Glossary

BIOINFORMATICS: The collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics.

BIOMARKER: A distinctive biological or biologically derived indicator (as a biochemical metabolite in the body) of a process, event, or condition (as aging or exposure to a toxic substance) used to measure or indicate the effects or progress of a disease, illness, or condition.

DNA MICROARRAY: DNA microarrays, or DNA chips are fabricated, typically on glass slides, using high-speed robotics and provide massively parallel gene expression and gene discovery information on thousands of genes simultaneously.

ECOSYSTEM: A system formed by the interaction of a community of organisms with their physical environment.

ELISA: A sensitive immunoassay that uses an enzyme linked to an antibody or antigen as a marker for the detection of a specific protein, especially an antigen or antibody. It is often used as a diagnostic test to determine exposure to a particular infectious agent by identifying antibodies present in a blood sample.

ENVIRONMENTAL BIOMARKER: Biomolecular signatures, such as a set of expressed proteins, genes, metabolites, and/or lipids, that when expressed together present a unique pattern of molecular change in an organism and that identify an exposure or response to a specific environmental stressor.

EPIDEMIOLOGY: The field of medicine that studies the causes, distribution, and control of disease in populations.

GENE EXPRESSION: Processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action at the level of transcription or translation. These processes include gene activation and genetic induction.

GENOMICS: A branch of biotechnology that applies the techniques of genetics and molecular biology to the genetic mapping and DNA sequencing of selected organisms using high-speed methods, organizing the results in databases, and applying the data to medicine or biologically-related fields.

HYPORHEIC MESOCOSM: A contained system for use in conducting controlled, laboratory-based studies to investigate the physical and biological dynamics of hyporheic zones as they relate to contaminants in groundwater that are released to surface waters.

HYPORHEIC ZONE: The interface or transition zone between groundwater and surface water systems, and the location or primary release point of contaminants from groundwater to surface water systems.

INFLAMMATORY RESPONSE: A host response to a stimulus (e.g., allergic stimulus; pulmonary irritant) causing inflammation that can be fairly rapid onset (an acute inflammatory response), quickly becomes severe, usually manifested for only a few days, but may persist for several days or even a few weeks; or may begin with a relatively rapid onset or in a slow, insidious, and even unnoticed manner, may persist for several weeks, months, or years and may have a vague and indefinite termination (a chronic inflammatory response)- the host's tissues may respond in a manner that is not sufficient to overcome completely the continuing effects of the injuring agent.

MACROPHAGE: A phagocytic tissue cell of the mononuclear phagocyte system that may be fixed or freely motile, is derived from a monocyte, and functions in the protection of the body against infection and noxious substances; the alveolar macrophage can be found in lung and can be obtained in lung lavage, responsible for clearance of inhaled particles and lung surfactant.

METABOLITE: The intermediates and products of metabolism; usually restricted to small molecules. A primary metabolite is essential for normal growth, development, and reproduction. A secondary metabolite is not essential for normal growth, development and reproduction, but usually has important ecological function (e.g., antibiotics).

METABOLOME: The collection of all metabolites in a biological organism, which are the end products of its gene expression.

METABOLOMICS: The study of the unique chemical fingerprints that specific cellular processes leave behind and the study of small-molecule metabolite profiles; metabolic profiling can give an instantaneous 'snapshot' of the physiology of that cell.

PATHOGEN: An agent that causes disease, especially a living microorganism such as a bacterium, virus, or fungus.

PERIPHYTON: Sessile organisms, such as algae and small crustaceans, that live attached to surfaces projecting from the bottom of a freshwater aquatic environment.

POLYCYCLIC AROMATIC HYDROCARBON (PAH): Any of a class of hydrocarbon molecules with multiple carbon rings that include numerous carcinogenic substances and environmental pollutants.

POLYMORPHISM: The occurrence of different forms, stages, or types in individual organisms or in organisms of the same species, independent of sexual variations.

PROTEIN MICROARRAY: A method whereby different molecules of protein have been affixed on glass at separate locations in an ordered manner thus forming a microscopic array. These are used to identify protein-protein interactions, to identify the substrates of protein kinases, or to identify the targets of biologically active small molecules.

PROTEOME: In genetics, the complete set of proteins from the information encoded on a genome that can be expressed and modified by a cell, tissue, or organism.

PROTEOMICS: A branch of biotechnology concerned with applying the techniques of molecular biology, biochemistry, and genetics to analyzing the structure, function, and interactions of the proteins produced by the genes of a particular cell, tissue, or organism, with organizing the information in databases, and with applications of the data.

SECRETOME: A subset of the proteome that is defined by its action, which is to be actively exported from the cell.

SUBTRACTIVE HYBRIDIZATION: A method to identify DNA/RNA present in one sample but not in the others.

TOXICOGENOMICS: A blending of functional genomics and molecular toxicology working to establish correlations between responses to toxicants and changes in the genetic profiles of an organism exposed to environmental stressors.

TOXICOLOGY: The study of the nature, effects, and detection of poisons/toxins and the treatment of their efforts on organisms.

TRANSCRIPTOME: The set of all mRNA molecules (or transcripts) in one or a population of cells for a given set of environmental circumstances. Unlike the genome, which is fixed for a given organism, the transcriptome varies depending upon the context of the experiment.

TRANSCRIPTOMICS: Depicting the expression level of genes, often using techniques capable of sampling tens of thousands of different mRNA molecules at a time (e.g., DNA microarrays).

TREE OF LIFE CHIP: A microarray that is taxonomically diverse and incorporates functional gene features.

ZOONOTIC DISEASE: Diseases caused by infectious agents that can be transmitted between (or are shared by) animals and humans.

Environmental Biomarkers