Antibody
A key protein of the immune system, which is produced by certain white blood cells in response to a foreign substance (antigen). Depending on the nature of a specific antigen, antibodies can function by either destroying the antigen directly, or facilitating white blood cells in eliminating the antigen.

Antigen
A molecule or substance that generates a host immune response including antibody production. These substances are usually foreign or potentially toxic to the host.

Assay
A laboratory test used to analyze the percentage of a particular compound in a mixture, the strength of a solution, the purity of a prepared material or the efficacy/potency of a drug.

Autoimmune disease/disorder
A disease in which the body attacks itself because the immune system mistakenly recognizes the body's own tissue as a foreign antigen.

B cells/B lymphocytes
Classified as white blood cells, they are important parts of the immune system that produce antibodies.

Biacore
Biacore is a surface plasmon resonance (SPR) based equipment that can provide real-time, label-free detection and monitoring kinetic and affinity parameters of a specific molecular interaction. For example, Biacore has been used for measuring the kinetic constants (k_on and k_off) of an sFv antibody binding to its antigen with minimal sample preparation requirements.

Bioinformatics
Bioinformatics is a new data-managing field designed to advance scientific research through acquiring, organizing, analyzing, visualizing and archiving large amounts of biological, medical, behavioral or other health-related information with use of computational tools.

Colony
A cluster of cells, usually bacteria, grows in or on a nutrient medium and originates from a single cell.

Disease targets
A disease target is normally a molecule (most times proteins) that is involved directly or indirectly in a biochemical or genetic process that may lead to a disease. Manipulation of the function or activities of such a molecule may have therapeutic potential to prevent or treat the disease.

Efficacy
Quantitative measurement of the effectiveness of a drug or a treatment in disease intervention.

ELISA
An abbreviation for "enzyme-linked immunosorbent assay". ELISA is a highly sensitive assay for detecting and measuring interactions between antigens and their specific antibodies. Either the antigen or the antibody can be immobilized on a solid surface, usually onto the wells of a 96-well plastic plate, to catch its specific binder present in a solution. The captured antibody or antigen can be verified and optically visualized with an application of a detecting antibody that is labeled in some way.

Epitope
Part of the antigen molecule that serves as the binding site for an antibody.

FACS
FACS stands for Fluorescence Activated Cell Sorting, also known as flow cytometry. FACS is a powerful technique for analyzing and characterizing cells that are marked with a fluorescent label (s) and is used widely in both basic research and clinical diagnostic applications. As the individual suspension cell passes through the sensing region of the FACS machine, fluorescent signals are acquired, analyzed, and stored in a computer. The size of cells as well as the expression of interested molecules (such as proteins) within a single cell can be determined. Specific cells can be further separated, sorted, and collected for further analysis.

Genes
The basic biological units of DNA that provide the blueprint for every protein synthesized in the body and can be transmitted from generation to generation.

Genome
The total DNA content or genetic information of an organism.

High-throughput screening
The process of using automated assays to conduct large-scale searches of substances for desired property. High-thoughtput screening is fast and cost-effective.

Humanized antibodies
Humanized antibodies are human antibodies that the complementarity determining regions (CDR) are replaced by the CDRs of murine (mouse) or other origin. A humanized antibody retains over 90 percent human material. The CDR (Complementarity Determining Regions) are the regions of an antibody molecule that interact/bind with antigens.

Hybridoma
A cell line produced in vitro by artificially fusing a tumor cell with a B-lymphocyte to produce monoclonal antibodies.

Immunogenic
The ability to induce a specific immune response.

Immunoglobulins
Structurally related proteins possessing known antibody activity (i.e. capable of recognizing and binding antigens). There are five different classes of immunoglobulins defined by their structure and function. Some immunoglobulins are expressed on cell surfaces, while others are secreted into the body fluid.

Immunological response
The reaction of a host immune system against foreign substances (antigens), consisting both antibody and cellular responses. For example, exposure to a cold virus or the administration of a murine antibody can generate an immunological response.

Immunotube Selection
A method for selecting phage-sFv antibody binders of target protein antigens immobilized on a solid surface (immunotube) that is treated for maximum protein absorption. Upon a few rounds of binding, elution, and amplification in bacteria, target-specific phage-sFv antibodies can be isolated from a large phage display library. (For more detail, view Phage Display Overview Animation)

Intrabodies
Antibodies that are directed against intracellular target molecules and expressed within a specific subcellular compartment as directed by the intracellular localization signals genetically fused to N- or C-terminus of a given antibody.

In situ
A material that is in its original position within a biological context.

Ligand
A molecule or compound that has the capacity to bind to a receptor and modulate its activity.

Monoclonal antibody
An antibody derived from a single clone of cells, and as a result, all antibody molecules produced recognize the same antigen-binding site (epitope).

Paramagenetic proteoliposomes
Paramagnetic proteoliposomes are liposomes that can be used in analogy to a cell surface in presenting specific membrane proteins in their native conformations. Streptavidin and a specific ligand such as an antibody to the membrane protein of interest can be covalently linked to the surface of nonporous magnetic beads. The conjugated beads can then be used to capture the membrane proteins in solution or cell lysate. Upon mixing, biotinylated lipid (biotinyl-DOPE) molecules form a lipid bilayer around the conjugated beads with the membrane proteins inserted in a fixed orientation. The paramagenetic proteoliposomes have been used to select antibodies against specific membrane proteins from a large phage display library. (For more detail, view Phage Display Overview Animation)

Pathfinder/Stepback/Subtraction Selection
Pathfinder selection is a method developed for in situ phage antibody selections, especially for the selection of antibodies to specific cell surface antigens. The phage antibodies from a large library are first bound to the cell surface together with a horseradish peroxidase (HRP)-conjugated ligand or antibody (pathfinder) that binds to the target of the interest. In the presence of hydrogen peroxide, the HRP on the "pathfinder" is capable of catalyzing covalent linkage of biotin tyramine molecules to those phage antibodies bound in the close proximity to the "pathfinder" on the cell surface. The biotinylated phage antibodies are likely to be the antibodies that recognize the target antigen and can be specifically recovered on streptavidin-coated magnetic beads. (For more detail, view Phage Display Overview Animation)

The biotinylated phage isolated through the Pathfinder selection could be further conjugated with HRP through streptavidin-biotin interaction and used as the "pathfinder" in new selections. Through this type of selection, namely "Stepback selection", it is possible to isolate those phage antibodies that recognize the original pathfinder (ligand or antibody) binding site.

Subtraction selection is a method for reducing the background phage binding during an antibody selection. It is widely used in all phage library related selections but especially useful in cell-related situation. For example, in a subtraction selection of phage antibodies specific to a transfected cell surface target protein, the phage library will be incubated with an untransfected parental cell line first in order to eliminate those phages that bind to the proteins on the parental cell surface. The post-absorption phage supernatant will then be allowed to interact with the same cell line transfected with the target of interest following the aforementioned Pathfinder procedure in order to isolate target-specific phage antibodies.

Phage
A short name for bacteriophage, which is a virus that infects bacteria.

Phage Display
Phage display is a process during which the phage, a bacterial virus, is made to expose or "display" different peptides or proteins including human antibodies on its surface. Through genetic engineering, millions of peptides or proteins are attached individually to a phage cell surface protein molecule (usually Gene III protein, g3p). In such a phage population – a library, each phage carries a gene for a different peptide or protein – g3p fusion and exposes it on its surface. Through a variety of selection procedure, phages that "display" binders to specific target molecules of interest can be identified and isolated. The phage display technique is very useful in discovery and development of pharmaceutical and/or diagnostic products. (For more detail, view Phage Display Overview Animation)

Panning
Panning refers to the multiple rounds of screening process in identification and isolation of phages carrying compounds such as antibodies with high affinity and specificity to a given target molecule.

Protein
Large biological molecules made of smaller building blocks known as 'amino acids'. Proteins carry a wide range of function that are critical for the biological process, and are major structural components of all living things, including humans.

Receptor
Typically a protein located on the surface or inside a cell that may interact with a different molecule, known as a ligand, to initiate or inhibit a biological response.

Single chain antibodies (sFv)
A single polypeptide consists of the variable region of the immunoglobulin heavy chain linked to the variable region of the light chain through a flexible interchain amino acid linker. The V_H-(Gly₄Ser)₃-V_L format is used in the Mehta I and II sFv phage display libraries but other formats such as V_L-(Gly₄Ser)₄-V_H have also been used by others.

Streptavidin/Avidin Bead Selection
A technique using streptavidin/avidin conjugated magnetic beads to select those phage-sFv antibodies that bind to biotinylated protein or peptide antigens. (For more detail, view Phage Display Overview Animation)

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