Perseus Proteomics Inc.
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Glossary

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Antibody
A protein (immunoglobin) that recognizes and interacts with a specific site (epitope) on an antigen, usually foreign, such as a virus or bacteria, and either neutralizes or facilitates the clearance of the antigen from the body by the immune system. The variety of antibodies is limitless. Antibodies can be utilized as tools to specifically recognize a particular molecule. Recombinant antibodies are used for diagnostic and therapeutic purposes.
Cancer
A general term, referring to any of variety of malignant tumors, whose cells grow and divide more rapidly than normal, invade surrounding tissue, and generally spread (metastasize) to other sites in the body often disturbing organ function resulting in death. Cancer currently stands as the major cause of death in the industrialized world.
Antibody medicine
Medicine made from humanized antibody, with their mode of action being their specific ability to recognize foreign objects.
Expression Technology
In this context, refers to recombinant DNA technology used to produce recombinant proteins.
Affinity
In this context refers to antibody affinity. The strength with which an antibody molecule binds an epitope is called its affinity. Affinity can be quantified by determining an association constant, K.
Cancer
Recent advances in genome analysis have revealed that certain forms of cancer exhibit specific gene expression profiles that may be linked to their tumorigenesis. As a result of this progress, new antibody-medicines are being developed which target specific molecules expressed by the tumor.
Baculovirus
A type of virus infectious to insects which is transmitted by larva (i.e. silk moth). It has no infectivity to mammalian cells and can be easily scaled up to express a protein in large quantities. It has been utilized as an expression tool, due to its ability to express proteins in their native structure, thus mimicking mammalian expression, while being easier to handle than bacterial expression.
Nuclear Hormone Receptors
Medicine based on the humanization of an established monoclonal antibody, with their mode of action being their specific ability to recognize foreign objects. Genome information can accelerate their development. Antibody medicines delivered by intravenous injection can recognize target molecules expressed on the target cells’ surface.
proteomics
Condition in which lipid (fatty material) is deposited within the walls of arteries. Metabolic syndrome, like hypertension or hyperlipidemia, causes inflammation and injury to the endothelial cells lining the artery. Long term chronic injury and inflammation thickens, hardens, and may finally block arteries resulting in decreased or blocked blood flow. In the terminal stages, it leads to myocardial infraction (i.e. heart attack) or cerebrovascular diseases (i.e. stroke).
Cytotoxic activitiy
An activity to exclude infected or cancer cells from body. Cytotoxic activity is carried by complement, antibodies, T cell, NK cell, or LAK cell. In antibody medicine, the activation of complement-dependent cytotoxicity (CDC) or antibody-dependent cellular cytotoxicity (ADCC) is the basis for the treatment of cancer.

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Gene expression (Transcriptome)
Overall process, pattern, or genomic plan by which the information encoded in the DNA of our genes is transcribed into RNA and converted into an observable phenotype. The Human genome consists of approximately 22,000 genes, with each organ of the body transcribing only a unique subset of the total genome. This normal pattern of gene expression may vary for each cancer or disease condition.
Epitope
The part of the antigen molecule specifically recognized by an antibody, which consist of sequence or higher order structure of amino acids, sugar chains, or DNA etc.
Epigenetics
Genomic information written not in the DNA sequence, but written on chromosomes through DNA methylation or chromatin modification. As an example, the cloned sheep "Dolly” has a shortened life span, nevertheless, it has a complete set of genomic information. This means that a source nucleus derived from mammary glands is different than that of an original embryo made from sperm and egg, thus lacking the proper DNA methylation and chromatin modifications. It suggests that some cancers or other diseases may be the result of loss of control or release from epigenesist.

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Life Style-related Disease
A group of diseases (diabetes, obesity, hyperlipidemia, and hypertension) caused by the patients’ long term habits or life-style, such as diet, exercise, smoking, drinking. Often referred to as silent killers, these diseases progress relatively unnoticed and result in various blood vessel malfunctions leading to heart or brain injury, or failure.
orphan receptor
Ligand refers to any molecule that binds tightly and specifically to a macromolecule, usually a protein, forming a macromolecule-ligand complex. In general, nuclear hormone receptors exist in the cytoplasm, and as a ligand (such as a steroid hormone) passes through the cell membrane, it can bind to its cognate nuclear receptor to form a ligand bound receptor complex which then moves into the nucleus and acts as a transcriptional factor to activate target genes. This is a major mechanism by which cells receive communications and respond to their outside environment.

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Monoclonal antibody
A technique for producing monoclonal antibodies was innovated by Milstein and Kohler, who in 1984 received the Nobel Prize for their work. In this technique, B-lymphocytes (which are the antibody producing cells of the body in mammals; importantly, each B-lymphocyte produces a single mono-specific antibody in response in to the target antigen) are isolated from the spleen of a mouse immunized with a specific target antigen, and subsequently each lymphocyte is fused with a myeloma cell. The resulting hybrid cell retains the cellular longevity of a cancer cell while continually producing that lymphocyte’s mono-specific antibody. This technology has become the predominant industrial application for developing antibody-based therapeutics and diagnostics.
Polyclonal antibody
Polyclonal antibodies refer to antibodies directly isolated from an animal immunized with a specific target antigen. The antibodies are produced from many different B lymphocytes, instead of a single B lymphocyte as in the case of monoclonal antibodies, and therefore represent a variety of antibodies specific to different epitopes on the target antigen. Unlike monoclonal antibodies, the quantity of polyclonal antibodies produced depends on the size of immunized animal and the quality is often unstable.
Protein
Molecules composed of amino acids. Proteins are one of three major building blocks of the human body, with lipids and carbohydrates.
Nuclear Hormone Receptors
A family of intracellular receptors that bind lipid-soluble molecules (i.e. steroid hormones, bile acids, etc.), and subsequently move to the nucleus and function as transcriptional activators, controlling gene expression. Some of these receptors termed orphan receptors, because the ligand molecules to which these receptors bind had not yet been identified, have recently been shown to be involved in carbohydrate and lipid metabolism.
proteomics
Systematic global analysis of protein information. DNA and its transcript(RNA) are referred to as a blue-print of the design plan for each cell type. However, information from DNA or RNA does not contain all of the protein information, since some proteins have variant isoforms with sugars attached or other modifications. Direct analysis of all proteins is desired once the genome information has been established. System wide protein analysis is difficult due to the fact that unlike DNA or RNA, there is currently no amplifying technology for proteins.
Nomenclature
In general, it refers to the technical vocabulary of a given profession or field of research. However, in the context of nuclear receptors, it refers to an unique ID named under Nuclear Receptors Committee (1999), A Unified Nomenclature System for the Nuclear Receptor Subfamily, Cell 97: 1-20. http://www.ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html It lists 48 kinds of nuclear receptor genes with its specific nomenclature and sequence with NCBI accession ID.
orphan receptor
It refers to any receptor in which no information regarding the ligand molecule is known. The glucocorticoid receptor gene was cloned in 1985, and since then, 48 nuclear receptor genes have been identified in the human genome. Half of these nuclear receptors still have an unknown function and their ligands are also unknown, hence they are referred to as orphan receptors. Recently, some of these nuclear receptors have been identified to be involved in sugar and lipid metabolism.

Q-T

Target Molecules
The term refers to protein(s) encoded by a gene product that may serve as diagnostic or therapeutic targets for disease or cancer therapy.
Specificity
In this context refers to antibody specificity. The specificity of an antibody is its ability to discriminate a single epitope among other epitopes.
Tolerance
animal against a target molecule, tolerance often blocks the establishment of a monoclonal antibody, since molecules important for biological function are often conserved between human and mice, and the target therefore often resembles the animals own molecules. The issue of tolerance is one of the largest hurdles to antibody production.

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