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Appendix C Glossary Adjuvant: substance (e.g., aluminum salt) that is added during production to increase the body’s immune response to a vaccine. Adventitious agents: microorganisms that have been unintentionally intro- duced into the manufacturing process of a biological product. They include bacteria, fungi, mycoplasmas, rickettsia, protozoa, parasites, transmissible spongiform encephalopathy agents, and viruses. Anthrax: infectious disease of humans and animals caused by the bacterium Bacillus anthracis. Antibody: an immune system protein that specifically recognizes a target site on an antigen. Antibodies are also commonly referred to as immunoglobulins (Ig). There are different classes of antibodies produced by different types of immune system cells, at different stages of the immune response, and that serve different immune system functions in response to different types of antigens. Antigen: a substance that triggers the immune system to produce an antibody against it. Bacteria (singular: bacterium): a large group of single-celled, prokaryote (or- ganisms that lack a cell nucleus or any other membrane-bound organelles) mi - croorganisms. Typically a few micrometers in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic hot springs, radioactive waste, water, and deep in the Earth’s crust, as well as in organic matter and the live bodies of plants and animals. 163

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164 APPENDIX C Biocontainment: concept, also called laboratory biosafety, pertaining to micro- biology laboratories in which the physical containment of highly pathogenic organisms (bacteria) or agents (viruses) is required, usually by isolation in environmentally and biologically secure cabinets or rooms, to prevent acci- dental infection of workers or release into the surrounding community during scientific research. Biological agent: a microorganism or a component of a microorganism, whether natural or synthesized, including bacteria, viruses, fungi, and microbial toxins. Biological Safety or Biosafety: the application of knowledge, techniques, and equipment to prevent personal, laboratory, and environmental exposure to potentially infectious agents or biohazards. Biosafety defines the containment conditions under which infectious agents can be safely manipulated. The ob - jective of containment is to confine biohazards and to reduce the potential exposure of the laboratory worker, persons outside of the laboratory, and the environment to potentially infectious agents. It can be accomplished through the following means: Primary Containment: Protection of personnel and the immediate labora- tory environment through good microbiological technique (laboratory practice) and the use of appropriate safety equipment. Secondary Containment: Protection of the environment external to the laboratory from exposure to infectious materials through a combination of facility design and operational practices. Combinations of laboratory practices, containment equipment, and spe - cial laboratory design can be made to achieve different levels of physical containment. The most important element in maintaining a safe work environment is strict adherence to good microbiological and laboratory practices and techniques. Everybody working with infectious agents or potentially infected materials must be aware of the potential risks. In addition, they must be trained and proficient in the practices and techniques required for handling such material. It is the responsibility of the principal investigator or person in charge of the laboratory to provide or arrange for appropriate training of all personnel. Biosafety Level (BSL): the level of the biocontainment precautions required to isolate dangerous biological agents in an enclosed facility. The levels of con - tainment range from the lowest biosafety level 1 to the highest at level 4. In the United States, the Centers for Disease Control and Prevention (CDC) has speci- fied these levels in the publication Biosafety in Microbiological and Biomedical Laboratories, 5th Ed. (December 2009).

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165 APPENDIX C Chimera: an individual organism whose body contains cell populations from different zygotes or an organism that is developed from portions of different embryos. A chimera virus or chimeric virus is defined by the Center for Vet - erinary Biologics (part of the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service) as a “new hybrid microorganism created by joining nucleic acid fragments from two or more different microorganisms in which each of at least two of the fragments contain essential genes necessary for replication. Containment: the combination of personnel practices, procedures, safety equip- ment, laboratory design, and engineering features to minimize the exposure of workers to hazards or potentially hazardous agent. Disease: an abnormal condition affecting the body of an organism. It is often construed to be a medical condition associated with specific symptoms and signs. It may be caused by external factors, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune diseases. In humans, “disease” is often used more broadly to refer to any condition that causes pain, dysfunction, distress, social problems, and/or death to the person afflicted, or similar problems for those in contact with the person. Formalin: an aqueous solution of formaldehyde that is 37% by weight. Formal- dehyde is a colorless, gaseous compound that is the simplest aldehyde, used for manufacturing melamine and phenolic resins, fertilizers, dyes, and embalming fluids and in aqueous solution as a preservative and disinfectant, especially in vaccines. Genome: the entirety of an organism’s hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA. Immunity: protection against a disease. There are two types of immunity, pas- sive and active. Immunity is indicated by the presence of antibodies in the blood and can usually be determined with a laboratory test. Active immunity is the production of antibodies against a specific disease by the immune sys - tem. Active immunity can be acquired in two ways, either by contracting the disease or through vaccination. Active immunity is usually permanent, mean - ing an individual is protected from the disease for the duration of their lives. Passive immunity is protection against disease through antibodies produced by another human being or animal. Passive immunity is effective, but protection is generally limited and diminishes over time (usually a few weeks or months). For example, maternal antibodies are passed to the infant prior to birth. These antibodies temporarily protect the baby for the first 4–6 months of life.

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166 APPENDIX C Immunization: the process of stimulating the immune system to respond to a biological agent. This can be accomplished by exposing the immune system to antigens from the biological agent, such as by injecting live or dead pathogens, in order to provoke the production of antibodies directed against the biological agent (referred to as generating active immunity). Immunization can also be accomplished by transferring antibodies produced by an already immunized individual to a non-immunized one (passive immunity). Inactivated vaccine: a vaccine in which a virus or bacteria has been rendered inactive through chemical or physical processes so that the microorganism can no longer grow and replicate. Intercurrent illness: a disease that develops during the course of another, un- related illness. Investigational vaccine: a vaccine that has been approved by the Food and Drug Administration (FDA) for use in clinical trials on humans. However, investigational vaccines are still in the testing and evaluation phase and are not licensed for use in the general public. Live, attenuated vaccine: a vaccine in which a live virus or bacteria is weak- ened through chemical or physical processes in order to produce an immune response without causing the severe effects of the disease. Live, attenuated vac - cines currently licensed in the United States include measles, mumps, rubella, polio, yellow fever, and varicella. Microorganism (or microbe): an organism that is unicellular or lives in a colony of cellular organisms. The study of microorganisms is called microbiology, a subject that began with Anton van Leeuwenhoek’s discovery of microorganisms in 1675, using a microscope of his own design. Microorganisms are very diverse; they include bacteria, fungi, archaea, and protists; microscopic plants (green algae); and animals such as plankton and the planarian. Some microbiologists also include viruses, but others consider these as nonliving. Most microorgan - isms are unicellular (single-celled), but this is not universal, since some multicel- lular organisms are microscopic, while some unicellular protists and bacteria, like Thiomargarita namibiensis, are macroscopic and visible to the naked eye. Pathogen: a microorganism, such as a bacterium, virus, or fungus, that is capable of causing disease or host damage, either through the action of the microorganism or through the host immune response to the microorganism. Plasmid: a DNA molecule that is separate from, and can replicate indepen - dently of, the chromosomal DNA. They are double stranded and, in many

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167 APPENDIX C cases, circular. Plasmids usually occur naturally in bacteria, but are sometimes found in eukaryotic organisms (e.g., the 2-micrometer ring in Saccharomyces cerevisiae). Plasmid size varies from 1 to over 1,000 kilobase pairs (kbp). The number of identical plasmids within a single cell can range anywhere from one to even thousands under some circumstances. Plasmids can be considered to be part of the mobilome (the total of all mobile genetic elements in a genome) since they are often associated with conjugation, a mechanism of horizontal gene transfer. The term plasmid was first introduced by the American molecu - lar biologist Joshua Lederberg in 1952. Plasmids are considered transferable genetic elements, or “replicons,” capable of autonomous replication within a suitable host. Recombinant: may refer to a recombinant organism, that is, an organism that contains a different combination of alleles from either of its parents, recombi - nant DNA, that is, a form of artificial DNA; or a recombinant virus, that is, a virus formed by recombining genetic material. Replicon: a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication. For most prokaryotic chro - mosomes, the replicon is the entire chromosome. The only exceptions found comes from archaea, where two Sulfolobus species have been shown to con- tain three replicons. Plasmids and bacteriophages are usually replicated as single replicons, but large plasmids in Gram-negative bacteria have been shown to carry several replicons. For eukaryotic chromosomes, there are multiple replicons per chromosome. The definition of replicons is somewhat confused with mitochondria, as they use unidirectional replication with two separate origins. Risk: the potential that a chosen action or activity (including the choice of in - action) will lead to a loss (an undesirable outcome). The notion implies that a choice having an influence on the outcome exists (or existed). Potential losses themselves may also be called “risks.” Almost any human endeavor carries some risk, but some are much riskier than others. Scarification: a process of immunization that involves scratching or puncturing the skin surface to break it and introduce the antigenic material. Select Agent: an infectious disease-causing pathogen or toxin that is subject to regulation by the U.S. government according to the Code of Federal Regulations (42 CFR Part 73 and 9 CFR Part 121). The lists of biological agents subject to the Select Agent regulations are maintained by the Centers for Disease Control and Prevention and the Animal and Plant Health Inspection Service.

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168 APPENDIX C Seroconversion: the development of antibodies in response to an immuniza- tion, indicated by a change from a negative response on a blood test for these antibodies to a positive test response. Titer (antibody): a measure of the concentration of a particular antibody in a sample. Serial dilutions of the sample are made and the highest dilution factor that still yields a positive reading for the presence of the antibody is the titer. Toxin: A toxin is a poisonous substance produced by living cells or organisms. It was the organic chemist Ludwig Brieger (1849–1919) who first used the term “toxin.” Toxins can be small molecules, peptides, or proteins that are capable of causing disease on contact with or absorption by body tissues interacting with biological macromolecules such as enzymes or cellular receptors. Toxins vary greatly in their severity, ranging from usually minor and acute (as in a bee sting) to almost immediately deadly (as in botulinum toxin, the toxin from Clostridium botulinum). Transduce: to cause transduction in (a cell). Transduction is the transfer of genetic material from one cell to another by means of a virus. Vaccination: A process that originally referred to a particular type of immuni- zation, namely, the inoculation of antigenic material from the cowpox virus in order to generate immune resistance to the related but more lethal disease of smallpox. In current usage, the term is frequently used synonymously with im - munization to indicate stimulation of the immune system by delivery of antigens in order to provoke an antibody response. Vaccine: a product that produces immunity, therefore protecting the body from the disease. Vaccines are administered through needle injections, by mouth, and by aerosol. Virus: a small infectious agent that can replicate only inside the living cells of organisms. Most viruses are too small to be seen directly with a light micro- scope. Viruses infect all types of organisms, from animals and plants to bacteria and archaea. Virus particles (known as virions) consist of two or three parts: the genetic material made from either DNA or RNA, long molecules that carry genetic information; a protein coat that protects these genes; and in some cases an envelope of lipids that surrounds the protein coat when they are outside a cell. The shapes of viruses range from simple helical and icosahedral forms to more complex structures. The average virus is about one one-hundredth the size of the average bacterium.

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169 APPENDIX C Zoonotic disease: an infectious disease that can be transmitted (in some in- stances, by a vector) from nonhuman animals, both wild and domestic, to humans or from humans to nonhuman animals (the latter is sometimes called reverse zoonosis or anthroponosis). Of the 1,415 pathogens known to affect humans, 61% are zoonotic.

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