Appendix D

Glossary

Abiotic: Nonliving chemical and physical factors in an environment.

Adaptive immune response: Response of the vertebrate immune system to a specific antigen that typically generates immunological memory.

Aggressive: In plant pathology, the quality of being able to cause more disease more quickly on susceptible host plants.

Anthropogenic: Caused or produced by humans.

Antibiotic: Class of substances that can kill or inhibit the growth of some groups of microorganisms. Used in this report to refer to chemicals active against bacteria. Originally antibiotics were derived from natural sources (e.g., penicillin from molds), but many currently used antibiotics are semi-synthetic and modified with additions of manmade chemical components.

Antibody therapy: Any therapeutic intervention in which a monoclonal or other concentrated antibody is used to manage a condition, such as cancer or severe infection.

Antifungal: Substances that can kill or inhibit the growth of fungal organisms.

Ascomycete: Any of various fungi belonging to the phylum Ascomycota, characterized by the presence of sexually produced spores formed within an ascus. Like



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Appendix D Glossary Abiotic: Nonliving chemical and physical factors in an environment. Adaptive immune response: Response of the vertebrate immune system to a specific antigen that typically generates immunological memory. Aggressive: In plant pathology, the quality of being able to cause more disease more quickly on susceptible host plants. Anthropogenic: Caused or produced by humans. Antibiotic: Class of substances that can kill or inhibit the growth of some groups of microorganisms. Used in this report to refer to chemicals active against bacte- ria. Originally antibiotics were derived from natural sources (e.g., penicillin from molds), but many currently used antibiotics are semi-synthetic and modified with additions of manmade chemical components. Antibody therapy: Any therapeutic intervention in which a monoclonal or other concentrated antibody is used to manage a condition, such as cancer or severe infection. Antifungal: Substances that can kill or inhibit the growth of fungal organisms. Ascomycete: Any of various fungi belonging to the phylum Ascomycota, charac- terized by the presence of sexually produced spores formed within an ascus. Like 413

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414 FUNGAL DISEASES most fungi, ascomycetes also reproduce asexually by the formation of nonsexual spores called conidia at the ends of filaments known as hyphae. Assembling the Tree of Life program: This National Science Foundation pro- gram was created in 2004 with the goal of constructing the evolutionary history for all major lineages of life. The program supports efforts to classify all major groups of organisms and to reveal the pattern of historical relationships that would explain similarities and differences among them. The program has three goals: (1) Creation and support of multidisciplinary teams of investigators to acquire and integrate molecular and morphological evidence on both extant and extinct organisms in order to resolve phylogenetic relationships of large, deep branches of the Tree of Life; (2) Research and de - velopment of tools for computational phylogenetics and phyloinformatics to improve assessment, predictive capabilities, and the visualization and navigation of the hierarchical structure in the Tree of Life; and (3) Outreach and education in comparative phylogenetic biology and paleontology. Asymptomatic: Presenting no symptoms of disease. Asymptomatic carriers: A person or animal that has contracted an infectious disease, but displays no symptoms yet has the ability to transmit it to others. Bacteria: Microscopic, single-celled organisms that have some biochemical and structural features different from those of animal and plant cells. Basidiomycetes: Any various fungi belonging to the phylum Basidomycota, bearing sexually produced spores on a basidium. All hyphae of basidiomycetes are divided into segments by septa and go through three stages of development. Biofuel: Fuel produced from renewable resources, especially plant biomass, vegetable oils, and treated municipal and industrial wastes. Biological invasion: The process by which species (or genetically distinct popu- lations), with no historical record in an area, breach biogeographic barriers and extend their range. Bioluminescence: Light produced by a chemical reaction that originates in an organism. Biota: The animal and plant life of a given region. Chronic: Relating to an illness or a medical condition that is characterized by long duration or frequent recurrence.

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415 APPENDIX D Climate: Average meteorological conditions over a specified time period, usually at least a month, resulting from interactions among the atmosphere, oceans, and land surface. Climate variations occur over a wide range of spatial and temporal scales. Climate change: A change of climate that is attributed directly or indirectly to human activity and alters the composition of the global atmosphere; this happens in addition to natural climate variability observed over comparable time. Colonize: The spreading of a species into a new habitat. Colony collapse disorder: A syndrome characterized by the disappearance of all adult honey bees in a hive while immature bees and honey remain. Colony-forming unit: A standard unit of measurement for environmental sam- pling. Colonies reflect the number of “viable” organisms (i.e., organism ca- pable of forming colonies when provided with nutritional elements necessary for growth). Commensals: Organisms in a mutually symbiotic relationship where both live peacefully together while not being completely dependent on one another (e.g., the gut microbiome). Communicable disease: An infectious disease transmissible (as from person to person) by direct contact with an affected individual or the individual’s dis - charges or by indirect means (as by a vector). Conidia: Asexually produced fungal spore. Most conidia are dispersed by the wind and can endure extremes of cold, heat, and dryness. When conditions are favorable, they germinate and grow into hyphae. Contagious: Capable of being transmitted by direct or indirect contact, as an infectious disease. Corn Belt: The area in the Midwestern United States—roughly covering west - ern Indiana, Illinois, Iowa, Missouri, eastern Nebraska, and eastern Kansas—in which corn (maize) and soybeans are the dominant crops. Cultivar: A variety of a plant that has been created or selected intentionally and maintained through cultivation. Detection: The act of discovering a novel, emerging, or reemerging disease or disease event.

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416 FUNGAL DISEASES Diagnosis: The identification of a condition, disease, or injury made by evaluat- ing the symptoms and signs presented by an individual. Dimorphic: The existence of two distinct types of individuals within a species, usually differing in one or more characteristics such as coloration, size, and shape. Disease: A situation in which infection has elicited signs and symptoms in the infected individual; the infection has become clinically apparent. Some exposures to infectious disease-causing agents can also produce asymptomatic illnesses that can be spread to others. Disease burden: The impact of a health problem in an area measured by financial cost, mortality, morbidity, or other indicators. It is often quantified in terms of quality-adjusted life years (QALYs) or disability-adjusted life years (DALYs), which combine the burden due to both death and morbidity into one index. Ecosystem: A community of organisms together with their physical environment, viewed as a system of interacting and interdependent relationships and including such processes as the flow of energy through trophic levels and the cycling of chemical elements and compounds of the system. Ecosystem services: Benefits derived from a multitude of resources and pro- cesses that are supplied by natural ecosystems (e.g., decomposition of waste, food, energy, nutrient dispersal, and cycling). Emerging infectious disease: Infections that are rapidly increasing in incidence or geographic range. Emigration: To leave one’s usual country of residence to settle in another. Endemic: Present in a community or common among a group of people; said of a disease prevailing continually in a region. Endophytes: Fungi that live inside the plant tissue, but without causing any obvious negative effects. Endosymbiont: An organism that lives inside another organism, most often for the benefit of the two (e.g., rhizobia [nitrogen-fixing soil bacterial] that live within root nodules—rhizobia cannot independently fix nitrogen, but need the plant as an energy source; in turn, rhizobia supply the plant host with ammonia and amino acids).

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417 APPENDIX D Environmental microbe: Microbe acquired from the environment (in contrast to acquisition from other living hosts). Enzootic: A disease of low morbidity that is constantly present in an animal community. Enzyme: Any of numerous proteins produced in living cells that accelerate or catalyze the metabolic processes of an organism. Epidemic: The condition in which a disease spreads rapidly through a com- munity in which that disease is normally not present or is present at a low level. Epidemiology: Study of the distribution and determinants of health-related states or events in specified populations. Epidemiology is the basic quantitative science of public health. Epizootic: A disease of high morbidity that is only occasionally present in an animal community. Eradication: Reduction of the worldwide incidence of a disease to zero as a result of deliberate efforts. Etiologic agent: The organism that causes a disease. Etiological: Of or pertaining to causes or origins. Etiology: Science and study of the causes of diseases and their mode of operation. Eukaryotic organism: One of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and lack several features characteristic of eukaryotes (e.g., cells containing a nucleus surrounded by a membrane and whose DNA is bound together by proteins [histones] into chromosomes). Animals, plants, and fungi are all eukaryotic organisms. Expression vectors: A plasmid that is used to introduce a specific gene into a tar- get cell. Once the expression vector is inside the cell, the protein that is encoded by the gene is produced by the cellular-transcription and translation machinery ribosomal complexes. The plasmid is frequently engineered to contain regula - tory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector. Extreme weather: Refers to weather phenomena that are at the extremes of the historical distribution and are rare for a particular place and/or time, especially

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418 FUNGAL DISEASES severe or unseasonal weather. Such extremes include severe thunderstorms, se - vere snowstorms, ice storms, blizzards, flooding, hurricanes, high winds, and heat waves. Fermentation: The process by which complex organic compounds, such as glu- cose, are broken down by the action of enzymes into simpler compounds without the use of oxygen. Food security: The availability of food and one’s access to it. A household is considered food secure when its occupants do not live in hunger or fear of starvation. Fungi/fungal/fungus: For the purposes of this publication, the terms fungi, fun - gal, and fungus are used inclusively to describe all organisms traditionally studied by mycologists—including species that are now excluded from Kingdom Fungi (e.g., Phytophthora ramorum and Phytophthora infestans) or whose relationship to the fungal kingdom has yet to be determined (e.g., the microsporidia Nosemus spp.). Genome: The complete genetic composition of an organism (e.g., human, bac - terium, protozoan, helminth, fungus), contained in a chromosome or set of chro - mosomes or in a DNA or RNA molecule (e.g., a virus). Genomics: The study of all the genes in a person, as well as interactions of those genes with each other and with that person’s environment. Genotype: The genetic makeup of an organism as distinguished from its physical characteristics. Genus: A group of species with similar characteristics that are closely related. Germinate: The beginning of growth, as of a seed, spore, or bud. Globalization: The increased interconnectedness and interdependence of peoples and countries. It is generally understood to include two interrelated elements: (1) the opening of borders to increasingly fast flows of goods, services, finance, people, and ideas across international borders, and (2) the changes in institutional and policy regimes at the international and national levels that facilitate or pro - mote such flows. Haploid: Having a single set of each chromosome in a cell or cell nucleus. In most animals, only the gametes are haploid.

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419 APPENDIX D Hibernacula: A protective case, covering, or structure, such as a cave, in which an organism remains dormant for the winter. Host: Animal or plant that harbors or nourishes another organism. Hyphae: Slender tubes that develop from germinated spores and form the struc- tural parts of the body of a fungus. A large mass of hyphae is known as a myce - lium, which is the growing form of most fungi. Immunocompetence: The ability of the immune system to respond appropriately to an antigenic stimulation. Immunocompromised: A condition (caused, e.g., by the administration of im- munosuppressive drugs or irradiation, malnutrition, aging, or a condition such as cancer or HIV disease) in which an individual’s immune system is unable to respond adequately to a foreign substance. Incidence: As used in epidemiology, the number of new cases of a disease that occur in a defined population within a specified time period; the rate of occurrence. Incubation period: The time from the moment of inoculation (exposure to the infecting organism) to the appearance of clinical manifestations of a particular infectious disease. Infection: The invasion of the body or a part of the body by a pathogenic agent, such as a microorganism or virus. Under favorable conditions the agent develops or multiplies; the results may produce injurious effects. Infection should not be confused with disease. Innate immune response: Immune response (of both vertebrates and inverte- brates) to a pathogen that involves the preexisting defenses of the body, such as barriers formed by skin and mucosa, antimicrobial molecules, and phagocytes. Such a response is not specific for the pathogen. Inoculum: Collective term for microorganisms or their parts (spores, mycelial fragments, etc.), which are capable of infection or symbiosis when transferred to a host. Internal transcribed spacer sequences: Internal transcribed spacer sequences are sections of non-functional RNA that are highly variable, even between closely related species, and are widely used for taxonomy purposes.

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420 FUNGAL DISEASES International Health Regulations (IHR): An international legal instrument that is binding on 194 countries across the globe, including all the Member States of the World Health Organization (WHO). Their aim is to help the international community prevent and respond to acute public health risks that have the poten - tial to cross borders and threaten people worldwide. The IHR, which entered into force on June 15, 2007, requires countries to report certain disease outbreaks and public health events to WHO. Building on the unique experience of WHO in global disease surveillance, alert, and response, the IHR define the rights and obligations of countries to report public health events, and establish a number of procedures that WHO must follow in its work to uphold global public health security. Invasive species: Non-native plants and animals that, when introduced to new environments, reproduce or spread so aggressively that they harm their adopted ecosystems. Also called: exotic, alien, and non-indigenous species. Latency: Delay between exposure to a disease-causing agent and manifestation of the disease (onset of infectiousness). Lichen: Symbiotic associations between fungi and photosynthetic partners (algae). Macrophage: Phagocytic cell derived from blood monocytes, typically resident in most tissues. It has both scavenger and antigen-presenting functions in immune responses. Meiosis: The process in cell division in sexually reproducing organisms that reduces the number of chromosomes from diploid to haploid (half the original number). Mendelian: A single gene disorder caused by a defect in one particular gene, and characterized by how they are passed down in families. Metabolites: A substance produced by the chemical processes by which cells produce the substances and energy needed to sustain life. Microbe: A microorganism or biologic agent that can replicate in humans (in- cluding bacteria, viruses, protozoa, fungi, and prions). Microbial flora: The microscopic organisms living within a particular region, including bodily organ or body part, such as the skin. Microbial threat: Microbes that lead to disease in humans.

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421 APPENDIX D Microbiology: A branch of biology dealing especially with microscopic forms of life. Microbiome: Term used to describe the collective genome of our indigenous microbes (microflora). Migration: The regular, usually seasonal, movement of all or part of an animal population to and from a given area. Mitigation: Initiatives that reduce the risk from natural and man-made hazards. Morbidity: Diseased condition or state. Mortality: Proportion of deaths to population or to a specific number of the population; death rate. Mutation: Genetic change that can occur either randomly or at an accelerated rate through exposure to radiation or certain chemicals (mutagens) and may lead to change in structure of the protein coded by the mutated gene. Mycelia, mycelium: The mass of fine branching tubes (known as hyphae) that forms the main growing structure of a fungus. Mycorrhizal fungi: Fungi that colonize plant roots. Natural history: The natural development of something (such as an organism or disease) over a period of time. Necropsy: An autopsy performed on an animal. Neutrophil: Most common blood leukocyte; a short-lived phagocytic cell of the myeloid series, which is responsible for the primary cellular response to an acute inflammatory episode, and for general tissue homeostasis by removal of damaged material. Notifiable disease: Disease that health professionals are required to report to state, national, or international authorities. Obligate: Capable of existing only in a particular environment; an obligate para- site cannot survive independently of its host. Old World: Refers to the Western Hemisphere; in a biological context: New World species are those from the Nearctic and Neotropic ecological zones; Old World species are those from the Palearctic and Afrotropic ecological zones.

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422 FUNGAL DISEASES One Health: Holistic approach to preventing epizootic disease and for maintain- ing ecosystem integrity for the benefit of humans, their domesticated animals, and the foundation biodiversity that supports all life. Oomycete: Not a “true fungi”; an oomycete or “water mold” that belongs to the Kingdom Stramenopila (a major eukaryotic group that includes diatoms and brown algae, and is distinct from plants, fungi, and animals). Like fungi, oomy - cetes “exhibit filamentous growth, produce sexual and asexual spores, and can feed on decaying matter or be obligate parasites of plants.” Opportunistic: Resulting from pathogen entry via wounds or weakened state of the host, or as a disturbance of a normally benign host–fungus relationship. Pandemic: Disease outbreak occurring over a wide geographic area and affecting an exceptionally high proportion of the population. Parasite, parasitic: An organism that lives in or on and takes its nourishment from another organism. A parasite cannot live independently. Parasitic diseases include infections by protozoa, helminths, and arthropods. Pathogen: Organism capable of causing disease. Pathogenic: Capable of causing disease. Pathogenicity: The ability of an organism, a pathogen, to produce an infectious disease in another organism. Pathology: The branch of medicine concerned with disease, especially its struc- ture and its functional effects on the body. Phagocyte/phagocytic cell: A cell that is capable of phagocytosis, or the uptake of particulate material by a cell. The main mammalian phagocytes are neutrophils and macrophages. Phenology: The scientific study of cyclical biological events, such as flowering, breeding, and migration. Phenotype: The physical appearance of an organism as distinguished from its genetic makeup (genotype). Phylogeny: The connections among all groups of organisms as understood by ancestor/descendant relationships.

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423 APPENDIX D Phylum: In taxonomy and systematics: the highest level of classification below the kingdom. Prevalence: Total number of cases (new as well as previous cases) of a disease in a given population at a point in time. Primary fungal pathogen: Pathogens able to induce symptoms of disease in otherwise healthy individuals. Propagules: Any of various structures that can give rise to a new individual or- ganism. (For fungi, propagules include spores or encapsulated yeast cells.) Psychotropic: Affecting mental activity, behavior, or perception. Public health: The art and science of dealing with the protection and improve- ment of community health by organized community effort and including preven- tive medicine and sanitary and social health. Quarantine: The enforced isolation or restriction of free movement imposed to prevent the spread of a contagious disease. Race (plant pathology): A subspecies group of pathogens that infect a given set of plant varieties. Recombination: A combining of genes or characters different from what they were in the parents. Recombine: The process by which the combination of genes in an organism’s offspring becomes different from the combination of genes in that organism. Reservoir: Any person, animal, arthropod, plant, soil, or substance (or combina - tion of these) in which an infectious agent normally lives and multiplies, on which it depends primarily for survival, and in which it reproduces itself in such manner that it can be transmitted to a susceptible vector or host. Saprophytic: Deriving nutrients from dead organic matter. Serotype: The characterization of a microorganism based on the kinds and com- binations of constituent antigens (a substance that stimulates the production of an antibody when introduced into the body) present in that organism; a taxonomic subdivision of bacteria based on the above.

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424 FUNGAL DISEASES Somatic cells: The cells of the body, with the exception of the reproductive cells (gametes). Species: The basic unit of taxonomy. A species is defined as a group of individu - als that are genetically related and can interbreed to produce fertile young of the same kind. Species barrier: Difficulty or impossibility for an infectious agent to pass from one species to another (due to differences between species). Spores: Well-protected structures that can survive in adverse environmental conditions, such as freezing or drying (better than mycelia and yeast cells), for months and even years. Surveillance: The continual scrutiny of all aspects of occurrence and spread of a disease that are pertinent to effective control, involves the systematic collection, analysis, interpretation, and dissemination of health data. Symbiotic: The close association between two or more organisms of different species, often but not necessarily benefiting each member. The association of algae and fungi in lichens and of bacteria living in the intestines or on the skin of animals are symbiotic. Syndrome: A group or recognizable pattern of symptoms or abnormalities that indicate a particular trait or disease. Systematics: The classification of organisms and the evolutionary relationships among them; taxonomy. Thermotolerance: Garcia Solache and Casadevall (2010) define thermotolerance as the ability to grow at mammalian (37°C) and higher temperatures. Most fungi thrive in the range of 12°C to 30°C, but there are wide temperature tolerances among species, with some growing at temperatures as low as –10°C or as high as 65°C. [Garcia-Solache, M. A., and A. Casadevall. 2010. Hypothesis: global warming will bring new fungal diseases for mammals. mBio 1(1):1–3.] Transformation: The genetic alteration of a bacteria cell by the introduction of genetic material from another cell or from a virus. Transmission: Process by which a pathogen passes from a source of infection to a new host.

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425 APPENDIX D Vaccine: A preparation of living, attenuated, or killed bacteria or viruses, frac - tions thereof, or synthesized or recombinant antigens identical or similar to those found in the disease-causing organism that is administered to raise immunity to a particular microorganism. Vector: A carrier, especially an arthropod, that transfers an infective agent from one host (which can include itself) to another. Vector borne: Transmitted from one host to another by a vector. Virulence: The degree of pathogenicity of an organism as evidenced by the severity of resulting disease and the organism’s ability to invade the host tissues. Virulence factors: Molecules produced by a pathogen that specifically cause disease, or that influence their host’s function to allow the pathogen to thrive. Weather: The state of the atmosphere over a short period of time, measured in terms of wind, temperature, humidity, atmospheric pressure, cloudiness, and precipitation. The difference between weather and climate is a measure of time: Climate is how the atmosphere “behaves” over relatively long periods of time. Xylose: A white crystalline sugar extracted from wood, straw, and corn. Yeast: Any of various one-celled fungi that reproduce by budding and can cause the fermentation of carbohydrates, producing carbon dioxide and ethanol. Zoonotic infection: Infection that causes disease in human populations but that can be perpetuated solely in non-human host animals (e.g., bubonic plague); may be enzootic or epizootic.

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