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A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Abiotic: Occurring in the absence of living organisms.
Accessory pigment: Pigments that trap light energy and transfer it to chlorophyll molecules in reaction centers. Carotenoids and phycobiliproteins are examples.
Accidental pathogen: A microorganism that does not generally cause disease in its normal life cycle. Can cause disease if introduced into a host as a result of a breach in barrier defense.
Aceticlastic: A methanoarchaeon that forms methane from the methyl group and CO2 from the carbonyl group of acetate.
Acetogenic bacteria: Species that produce acetic acid via sugar fermentation or from H2 + CO2 in anaerobic environments.
Acetyl-CoA pathway: An autotrophic CO2 fixation pathway utilized by selected anaerobic bacteria. The assimilation of two molecules of CO2 results in formation of acetyl-CoA.
Acid dyes: Staining compounds that are negatively charged.
Acid-fastness or acid-alcohol fastness: A property of some organisms, such as mycobacteria, that have a high lipid content in their outer wall. These organisms retain hot carbol-fuchsin stain when rinsed with acid alcohol.
Acid mine drainage: Low pH water emanating from mines.
Acid rain: Rainfall that has low pH due to sulfuric acid.
Acidophile: An organism that preferentially grows at a pH below 5.4. Sulfolobus is one example.
Acne: An inflammatory reaction in the sebaceous glands and hair follicles of the skin.
Acquired immunity: Most often called adaptive immunity. A specific immunity acquired by exposure of B lymphocytes and T lymphocytes to an antigen.
Acridine orange: A fluorescent dye that stains nucleic acids.
Actinobacteria: Bacteria from the phylum Actinobacteria, some of which produce mycelia.
Activated sludge process: An aerobic wastewater treatment process.
Activation energy: Energy added that renders molecules capable of chemical interactions.
Activator: A protein capable of enhancing transcription of a gene.
Active immunity: An immune state generated by challenge with a specific antigen.
Active site: The specific area of an enzyme where substrate is bound, forming an enzyme-substrate complex.
Active transport: Movement of ions or molecules across the cell membrane at an expenditure of energy.
Acute infection: An infection that causes abrupt onset of symptoms and is resolved rapidly by the host, or that kills the host rapidly.
Acute phase response: A group of physiological processes occurring soon after the onset of infection, trauma, inflammatory processes, and some malignant conditions. It includes an increase in acute phase proteins in serum many of which arise from the liver, fever, increased vascular permeability, and metabolic and pathologic changes.
Acute stage: The stage in the infection cycle where symptoms are most pronounced.
Acyl carrier protein (ACP): A small protein bound to a growing fatty acid during synthesis and released when the chain attains full length.
Acyl-homoserine lactones (AHLs): A class of signaling molecules involved in microbiological quorum sensing.
Adaptive immunity: Immune responses characterized by exquisite specificity for the antigen and memory (recall) responses upon secondary encounter with antigen. Such responses are conveyed by lymphocytes known as T cells and B cells.
ADCC: Antibody dependent cellular cytotoxicity.
Adenosine-5′-triphosphate (ATP): The energy carrier in all living cells.
Adenylate cyclase toxin: A protein toxin produced by Bordetella pertussis, catalyzing formation of cyclic AMP in mammalian cells.
Adherence factors: Molecules on the surface of pathogens that allow them to attach to host cells and tissues.
Adhesin: A cell surface protein that allows pathogenic bacteria to adhere to other cells or a substrate. Adhesins are important in attachment of pathogens to host cells during infection.
ADP ribosylation: Transfer of the ADP-ribose moiety from NAD to a protein, a reaction catalyzed by various bacterial toxins.
Aerial mycelium: The cellular network of Actinobacteria that is produced in the air above the cells on the growth substrate.
Aerobe: An organism that utilizes molecular oxygen as terminal electron acceptor in aerobic respiration.
Aerobic respiration: A process in which oxygen serves as the electron acceptor in metabolism.
Aerosol: Liquid droplets suspended in air.
Aerotolerant: An organism that does not utilize molecular oxygen as terminal electron acceptor but is not harmed by O2.
Affinity maturation: The process by which B-cells produce antibodies with increased affinity for antigen. This results from somatic hypermutation of bases encoding the antigen combining site of the B cell antigen specific receptor followed by affinity based selection.
AFM: Atomic force microscopy.
Agar: A sulfur-containing polysaccharide of marine algal origin that is used as a solidifying agent in culture media.
Agarose gel electrophoresis: A method of separating DNA fragments based on size and charge.
Agglutination: Sticking together of microbes or cells, often caused by an interaction with an antibody, resulting in an observable clump.
AIDS: Acquired immune deficiency syndrome. An infection caused by HIV, the human immunodeficiency virus.
Airborne droplets: Liquid suspended in air that may contain pathogens, particularly when of human origin, such as from a sneeze.
Akinetes: Resting bodies formed by some cyanobacteria.
Alcoholic fermentation: Anaerobic metabolism where alcohol (ethanol, butanol, etc.) and CO2 are major products.
Algae: Photosynthetic eukaryotic aquatic organisms.
Alkaliphiles: Organisms that inhabit alkaline lakes and grow at a pH up to 11.5.
Allergic contact dermatitis: Allergic response mediated by T cells and activated macrophages.
Allergy: Inappropriate immune response to an antigen (allergen).
Allophycocyanin: A blue-green colored pigment of cyanobacteria.
Allostery: Change in the conformation of a protein resulting from the attachment of a compound at a site other than the reactive site. Generally a reversible inactivation of a protein, such as an enzyme.
Alpha-hemolysis: An effect observed on blood agar plates in which bacterial toxins cause a green coloration of the hemoglobin.
Alternative pathway of complement activation: Complement activation by generation of a C3 convertase on the surface of pathogens.
Alternative σ factors: A family of sigma subunits of RNA polymerase that are different from the major sigma factor (σ70 in E.coli).
Amebiasis: Infection caused by pathogenic amoebas.
Ames test: A procedure for determining the mutagenic potential of a chemical.
Aminoacyl-tRNA synthetase: An enzyme responsible for linking amino acids to transfer RNAs.
Ammonia oxidizers: Bacteria or archaea that oxidize ammonia as an energy source.
Ammonification: Release of ammonia from cell material during decomposition.
Amylases: Enzymes that hydrolyze starch or glycogen.
Anabolism: See biosynthesis.
Anaerobe: An organism that does not employ oxygen as terminal electron acceptor.
Anaerobic respiration: Electron transport oxidation where sulfate, sulfur, nitrate, CO2, or other oxidized compounds are utilized as a terminal electron acceptor.
Anaerobic sludge digester: A wastewater treatment process that occurs anaerobically.
Anammox reaction: A reaction in which ammonia and nitrite are converted to nitrogen gas.
Anammoxosome: A compartment in certain members of the Planctomycetes in which the anammox reaction occurs.
Anamnestic response: Rapid immune response to antigens to which the host has previously been exposed. Also known as an immunological or recall response.
Anamorphs: Asexual growth morphology in fungi.
Anaphylactic shock: A destructive reaction between an antigen and antibody. Results in smooth muscle contraction.
Anaphylatoxins: Molecules that attract cells to a site of inflammation. Includes complement factors C3a, C4a and C5a.
Anaplerotic reactions: Replacement reactions that permit the tricarboxylic acid (TCA) cycle to continue. The replenishing of oxaloacetic acid by carboxylation of pyruvate is a key anaplerotic reaction.
Anastomosis: Fusion of cytoplasmic extensions and pseudopodia between the same or different individuals.
Angular aperture: The angle through which light enters the objective lens.
Anion: A negatively charged atom.
Annotation: Notes explaining the putative biological roles of gene products deduced from genome sequencing.
Anoxic: An environment that lacks oxygen.
Anoxygenic photosynthesis: Photosynthesis in which O2 is not produced. Employs electron donors other than H2O. H2S, H2, and reduced organic compounds would donate electrons in anoxygenic photosynthesis.
Antenna pigments: Light harvesting substances other than chlorophyll α used by photosynthetic organisms.
Antheridia: One of two types of hyphae in conjugating Ascomycetes. Antheridia transfer haploid nuclei to asconia.
Antibiotic: A metabolite produced by a microorganism that inhibits or destroys other microorganisms.
Antibiotic-resistance gene cassettes: Segments of DNA, often part of a mobile genetic element such as an integron, encoding antibiotic resistance determinants.
Antibody: A glycoprotein present in body fluids that can bind specifically to an antigen. An immunoglobulin.
Anticodon: The three-base sequence on tRNA that is complementary to the three-base codon of mRNA.
Antigen: A substance recognized by the body as nonself and which elicits the immune response. An immunogen.
Antigen presentation: A process wherein certain immune cells (i.e., macrophages, dendritic cells, and B cells) capture and process foreign proteins, display peptide fragments of these on their plasma membrane attached to major histocompatibility antigens, and stimulate T cells, which then mount an immune response.
Antigen-presenting cell (APC): Phagocytic cells that process antigens and present them to T cells in the immune response.
Antigenic determinants: Regions of an antigen that elicit an immune response. Also termed epitopes.
Antigenic drift (shift): Antigenic variation resulting from alterations in antigen genes.
Antigenic variation: See antigenic drift.
Antimetabolite: Compound that inhibits metabolism in microorganisms. General structure resembles a natural metabolite and competes for active sites on enzymes.
Antimicrobial agent: Anything that inhibits or kills microbial cells.
Antiparallel: The strands in double stranded DNA are oriented in opposing directions-one 3′ → 5′ the other 5′ → 3′.
Antiseptic: A chemical generally applied externally that destroys microbes without serious harm to the tissue.
Antiserum: A serum that contains specific antibodies.
Anti-sigma factors: Proteins that interfere with transcription by sequestering sigma factors.
Antitermination: The ability of RNA polymerase to overcome premature termination caused by a hairpin structure called a terminator.
Antiterminator: A secondary RNA structure that disrupts the structure formed by a terminator.
Antitoxin: An antibody specific for a toxic substance.
Apical complex: Set of organelles for host cell invasion found in Apicomplexa.
Apoptosis: Elimination of aberrant cells by programmed cell death.
Apothecium: Disk-shaped ascocarp.
Aquifex: A deep-branching phylum of the Bacteria.
ARC: Aids Related Complex is a series of symptoms associated with an HIV infection and may lead to an active case of AIDS.
Archaea: One of the three domains of living organisms; formerly termed Archaebacteria.
Artificial classifications: Taxonomies that not based on evolutionary principles.
Artificial competence: The ability of bacteria to take up exogenous DNA following treatment with certain chemicals.
Ascocarp: In Ascomycetes, hyphae assembled into a single structure that holds the crozier for sexual reproduction.
Ascogonia: One of two types of hyphae in conjugating Ascomycetes. Ascogonia are the recipient of haploid nuclei from antheridia.
Ascospores: Haploid spores formed inside the ascus of Ascomycetes.
Ascus: The terminal hyphae in the ascocarp where meiosis occurs.
Aseptic technique: The manipulation of microorganisms such that contamination by undesirable organisms is prevented.
Assimilation: Uptake of nutrients and conversion to cellular components.
Assimilatory sulfate reduction: Uptake of sulfate to fulfill nutrient requirements of an organism.
Astrobiology: The study of early life on Earth and the exploration of life in the Universe.
ATP-Binding Cassette (ABC) transporters: Membrane protein complexes that use ATP to transport substrates without alteration of the compound transported.
attB: A specific sequence on DNA which serves as a site for integration of bacteriophages or plasmids through recombination with their attP sites.
Attenuation (transcriptional): Temporary pause by RNA polymerase during transcription, usually in response to specific signals.
Attenuation (of a microbe): Weakening of a pathogen to be employed in immunization.
Autecology: The study of a species in its natural environment.
Autochthonous: Indigenous microbial populations.
Autoclave: An instrument that uses heat and steam under pressure to destroy all microbes present.
Autoimmune disease: A state in which antibodies are formed against self-antigens.
Autoinducers: Signaling molecules produced by bacteria for the purpose of coordinating gene expression during quorum sensing.
Autolysin: Enzymes in bacteria that form breaks in peptidoglycan, permitting incorporation of newly formed wall units during growth.
Autolysis: Process in which peptidoglycan is disrupted, causing cell lysis mediated by autolysins.
Autophosphorylation: Modification of an amino acid on an enzyme by self-phosphorylation; often carried out by sensor kinases of the two-component signal transduction systems.
Autotroph: An organism that can utilize CO2 as sole source of carbon.
Auxotroph: A mutant that has lost the ability to synthesize a metabolite normally synthesized by the microbial strain.
Avirulent: An infectious disease agent that does not have virulence and thus does not cause pathology.
Axenic culture: A culture free of contaminating organisms. A pure culture.
Axial filament: An endoflagellum produced by members of the phylum Spirochaetes.
Axoneme: Arrangement of microtubules in the cilium.
Bacillary dysentery: A bacterial disease caused by enteric bacteria, esp. Shigella dysenteriae.
Bacillus (bacillary): An oblong bacterium; also called a rod; a name for a bacterial genus.
Bacitracin: An antibiotic that prevents recycling of the undecaprenol pyrophosphate carrier during peptidoglycan synthesis.
Bacteremia: Presence of bacteria in the bloodstream; generally transient.
Bacteria: One of the three domains, along with Archaea and Eukarya.
Bacterial enumeration anomaly: The inability to cultivate most of the microorganisms from most natural habitats.
Bactericide: Agent that kills bacteria. Mercuric chloride is a bactericide.
Bacteriochlorophyll: Chlorophyll pigments of anoxygenic photosynthetic bacteria.
Bacteriocin: Protein produced by a bacterial strain that kills related strains.
Bacteriocinogenic plasmids: Plasmids carrying genes for bacteriocins.
Bacteriolytic agent: An agent that causes dissolution of the bacterial membrane.
Bacteriophage: Virus that infects Bacteria or Archaea.
Bacteriorhodopsin: A carotenoid in the purple membranes of halophiles that resembles rhodopsin in the visual cells of animals. It is involved in light-driven ATP synthesis.
Bacteriostatic: Inhibits bacterial reproduction or growth but does not kill.
Bacterivores: Species that consume bacteria.
Bacteroid: An osmotically fragile bacterium that lives within protected areas such as plant root nodules or the intestinal tract.
Bacteroidetes: A major phylum of the Bacteria.
Bactoprenol: A lipid that carries the saccharide units of peptidoglycan or lipopolysaccharide core across the cytoplasmic membrane. Also called undecaprenol.
Baeocyte: A reproductive cell produced by some cyanobacteria.
Balanced growth condition: When all metabolic intermediates required for growth are available at the appropriate level.
Banded-iron formations (BIFs): Bands of ferric iron deposited in geologic strata during the era when oxygenic photosynthesis evolved.
Barophiles: Organisms that thrive at high hydrostatic pressure. Also termed piezophiles.
Barotolerant: Can grow under high pressure but generally grows better at normal pressure.
Barrier defense: The first level of host defense against infection; includes chemical, mechanical, microbial, and physical components.
Basal body: A structure equivalent to the centriole, found at the base of cilia.
Basal structure: The component of the flagellum in the cell envelope. Anchors the flagellum to the various layers of the cell wall and includes the flagellar motor.
Base composition: Relative percent of the total cellular DNA that is guanine-cytosine (G + C). Remainder is adenine-thymine (A + T).
Base-pairing: Hydrogen bond formed between specific bases of DNA and RNA: A with T (or U) and G with C.
Basic dyes: Positively charged staining compounds that are most commonly used to stain microorganisms.
Batch culture: Growth of a microorganism in a closed vessel, on a suitable medium, at an appropriate temperature, and for a selected time.
B cell (lymphocyte): An antibody-bearing cell that can differentiate during the immune response to secrete antibody (plasma cell) or to form a memory cell.
B-cell receptor: Membrane-bound surface immunoglobulin (antibody) on a B lymphocyte; allows it to recognize and react with antigens.
Bdelloplast: The spheroidal cell resulting from an infection by Bdellovibrio.
Beta (β): A subunit of RNA polymerase.
Beta-hemolysis: The lysis of red blood cells due to specific bacterial toxins that produce transparent zones around colonies on blood agar plates.
Beta-hydroxybutyrate: A storage polymer produced by many bacteria.
Binary transverse fission: Simple symmetrical division of a bacterium to yield two cells.
Binomial system: A system for naming organisms with a genus name and a specific epithet.
Bioaugmentation: The process of amending contaminated sites with bacteria that are capable of degrading toxic compounds.
Biochemical oxygen demand (BOD): A test in which the oxygen required by microorganisms to catabolize organic matter present in a water sample is measured.
Bioconversion (biotransformation): Biologically induced modification of a substrate to generate a more useful product. The substrate converted is not utilized for growth.
Biodegradation: Destruction of organic compounds by microorganisms.
Biodiversity: The extent of species richness in habitats.
Biofilms: A layer produced by microorganisms on solids in environments that contain fluids.
Biogeochemical cycles: The processes whereby chemical materials such as carbon, nitrogen, and sulfur are recycled by biological and geological processes.
Biogeography: The distribution of organisms in the environment.
Biological insecticides: Organic materials that are produced by organisms and are toxic to insects.
Biological tertiary treatment: The processes whereby nitrogen and phosphorus are removed in wastewater treatment.
Bioluminescence: Production of light by living organisms.
Biomagnification: Accumulation of substances, generally deleterious, by consumer organisms.
Biomarker: A chemical substance produced by an organism that serves as a signature for the presence or activity of that organism or group of organisms.
Biomass: Total living cellular material in an environment.
Bioremediation: Removal of toxic or undesirable environmental contaminants by microorganisms.
Biosynthesis (anabolism): Synthesis of macromolecules from monomers during cell growth.
Biotechnology: Use of living organisms to generate useful industrial products. Usually involves genetic manipulation.
Biotic: Produced or caused by organisms.
Biotransformation: Use of microbes or enzymes to convert a substrate to a modified form.
Biovars: A term used to identify a particular sub-species or organism; a biological variety.
Botulism: A food-borne disease caused by ingestion of toxin and/or Clostridium botulinum.
Bridging immune system: A group of defense processes that have some characteristics of both the adaptive and innate immune systems.
Broad-spectrum antibiotic: Antimicrobial that is effective against both gram-positive and gram-negative bacteria.
Brucellosis: A disease caused by Brucella species.
Bt protein: A protein produced by Bacillus thuringiensis that is toxic to insects.
Bubo: Swelling of lymph nodes following infecion with Yersinia pestis.
Bubonic plague: A disease caused by Yersinia pestis and characterized by the appearance of buboes; also called the Black Death.
Budding: Asexual reproduction in which progeny arise from protuberances on the surface of the parent cell.
Bulking: A microbial process that prevents settling in secondary clarifiers and is therefore deleterious to sludge removal.
Butanediol fermentation: A specific type of low-acid fermentation typical of some enterics.
Butyric acid bacteria: Bacteria that produce butyric acid in sugar fermentation such as some Clostridium species.
Cachexia: A response to tumor necrosis factor alpha that results in wasting or severe weight loss.
Calorie: Amount of heat energy required to raise a gram of water from 14.5°C to 15.5°C.
Calvin cycle: The major pathway for CO2 fixation during photosynthesis in plants, algae, cyanobacteria, and many photosynthetic bacteria. Some chemolithotrophs also utilize this pathway. Sometimes referred to as the Calvin-Benson cycle.
Capsid: The protein coat that surrounds viral nucleic acid.
Capsomers: Protein subunits that together form an icosahedral capsid.
Capsule: An organized layer of biosynthetic origin, often a polysaccharide, that surrounds the outer wall or envelope of the bacterium.
Carboxysomes: Inclusion bodies present in autotrophs composed of ribulose-1,5-bisphosphate carboxylase (Rubisco). This enzyme is involved in CO2 fixation via the Calvin cycle.
Carcinogen: An agent, generally a mutagen, that causes cancer.
Carotenoid: Red to yellow pigments found in many bacteria. Can serve as accessory pigments in photosynthetic organisms. Also a pigment in many nonphotosynthetic microorganisms.
Carrier: An infected individual that transmits disease to others. Usually a carrier has a subclinical infection.
Catabolism: Reactions involved in reduction of larger molecules to smaller molecules, generally with the release of energy.
Catabolite repression: Curtailment of the synthesis of selected enzymes by the availability of glucose or other metabolites as substrate.
Catalase: An enzyme that breaks down hydrogen peroxide to water and oxygen.
Catalyst: A compound that increases the reaction rate without itself being altered.
Cationic: Having a positive charge.
CD3: A set of glycoproteins on the surface of T cells that provide the signaling component of the T cell receptor for antigen.
CD4: Specific antigen on selected cells such as T cells. CD4+ cells are host for HIV.
CD8: A specific antigen on selected T cells that often have the property of being cytotoxic (kill other cells).
CD28: A costimulatory surface molecule of T cells that must interact with its ligand in order for naïve T cells to be activated by antigen.
cDNA: A DNA copied from an RNA template using the enzyme reverse transriptase.
Cell: Basic unit of living matter.
Cell cycle: Sequence involved in growth/division of a cell.
Cell envelope: The layers that lie outside the cell membrane of microorganisms.
Cell growth: Increase in cell size in absence of division.
Cell-mediated immunity: T cells and activated macrophages are involved in clearing the host of infection.
Cell sorters: Flow cytometers used to count and separate cells.
Cell theory of life: The concept that all organisms consists of subunits termed cells.
Cell wall: A tough structure surrounding the bacterial cytoplasmic membrane that gives the cell shape and protection.
Cellular differentiation: The process whereby cells undergo morphological changes or morphogenesis.
Cellular immunity: See cell-mediated immunity.
Centers for Disease Control and Prevention (CDC): A division of the U.S. Public Health Service involved in tracking diseases, providing information on diseases, and advising government agencies on disease prevention.
Centric diatoms: Diatoms with radial symmetry.
Centromere: Short repeated DNA sequences in eukaryotic chromosomes that bind kinetochore proteins.
Chancre: An early lesion that occurs in the primary stages of syphilis.
Chaperones: Specific proteins that are involved in the folding and assembly of other proteins.
Chasmolithic: Organisms that live in the cracks of rocks.
Chemical mutagens: Compounds that modify bases on DNA, resulting in mutations.
Chemical oxygen demand (COD): Amount of chemical oxidant necessary to oxidize organics in water to CO2.
Chemiosmosis: Development of a chemical potential across a cytoplasmic membrane that can drive ATP synthesis. Protons are driven outward by electron carriers or light.
Chemoautotrophic: Organisms that obtain their energy from reduced chemical compounds and are capable of synthesizing organic material from carbon dioxide.
Chemoheterotrophic: See chemoorganotrophic, also heterotrophic.
Chemolithotroph (chemoautotroph): A microorganism that obtains its energy by oxidation of inorganic compounds and utilizes CO2 as its carbon source.
Chemoorganotroph (heterotroph): A microorganism that obtains its energy by oxidation of organic compounds and utilizes carbonaceous substrates other than CO2 for growth.
Chemoreceptors: Proteins in the cytoplasmic membrane or periplasm that bind chemicals involved in chemotaxis.
Chemostat: A continuous culture apparatus that feeds growth medium, with one substrate at limiting concentration, into a culture vessel and permits removal of cells at a rate that maintains steady state growth.
Chemotaxis: Movement of a microorganism toward a chemical attractant or away from a repellent chemical.
Chemotherapy: Treatment of disease with chemicals that destroy the agent without serious harm to the host.
Chi site: A site on DNA nicked by RecB, RecC, and RecD nucleases during homologous recombination.
Chlamydiae: One of the major phyla of Bacteria.
Chlorination: The process in which chlorine is used to disinfect drinking water and water in swimming pools.
Chlorobi: A major phylum of the Bacteria.
Chloroflexi: A major phylum of the Bacteria.
Chlorophyll: A tetrapyrrole with a molecule of magnesium in the center that captures light energy during photosynthesis.
Chloroplast: The chlorophyll-containing organelle in photosynthetic eukaryotes.
Chlorosome: An oblong protein-bound structure in green sulfur bacteria that contains the light-gathering pigments. It is located on the inner surface of the cytoplasmic membrane.
Cholera: A water-borne enteric disease caused by Vibrio cholerae.
Cholera toxin: A secreted toxin produced by Vibrio cholerae, responsible for the major symptom (diarrhea) of cholera.
Chromatic aberration: Lens defects caused by the differences in wavelengths of white light.
Chromophore: The pigmented or colored portion of a dye.
Chromosome: The site of cellular DNA. The Archaea and Bacteria generally have one circular chromosome. One microorganism (Borrelia burgdorferi) is known that has a linear chromosome. Eukarya are multichromosomal.
Chromosome mobilizing ability: The ability of integrated plasmids to mediate transfer of chromosomal genes.
Chronic infection: Long-term infection.
Cilia: Projections on the surface of cells that move substances over the cell, or in some cases, move the cell itself.
Classification: Placing organisms in groups based on phylogenetic relatedness.
Cleistothecium: Spherical ascocarp.
Climax state: The stable end-state of a biological succession.
Clonal selection: Theory that clones of specific B or T cells are stimulated to reproduce when an appropriate antigen binds to their surface.
Clone: Genetically identical progeny of a single parent.
Cloning: Generation of multiple copies of the same organism. In genetic engineering, it refers to the capture and propagation of a copy of a gene.
Cloning vector: A bit of replicative DNA that can transport inserted foreign DNA into a recipient cell.
Clonotypic population: A group of cells that arise from a single progenitor.
Coagulase: An enzyme capable of inducing the coagualtion cascade in blood.
Coccus (coccoid): A spherical bacterium.
Codon: A sequence of three bases (purines or pyrimidines) in messenger RNA that codes for a specific amino acid.
Coenocytic: A filamentous organism that contains nuclei that are not separated from one another by cell septa. Results from repeated nuclear division without cell division.
Coevolution: Parallel changes in ecologically interdependent species to maintain an interaction.
Colicins: Plasmid-encoded proteins produced by enterics that harm other enteric bacteria.
Coliform bacteria: Gram-negative facultative aerobic bacteria that ferment lactose with formation of gas within 48 hours at 35°C.
Colonize: To take up residence in a host.
Colony: A visible assemblage of microorganisms growing on a solid surface. Generally from reproduction of a single cell.
Colony forming unit (CFU): Single cell that can form a colony on a solid medium.
Colony hybridization: Detection of a specific DNA sequence in a bacterial colony by DNA hybridization with a labeled probe.
Cometabolism: Transformation of a nongrowth substrate by microorganisms grown or growing on a utilizable substrate.
Commensalism: A symbiotic association where one organism benefits and the other(s) is unaffected.
Common-source epidemic: One in which all victims are infected from a single source. Food poisoning is an example.
Community: A mixed population of microorganisms in a natural habitat or microcosm.
Comparative biochemistry: Examination of the universality of equivalent biochemical reactions among all species.
Comparative genomics: Elucidation of structure, function, and evolution of genes by comparison of two or more genome sequences.
Compatible solute: Organic or inorganic compound that increases the internal osmotic pressure inside a bacterium to that outside.
Competent: A bacterial cell that can take up DNA fragments and be transformed.
Competitive inhibitor: A chemical analogue that replaces a natural substrate and competes for active sites.
Complement: A series of proteins in the blood that act sequentially (cascade) and are involved in the removal of antigen/antibody complexes and microbes by tagging them for phagocytosis (opsonization). Produces pores in cells and microbes, thus killing or inactivating them and attracting phagocytic cells to sites of inflammation.
Complement receptor: A cell surface component that binds a fragment of complement.
Completed test: The final tests used to identify a fecal coliform bacterium.
Complex medium (undefined): A culture medium in which the chemical composition of the ingredients is not precisely determined.
Composite transposon: A transposon consisting of one or more genes (usually antibiotic resistance genes) flanked by two insertion sequences.
Composting: Process of degrading plant material, typically in bins.
Compound light microscope: A microscope that uses two lens systems, the objective and the ocular, for viewing specimens.
Concatemer: Viral genomic material in which individual genomes are linked end-to-end. The linear structure is split to individual genomes upon viral assembly.
Condenser lens: A lens used to direct intense light onto the object being viewed.
Confirmed test: The second test in the identification of coliform bacteria from natural samples.
Conformation: Three-dimensional structure of a folded protein.
Congenital: Disease contracted maternally during gestation or birth.
Conidia: Hyphae that form asexual dispersal spores.
Conidiospores: Aerial spores produced by actinobacteria and fungi; used for dispersal.
Conjugal (sex) pili: Organelles used by the donor bacteria to recognize recipients during conjugative transfer of DNA.
Conjugation: Transfer of DNA from donor to recipient by direct cell to cell contact.
Conjugative transposon: A transmissible genetic element that can excise from the chromosome of a donor cell and transfer to a recipient, where it inserts into a new site.
Consortium: An assembly of several bacteria in which all benefit to some degree from the association.
Constitutive enzyme: An enzyme not subject to regulation; always expressed during growth.
Consumer: An organism that ingests other organisms as a source of nutrients and energy.
Contig: A contiguous sequence of DNA generated by assembly of overlapping sequences.
Continuous culture: A system where the addition of nutrients and removal of wastes permits long-term active growth.
Contractile vacuole: Vacuole system found in many eukaryotes responsible for excretion of excess water and ions by osmoregulation.
Convergent evolution: Development of similar characteristics by unrelated organisms because they adapt similarly to an environmental challenge.
Cord factor: A component of the cell wall of virulent M. tuberculosis consisting of molecules of mycolic acid that are attached to trehalose.
Corepressor: A low-molecular-weight compound that functions in enzyme repression.
Cortex: Dense area between the endospore coat and core in endospore-forming bacteria.
Coryneform bacteria: Bacteria such as the genus Corynebacterium that divide by a snapping division process that produces unusual shapes.
Co-translational protein translocation: A type of secretion mechanism where the signal peptide of a protein interacts with the Sec secretion apparatus prior to completion of its synthesis by the ribosome.
Covalent bond: A chemical bond resulting from sharing of electrons.
Crateriform structures: Distinctive pits produced on the outer surface of members of the Planctomycetes.
Cristae: In-folding membranes in mitochondria that hold some respiratory enzymes.
Critical point drying: A process in which water is removed from a specimen as a gas.
Crossbands: "Septum-like" structures in caulobacter stalks that are produced during cell division.
Cross-resistance: The development of resistance to one antimicrobial agent effects resistance to another.
Crossing-over: In meiosis, where adjacent DNA strands are exchanged.
Crown gall: A plant tumor produced by Agrobacterium tumefaciens.
Crozier: Structure that forms at terminal hyphae in Ascomycetes where conjugation occurs.
Crustose: Form of a lichen that is compact and grows close to a substrate.
Culture: A strain growing on a laboratory medium.
Culture collection: A place that holds microbial cultures in a living state so that they can be used by others for comparative purposes.
Culture medium: A liquid or solid nutrient on which microorganisms can be grown.
Curing: Loss of a plasmid in one of the daughter cells during cell division.
Cyanobacteria: The Bacteria that can grow photosynthetically via oxygenic photophosphorylation. Morphologically diverse.
Cyanophycin: A non-protein polymer consisting of the two amino acids aspartate and arginine.
Cyanosis: Blueish appearance of the skin caused by lack of oxygen in the blood.
Cycles of matter: Natural processes whereby major constituents of living cells (C, N, S) are recycled.
Cyclic photophosphorylation: Cyclical movement of electrons in photosystem I.
Cycloserine: An antibiotic that inhibits addition of alanines to UDP-N-acetyl muramic acid during early stages of peptidoglycan synthesis.
Cyst: Cell temporarily protected inside a cell wall, usually during dormancy.
Cyst (parasites): A sac like structure that forms around parasites.
Cyst (pathology): An abnormal membranous sac containing a gaseous, liquid, or semisolid substance.
Cysticercoid: The larval stage of certain tapeworms.
Cytochromes: Heme proteins involved in electron transport.
Cytokines: A group of proteins produced by leukocytes that direct the functions of cells with specific receptors for them.
Cytokinesis: Division of the cytoplasm of a dividing cell.
Cytolethal distending toxin: A DNA damaging toxin produced by Campylobacter jejuni.
Cytoplasm: The liquid contents of a cell. Surrounded by a cytoplasmic membrane.
Cytoplasmic domains: The portion of a membrane-bound molecule that is within the cell cytoplasm.
Cytoplasmic inclusion: An intracellular storage granule in a bacterium.
Cytoplasmic membrane or cell membrane: The protein and lipid structure that surrounds the cytoplasm of cell.
Cytoproct: A region of the eukaryotic cell cortex specialized in the excretion of undigested food vacuole contents.
Cytoskeleton: Network of microtubules and microfilaments that gives a eukaryotic cell its shape and the ability to arrange organelles and move.
Cytostome: The oral structure, or specialized feeding area found in many protists.
Cytotoxic: A frequent property of CD8 T lymphocytes which allows these cells to kill virus-infected host cells.
Cytotoxin: A toxic material that destroys cells. Some pathogens produce these compounds.
Cytotrophs: Species that consume eukaryotic cells.
Dark-field microscopy: A process for indirect illumination such that the specimen is illuminated against a dark background.
Dark reactions: The Calvin cycle of carbon dioxide fixation that accompanies the light reactions of photosynthesis.
Death phase: The phase in batch culture in which the viable population is in decline.
Decomposition: The degradation or breakup of complex organic material to constituent parts culminating in the production of inorganic materials.
Defensins: Host peptides that lyse bacteria and some protozoa.
Defined medium: One in which the composition and quantity of all components are known.
Delayed type hypersensitivities: A type of host immune response characterized by the presence of T lymphocytes and macrophages and which takes 48 hours to develop. Contact dermatitis is an example.
Deletion: Absence of a DNA segment in a mutant, relative to the same region in the chromosome of the wild-type parent.
Denaturation: Change in a protein or other macromolecule that destroys activity.
Dendritic cell: An antigen-presenting cell; present in lymph nodes and spleen.
Denitrification: Reduction of oxidized forms of nitrogen to N2 gas via anaerobic respiration.
Deoxyribonucleic acid (DNA): A nucleotide polymer composed of deoxyribonucleotides joined by phosphodiester bonds. The genome of an organism is composed of DNA.
Dermatomycosis: Fungal skin infections.
Detritus: Particulate material that is nonliving.
Dextrans: Polymers of glucose or dextrose.
Diamino acid: An amino acid such as lysine that has more than one amino group.
Diaminopimelic acid: An example of a diamino acid found in the peptidoglycan of some gram-negative bacteria.
Diapedesis: Movement between cells, e.g., the process by which a neutrophil migrates from the bloodstream into the tissues.
Diauxie: Biphasic growth that can occur when two substrates are available in a culture medium.
Differential media: Culture media that permit growth of one bacterial type and inhibit others or permit a microorganism to demonstrate specific biological properties.
Differential stains: Stains such as the Gram stain that distinguish one type of bacterium from another.
Differentiation: Changes in the structure of a microorganism during the growth cycle.
Dimer: Compound formed by joining of two monomers.
Dimorphic life cycle: A life cycle in which two different cell types are found.
Diphtheria: An infection by Corynibacterium diphteriae expressing diphtheria toxin.
Diphteria toxin: A protein toxin produced by C. diphteriae capable of killing mammalian cells by inhibiting their protein synthesis.
Dipicolinic acid: An acid uniquely produced by endospore-forming bacteria.
Diploid: A state in eukaryotes in which two copies of each chromosome are found.
Diploid nucleus: A nucleus that holds two complete sets of chromosomes.
Disease: Disturbance of normal structural or functional capacity of an organism.
Disinfect: A way to destroy all microorganisms.
Disproportionation: A type of metabolism which requires that part of the substrate is metabolized by one pathway and part is metabolized by another pathway. For instance, a part of the substrate may be oxidized so that the remainder may be reduced.
Dissimilatory sulfate reduction: The use of sulfate in anaerobic respiration.
DNA library (gene library): Cloned DNA fragments that represent the genes in the entire genome of an organism.
DNA ligase: An enzyme catalyzing the joining of ends of DNA strands.
DNA microarrays: A collection of genes or segments of genes, attached to solid support, usually chemically derivatized glass slides.
DNA Pol I, II, III: Forms of DNA polymerases used in replicating the bacterial chromosome.
DNA vaccine: Immunization by injection of DNA encoding a protective antigen into host cells, resulting in its transcription and induction of an immune response by the transcribed protein.
Domain: The highest level of classification of all life based on rRNA analysis. The three domains are Bacteria, Archaea, and Eukarya. A domain is also used to describe an area of a macromolecule.
Donor: A cell that is the source of plasmid during conjugative DNA transfer.
Double-crossover: Two homologous recombinations at proximal sites, resulting in the replacement of one DNA segment by another.
Doubling time: Time required for a population to double in number.
Duodenum: A region of the small intestine.
D value: Decimal reduction time. Time required to reduce a population to one-tenth the original.
Early message: Messenger RNA formed immediately after viral infection, which is translated to catalytic proteins that disrupt host cell function.
Ecosystem: Total organismic community and associated abiotic components of a selected environment.
Ecovars: Ecological varieties of species.
Ectomycorrhizae: Association between fungi and root tip, in which the fungi form a sheath about the root.
Ectosymbionts: Symbionts that reside on the outer surface of organisms.
Edema: Accumulated fluid that results in swelling of a tissue.
Electron acceptor: The component that accepts electrons during an oxidation-reduction reaction.
Electron donor: The component that donates electrons during an oxidation-reduction reaction.
Electron micrograph: A photograph taken with an electron microscope.
Electron transport chain: Series of electron acceptors and donors that transfer electrons from an electron carrier, such as NADH, to a terminal acceptor, such as O2. Also functions during photophosphorylation.
Electrophoresis: Separation of charged molecules, such as protein or DNA, in an electrical field.
Electroporation: Use of an electrical pulse to alter the cytoplasmic membrane, thus promoting uptake of DNA fragments.
Elemental sulfur granules: Small spherical deposits of elementary sulfur (S0) produced by some heterotrophic and photosynthetic bacteria.
Elongation factors EF-G, EF-Ts and EF-Tu: Factors responsible for the movement of ribosomes along the mRNA following initiation of protein synthesis.
Embden-Meyerhof pathway (glycolysis): A pathway that catabolizes glucose to two pyruvic acid molecules and generates two molecules of ATP.
Empty magnification: Magnification without commensurate increase in resolution.
Enantiomers: Molecules whose chemical structures are mirror images of one another.
Encystment: The process of forming a cyst.
Endemic disease: One that is present at a constant low level in a population.
Endemic species: Species, such as kangaroos, that are found in only one geographic area.
Endemic typhus: See murine typhus.
Endergonic reaction: One that requires energy input to proceed.
Endocarditis: Infection of heart valves.
Endocytosis: Uptake of a particle, such as a virus, by enclosing it via membrane extension and pinching off of the vesicle formed.
Endoflagella or periplasmic flagella: Produced by members of the Spirochaetes; lie outside the cell membrane but inside the cell wall.
Endogenous pathway of antigen presentation: Presentation of antigens by antigen-presenting cells, with the peptides being generated by digesting proteins in the cytoplasm of the host cells. These are normally complexed with MHC class II molecules on the surface of the host cell. They are often derived from pathogens that are living inside the host cell.
Endogenous pyrogen: A protein that induces fever in a host.
Endomycorrhizae: A fungus-plant root association in which the fungus penetrates into the root cells.
Endophyte: A microorganism, often a cyanobacterium, that lives within a plant.
Endospore: A heat-resistant dormant cell that forms within the cell of selected bacteria.
Endosymbiosis: Growth of a microorganism within another organism that is generally beneficial to both.
Endosymbiotic theory: The theory that the mitochondrion, chloroplast, and other organelles arose through an endosymbiotic association of bacteria with eukaryotic ancestors.
Endotoxemia: A host response to endotoxin which results in intravascular coagulation of blood, edema, and sometimes death.
Endotoxin: The lipopolysaccharide portion of the outer envelope of gram-negative bacteria released by cell lysis or during growth; toxic to animal hosts.
Energy: Capacity to do work.
Enrichment culture: Addition of a selected substrate to a culture medium to isolate an organism that can grow on that substrate. Physical conditions may also be adjusted to obtain a specific type of organism.
Enteric: Intestinal; often used to describe microorganisms associated with the intestinal tract.
Enterocolitis: Inflammation of both the small and large intestine.
Enterohaemorrhagic E. coli: A strain of shiga-like toxin producing E.coli.
Enteropathogenic E. coli: A strain of E. coli capable of destruction of intestinal lining.
Enterotoxigenic: Enterotoxin-producing strain of E. coli causing severe diarrhea.
Enterotoxin: A toxin that adversely affects the intestinal tract.
Entner-Doudoroff: A nonglycolytic pathway of glucose catabolism that produces pyruvate and glyceraldehyde-3-phosphate.
Envelope: The outer structure in gram-negative bacteria of the membranous layer that surrounds the capsid of some viruses.
Enzyme: A highly specific protein catalyst.
Enzyme-linked immunosorbent assay (ELISA): A technique to detect specific antigens or antibodies, using enzymes as the detector system.
Eosinophils: A type of white blood cell that is in the myeloid lineage and has cytoplasmic granules.
EPA superfund sites: Locations in the USA that have been designated by the Environmental Protection Agency as sites that are highly contaminated with toxic materials.
Epidemic: A marked increase in the number of individuals affected by an infectious disease during a given period of time.
Epidemic typhus: An infection caused by Ricketsia prowazekii.
Epidemiology: The study of prevalence, incidence, and transmission of infectious diseases.
Epilimnion: Aerobic, relatively warm layer of water in a stratified lake; lies above the thermocline.
Epilithic: Organism that grows on the surface of a rock.
Episome: A plasmid that can integrate into the host genome or function separately.
Epitope: A specific area on an antigen that elicits an antibody response.
Erythrogenic toxin: A toxin produced by Streptococcus pyogenes responsible for the symptoms (rash) of scarlet fever.
Etiologic agent: The specific cause of a disease.
Eukarya: One of the three domains. Composed of organisms that have a membrane-bound nucleus and division of DNA by mitosis.
Eutrophic: An environment, usually aquatic, overly rich in nutrients.
Excystment The process of coming out of a cyst.
Exergonic: A reaction that liberates energy.
Exoenzyme: An enzyme that is secreted by the organism.
Exogenous pathway: Presentation of killed foreign antigens by antigen-presenting cells. Normally these are degraded in the endosomal pathway and the resulting peptides complexed with MHC class II molecules on the surface of the host cell.
Exon: Sequences in a split gene that code for messenger RNA.
Exotoxin: A toxin released by cells, generally during growth.
Exponential growth: Balanced growth in which each microbial cell is dividing during a fixed period of time.
Expression vector: Type of plasmid used in recombinant DNA technology, where the expression of the cloned gene(s) is directed from a promoter on the vector.
Extracellular enzyme: An enzyme excreted by a microorganism to cleave large molecules to a size transportable into the cell.
Extracellular polymeric substances (EPS): Polymeric materials that are produced outside the cell wall.
Extrachromosomal elements: DNA found in bacteria that is not part of the chromosome, such as plasmids.
Extreme: Employed with thermophiles or halophiles to indicate that they grow at the highest temperature or salt concentration of microorganisms presently described.
Extremophile: Term employed with organisms that live under environmental extremes such as thermophiles or halophiles to indicate that they grow at the highest temperature or salt concentration of microorganisms presently described.
Extrusomes: Exocytotic vesicles that contain material to be discharged outside of the cell membrane for defense or offense.
F prime (F′): The F plasmid carrying a segment of chromosomal DNA.
Facilitated diffusion: Carrier mediated transport across a cytoplasmic membrane.
Facultative: Term applied to aerobes and autotrophs to indicate that the organism can grow either aerobically/anaerobically or autotrophically/heterotrophically under appropriate conditions.
Fall turnover: The period in the autumn in which the surface waters of a lake (the epimilinion) of thermally stratified lakes become colder and mix with the deeper waters of the lake hypolimnion.
Fastidious: A microorganism with complex growth requirements, generally due to its inability to synthesize requisite monomers.
Fatty acids: Organic acids such as acetate and butyrate.
Fc region: A fragment of an immunoglobulin composed of the C terminal regions of the heavy chains, which conveys function, such as complement activation, to the antibody molecule. The Fab region combines with a specific antigen.
Fecal coliform: Enteric bacteria that can grow at elevated temperature, about 44°C; also see coliform bacteria.
Feedback inhibition: Condition in which the end product of a biosynthetic pathway can curtail activity of enzymes at earlier steps in the sequence of synthetic reactions leading to that end product.
Fermentation: Production of ATP via catabolic sequences in which organic compounds serve as electron donor and organic intermediates as electron acceptor.
Fermenter: An organism that carries out fermentation.
Fermentor: A growth chamber used to culture microbes for commercial operations.
Fever: An increase in body temperature above the norm.
Filament (flagellar): The external portion of the flagellum, attached to the hook. Consists of thousands of assembled flagellin proteins.
Filamentous: A microorganism that, in normal growth, forms long strands.
Filamentous hemagglutin: A surface adhesin of Bordatella pertussis.
Fimbriae: Filamentous structures on bacteria that play a role in adherence or in formation of pellicles or masses of cells.
Fine filaments: Fibrous cytoskeletal proteins that assemble into fine filaments.
Fixation (metabolism): The process whereby gases in the atmosphere are fixed into non-gaseous forms, e.g., nitrogen fixation and carbon dioxide fixation.
Fixative (microscopy): A chemical substance, such as formaldehyde or glutaraldehyde, that is used to preserve organisms for observation.
Fixed tissue macrophages: Macrophages that were derived from blood monocytes, but which now reside in host tissues and organs permanently.
Flagella: Structures involved in motility of bacteria.
Flagellin: The principal protein of flagella.
Flavoproteins: Riboflavin derivatives that are electron carriers.
Flocs: Particulate material that can be suspended in aqueous environments; may or may not be organic.
Flow cytometers: Instruments used for the separation of cells; see also cell sorter.
Fluid mosaic model: The accepted structure of cytoplasmic membranes with the phospholipids forming a bilayer. Proteins are embedded within the membrane or associated peripherally at either surface.
Fluorescence: Emission of light of distinct wavelength after activation with light of a different wavelength.
Fluorescent antibodies: Specific antiserum that has been tagged with a fluorescent dye; used for the microscopic identification of organisms and localization of specific proteins.
Fluorogenic compound: A chemical substance that becomes fluorescent when cleaved enzymatically.
Flux: The rate at which a chemical substance is moved from one place to another.
Foliose: Lichens that have a leaflike appearance.
Follicles (within lymphoid organs): Structures in the germinal centers of the spleen and lymph nodes.
Follicular dendritic cells: Specialized antigen-presenting cells within follicles of germinal centers.
Fomites: Inanimate objects that can harbor pathogens and transmit them to hosts.
Food chain: The carbon cycle in which organisms at successively higher levels ingest smaller organisms at lower levels as their source of carbon and energy; photosynthesis is the ultimate source of carbon for consumers in the food chain.
Food infection: An infection caused by ingestion of food contaminated with disease-causing pathogens.
Food poisoning: Illness caused by toxins present in food due to growth of microorganisms on the foodstuff prior to ingestion.
Food web: Interlinked food chains.
Fragmentation: Reproduction in actinomycetes in which filaments break into individual cells.
Frameshift mutations: Mutations that change the reading frame of a gene, usually by insertion or deletion of one or two (but not three) base pairs.
Free energy: Total energy available to do work.
Fruiting body: A reproductive structure in some bacteria, such as myxobacteria or actinomycetes. Fungi commonly produce fruiting structures.
Fruticose: A lichen that is bush- or treelike.
Functional genomics A study of the biological function of genes and their products.
Fungi: Heterotrophic eukaryotes that have rigid walls.
Fungicide: An agent that kills fungi.
Fungistatic agent: An agent that prevents fungal growth.
G + C: The DNA of an organism has guanine paired with cytosine and adenine with thymine. G + C refers to the percent of the total DNA that is guanine-cytosine pairs.
Gametocyte: A form of the protozoan Plasmodium in infected red blood cells.
Gas vesicles: Organelles with protein membranes that fill with gas in aquatic bacteria; serve as flotation devices.
Gastroenteritis: Inflammation of the stomach lining or intestines; often caused by food poisoning or infections.
Gene: A segment of the genome that codes for a specific polypeptide, protein, tRNA, or rRNA.
Gene replacement: Swapping of genes, usually involving homologous recombination.
Gene transfer: The process by which genes are transferred from one species to another.
Generalized transduction: Transfer of any part of a bacterial genome when packaged randomly in a phage capsid.
Generation time: Time required for a population to double in number.
Genetic code: Triplet nucleotide sequences that specify a specific amino acid in a protein chain.
Genetic engineering: Modification of the genome of an organism.
Genetic map: The precise sequence of genes in the genome.
Genome: The complete genetic repertoire in a cell or virus.
Genomic island: A segment of DNA acquired by horizontal gene transfer.
Genomic library: A collection of bacteria carrying segments of DNA, representing the entire genome of an organism.
Genotype: Heritable genetic information in a cell.
Genus: A grouping of organisms that are closely related phylogenetically.
Geosmin: Organic molecules produced by actinomycetes and some cyanobacteria that give soil or water a distinct aroma.
Germicide: An agent that kills bacteria.
Germinal center: A structure that forms within the spleen and lymph nodes after antigen stimulation and supports developing antibody responses.
Germination: Loss of dormancy in an endospore.
Giardiasis: Infection of the intestinal tract with Giardia lamblia.
Glider: An organism that is motile without aid of flagella. Gliders move only when on a semi-solid surface.
Gliding motility: Motility that occurs without the aid of flagella. Gliding bacteria move on a semi-solid surface such as an agar plate.
Glomerulonephritis: Inflammation of kidneys often following bacterial infections.
Glucan: A glucose polymer, see dextran.
Glycocalyx: Equivalent to capsule, the layer outside the cell envelope or wall.
Glycogen: A branched polysaccharide composed of glucose; used as a storage granule.
Glycolysis: Anaerobic conversion of glucose to pyruvate via the Embden-Meyerhof pathway, generating ATP.
Glycosidic bonds: Covalent bonds between sugars in polysaccharides.
Glyoxylate cycle: A modification of the tricarboxylic acid cycle in which isocitrate is cleaved to form succinate and glyoxylic acid. The latter condenses with acetate to form malate. Functional in organisms growing on two-carbon compounds, such as acetate.
Gonorrhea: A sexually transmitted disease caused by Neisseria gonorrhoeae infection.
Gram stain: A differential stain that separates bacteria on the basis of retention of the dye crystal violet. Those with an outer envelope are decolorized by an ethanol wash (gram-negative), whereas those without an outer envelope retain the dye (gram-positive).
Granuloma: A nodule that forms in inflamed tissues. This is usually composed of myeloid and lymphoid cells.
Group translocation: Transport where a molecule moves across the membrane and is chemically modified during the process.
Growth factor: Low molecular weight compounds that must be added to growth media for selected organisms because they cannot synthesize them.
Growth rate: The rate at which bacteria reproduce.
Growth yield: A measure of cellular mass generated per ATP produced from a substrate.
Gyrase: A topoisomerase capable of introducing supercoils into DNA.
Hairpin structure: A double-stranded RNA structure formed by the complementary pairing of proximal inverted repeats.
Halophile: An organism that requires very high salt (sodium chloride) for growth.
Halorespiration: The process of using halogenated compounds as oxidants in respiration.
Halotolerant: Able to grow in high salt concentrations, although not requiring it.
Haploid nucleus: A nucleus with one complete set of chromosomes.
Hapten: A molecule (generally low molecular weight) that cannot elicit an antibody response against self unless coupled with a larger molecule.
Haustoria: Specialized tip of a hypha that makes contact with a host cell.
Heat shock proteins: Proteins produced under stress, particularly heat, which protect the cell.
α-helix: A helical structure present in DNA and some proteins formed by hydrogen bonding.
Helper T cell: A T lymphocyte that cooperates with a B cell in initiating the antibody response.
Hemagglutination: Coagulation of red blood cells.
Hemagglutinin: Adherence molecule on the surface of influenza virus.
Hematopoietic stem cell (HSC): A cell that can mature or differentiate into any of the lymphoid or myeloid cells that make up the host immune system.
Hemolysins: Bacterial toxins that can disrupt cytoplasmic membranes of cells. Generally hemolysins are assayed by use of red blood cells. Important in tissue invasion to release substrates for growth of pathogens.
Hemolysis: Lysis of red blood cells.
Hemorrhagic fever: A fever caused by a virus that leads to hemorrhage and shock. Death is frequently the result.
Herd immunity: Immunity to a pathogen in the majority of potential hosts; results in the inability of the pathogen to cause disease.
Heterocyst: Specialized cells in cyanobacteria that are sites of nitrogen fixation.
Heterofermentation: Fermentation of sugars to a mixture of products.
Heteropolymers: Polymers that contain two different types of chemical subunits.
Heterotroph: An organism that utilizes preformed organic substrates as its major source of carbon.
Hexose monophosphate shunt (HMS): Metabolism of glucose through 6-phosphogluconate leading to 5-carbon sugars for synthesis of nucleotides and other cellular components.
Hfq: A protein chaperone stabilizing the interaction between ncRNAs and target mRNAs.
High endothelial venules: Vessels that support the migration of lymphocytes from blood into lymph nodes.
High-energy compound: One that yields free energy on hydrolysis.
High-frequency recombinant (Hfr) strain: A strain with a self-transmissible plasmid integrated in its chromosome.
Histones: DNA binding proteins that package the DNA in eukaryotes.
Holdfast: Material produced by some sessile microorganisms that aids in attachment to solid surfaces.
Holoenzyme: A complex of RNA polymerase core enzyme with sigma factor.
Homofermentation (homolactic): Fermentation of sugars, mostly to lactic acid.
Homogeneous immersion: The procedure in microscopy in which a uniformly high refractive index is provided between the specimen and the objective lens to provide highest resolution in image formation.
Homologous recombination: Recombination between nearly identical DNA segments.
Hook: Component at the base of the flagellar organelle, which transmits the rotary movement from the shaft to the filament.
Hopanoids: Steroid-like compounds produced by cyanobacteria.
Horizontal evolution: Gene transfer between distantly related organisms.
Horizontal (lateral) gene transfer: Acquisition of new genes from other organisms.
Hormogonia: Specialized cells produced by some cyanobacteria.
Host: An organism on which a parasite or pathogen can grow.
Human immunodeficiency virus (HIV): The retrovirus that is the etiological agent of AIDS.
Humoral immunity: An immune response involving antibodies.
Humus: Organic component of soil.
Hybridization: Annealing of one single-stranded DNA or RNA to its complementary copy of DNA or RNA.
Hybridoma: Fusion of a cancer cell to a specific B cell to generate monoclonal antibodies.
Hydrogen bond: A weak, but important, bond between a hydrogen atom and an electronegative atom, such as oxygen or nitrogen. Important in helix formation and other macromolecular interactions.
Hydrogenosomes: Organelle evolutionarily derived from mitochondrion, involved in the anaerobic production of about 1 ATP from pyruvate.
Hydrogenotrophic: An organism that utilizes or "eats" H2 as a substrate for growth.
Hydrolysis: Cleavage of a compound by addition of water.
Hydrophilic: Affinity for, and solubility in, water.
Hydrophobic: Lacking affinity for water; mostly insoluble in water.
Hypersensitivity: Harmful, exaggerated immune responses, some of which are known as allergies.
Hyperthermophiles: Archaea or Bacteria that have an optimal growth temperature above 80°C.
Hyphae: Filamentous cellular extensions from some fungi.
Hyphal growth: Filamentous form of growth in many fungi.
Hypolimnion: The layer in a stratified lake that has a uniform cold temperature and a low level of oxygen.
Hypolithic: Growth of organisms on surface of rocks.
Icosahedral: A virus capsid having 20 equilateral triangular faces and 12 corners.
Identification: The part of taxonomy that entails the determination of the species to which an unknown organism belongs.
Idiophase: End of the exponential growth phase, when secondary metabolites are synthesized in certain organisms, such as antibiotic producing actinomycetes.
Ig class switching: The process through which antibody-forming cells couple the antigen-binding parts of an immunoglobulin with different Fc pieces.
Ileum: A region of the small intestine.
Immediate hypersensitivity: Allergic response characterized by involvement of the antibody class IgE and release of histamine from mast cell granules. The response can result in death within 30 minutes.
Immobilized enzyme: One attached to a solid support. May efficiently convert substrate to product.
Immune: Resistant to infectious agents, generally due to adaptive immune responses.
Immune response: Bodily response to the presence of an antigen; has three components: barrier defense, innate immunity, and adaptive immunity.
Immunization: Eliciting of an immune response by introduction of a specific antigen into a host.
Immunodeficiency: Inability to generate normal antibody or cellular responses to specific antigens or for phagocytic cells to migrate to areas of inflammation.
Immunogen (antigen): Substance that will elicit an immune response.
Immunoglobulin (Ig): Blood protein fraction that is composed of antibodies.
Immunopathology: Host cell, organ, or tissue damage resulting from the host's own immune response.
Immunosuppressant: An agent that decreases the immune response.
Incidence: Number of cases of a disease in a subset of the general population.
Incompatability group: Classification of plasmids based on the inability of closely related plasmids to coexist in the same cell.
Indicator organism: A bacterial species that is employed to determine whether an environment is contaminated by human waste. An organism that does not survive for extended periods, but generally outlives enteric pathogens, would be an effective indicator.
Induced phagocytosis: Phagocytosis that occurs when the pathogen stimulates the host cells to do so either by binding to receptors on the host cell or inserting bacterial components into the membrane of the host cell.
Inducers: Molecules capable of facilitating transcription by their action through transcriptional regulators.
Inducible enzyme: Enzyme that is synthesized in the presence of a specific substrate (inducer).
Infection: Presence and growth of an organism within a host.
Infection thread: A minute tunnel through the roots of a legume, by which rhizobial cells migrate to the host cells that will give rise to a nodule.
Inflammation: A response to tissue injury that is generally localized but can become systemic in some cases. The local responses are characterized by pain, swelling, heat, and redness. The host's mechanism for attracting leukocytes, including phagocytic cells, to the site of tissue injury and infection.
Initiation codon: The first codon in mRNA that defines the beginning (amino terminus) of a protein.
Initiation site: Area of the genome where replication originates.
Innate immunity: A group of defense processes that are rapidly deployed after infection and generally involve cells in the myeloid lineage, including granulocytes and phagocytes.
Inoculum: Cell mass used to start a microbial culture.
Insertion: Placing of a piece of DNA into another sequence of DNA.
Insertion sequence: A small transposon that caries the genes for enzymes needed for its integration into a new site in a chromosome or a plasmid.
Integrase: An enzyme that promotes recombination between two sequences, resulting in integration of a DNA element into a new site.
Integrase inhibitor: A compound that inhibits the incorporation of a DNA sequence into a genome.
Integration: Incorporation of a DNA sequence into the genome.
Integrins: A family of adhesion molecules that promote stable interactions between cells and their extracellular matrix
Integron: A genetic element consisting of an integrase gene and an adjacent att site that serves as a site for capturing antibiotic resistance-specifying gene cassettes by site-specific recombination.
Interference: Resistance in a lysogenized bacterial cell to invasion by another virus.
Interferons (IFN): There are 3 types of interferons: gamma, alpha, and beta. They have antiviral properties and thus "interfere" with virus replication. Interferon-gamma also activates macrophages for increased anti-microbial activities.
Interspecies hydrogen transfer: The process in which hydrogen gas produced by a fermentative bacterium is quickly utilized by a nearby methanogen.
Intimin: An E. coli surface molecule that allows the bacteria to adhere to host gut cells by interacting with the bacteria-encoded translocated intimin receptor (TIR).
Intracellular pathogens/parasites: Microorganisms, including bacteria and protozoa, that survive and replicate inside of host cells.
Intron: Noncoding intervening sequences in a split gene. Does not appear in the ultimate RNA product.
In vitro: Outside a living organism, such as a test-tube experiment.
In vivo: Inside a living organism.
Invasiveness: Innate ability of a pathogen to produce substances that aid in dissemination of the organism within the host.
Inverted repeats: Two proximal segments of identical DNA sequence that are inverted relative to one another.
Ionizing radiation: High-energy radiation that causes loss of electrons from atoms.
Ionophore: A compound that disrupts cytoplasmic membranes, resulting in leakage of cytoplasm or transfer of materials (such as calcium) into the cell.
Iris diaphragm: An annulus that can be opened and closed to control the amount of light that is focused on the specimen in a compound light microscope.
Iron bacteria: Bacteria involved in the oxidation or reduction of iron.
Isomerization: Rearrangement of the direction of DNA during recombination.
Isotopes: Elements with an increased number of neutrons, but normal electron and proton complement.
Isotopic fractionation: The process in which the lighter isotope of an element or compound is preferentially utilized by an organism.
Jejunum: A region of the small intestine.
Joule: A unit of energy.
Kerogen: Organic compounds derived from organisms, but whose degradation over time has rendered the source compounds unidentifiable.
Kilobase pairs: 1,000 base pairs in a fragment of DNA.
Kineties: Ordered rows of cilia found in ciliates that coordinate the ciliary beat to control swimming.
Kinetochore: An assemblage of proteins on the centromere of eukaryotic chromosomes where the mitotic spindle attaches.
Kirby-Bauer: An antibiotic disk diffusion assay for testing susceptibility of a clinical isolate to antibiotics or chemotherapeutics.
Koch's postulates: Expression of rules for proving the relationship between a specific microorganism and a disease.
Lactic acid bacteria: Bacteria that produce lactic acid by fermentation.
Lactic acid fermentation: Anaerobic degradation of sugars by glycolysis to produce lactic acid as a major end product.
Lactoperoxidase: A peroxidase in milk.
Lag phase: Period after inoculation of a culture in which there is no increase in population.
Lagging strand: The strand of new DNA that is made during replication by joining short segments of DNA synthesized in the opposite direction as the movement of the replication fork.
Landfill: Improved system for treating household food wastes.
Late message: Messenger RNA produced sometime after viral infection coding for proteins that are involved in virion synthesis.
Latent virus: One present in a host without causing detectable symptoms.
Leaching: Release of minerals from ore by microbial action.
Leading strand: A DNA strand synthesized during replication that is made in the same direction as the movement of the replication fork.
Lectin: Surface protein of a plant cell where microorganisms, such as nitrogen-fixing bacteria, can attach.
Legionellosis (Legionnaires' disease): A respiratory infection by Legionella pneumonia.
Legume: Plant that can develop nodules for nitrogen fixation.
Leprosy: An infection by Mycobacterium leprae characterized by severe nerve damage.
Leptospirosis: A disease caused by the spirochete genus Leptospira.
Lethal dose 50 (LD50): Number of microorganisms or level of toxin that will kill 50% of a test population within a fixed time.
Leukocidin: A microbial toxin that will destroy phagocytes.
Leukocyte: A white blood cell.
Leukocyte adherence deficiency (LAD): A recessive genetic mutation that prevents leukocytes adhering to blood vessel walls, thus limiting their capacity to migrate from the blood into tissues and consequently reducing the efficacy of inflammatory defenses.
Leukocytosis: A decrease in the number and concentration of white blood cells in the host.
Levan: Polymer whose subunit is levulose or fructose.
Lichen: A beneficial symbiotic association between a fungus and a cyanobacterium or alga.
Light reactions: The systems in photosynthesis that covert sunlight into ATP.
Lipopolysaccharide (LPS): Complex structure containing fatty acids and sugars present on the outer envelope of gram-negative bacteria.
Lipoprotein: A protein found in either the outer or cytoplasmic membrane of gram-negative bacteria, which is modified by attachment of fatty acids during secretion.
Log phase: Exponential phase in growth curve of a culture.
Lophotrichous: Tuft of flagella at one or both poles of a rod-shaped bacterium.
Lymph: Clear, yellowish fluid that is the interstitial fluid that bathes tissue. Returns to the blood system by flowing through the lymphatic vessels and organs carrying lymphocytes and antigen-presenting cells. Eventually it is dumped into the blood system, although the cells within it may stay in lymphoid tissues along the way.
Lymph node: An encapsulated organ that is largely composed of lymphocytes.
Lymphocyte: A leukocyte that produces antibodies or is involved in cellular immune responses, including production of cytokines and killing of infected host cells.
Lymphogranuloma venereum: A sexually transmitted infection of males by Chlamydia trachomatis.
Lymphokine: Now generally referred to as a cytokine. Protein secreted by lymphocytes following activation. Mediators in the immune response that transmit signals from cell to cell.
Lyophilization: Rapid dehydration of frozen material in a vacuum.
Lysis: Physical disintegration of a cell.
Lysogenized cell: An archaeal or bacterial cell bearing a prophage.
Lysosome: An organelle in eukaryotic cells that contains digestive enzymes.
Lysozyme: Enzyme that disrupts the β(l-4) bond in peptidoglycan, causing cell disruption.
Lytic cycle: Life cycle of a virus that effects lysis of the host cell.
M cells: Cells that are part of the intestinal epithelia lining the gut lumen and through which some microbes pass to access the underlying tissue.
M protein: A major surface protein of S. pyogenes with antiphagocytic properties.
Macromolecule: A large molecule formed by polymerization of small molecules.
Macrophage: Phagocytic cell present in blood, lymph, and tissue. These cells destroy pathogens, and some are involved in the immune response by presenting antigen and secreting cytokines.
Magnetosomes: Magnetite (Fe3O4) particles that are present in certain bacteria. They are tiny magnets that align the bacterium in a magnetic field.
Magnetotactic: Bacteria that produce magnetite and orient themselves in a magnetic field.
Maintenance energy: Energy required by a cell to remain viable.
Major histocompatability complex (MHC): Cell surface antigens present in all individuals that are the unique marker of self. They are encoded by a family of genes.
Malaria: A parasitic infection by members of genus Plasmodium.
Marginate: To crawl out of the blood through the wall of a blood vessel.
Mast cell: Cells that are found in skin tissues, sometimes near blood vessels, and secrete histamine and other active products in the inflammatory response and in hypersensitivity.
Mastigonemes: Fine fibrous proteins extending from the cilium membrane, found in many protists.
Mat communities: Natural aggregations of microbial species in marine and hot spring environments that form layers of different species.
Mating types: Cell membrane proteins in eukaryotes that are responsible for cell-cell recognition and attachment for conjugation. Different alleles in the species provide a diversity of mating types.
Medium: The mixture of nutrients employed in the growth of a microorganism.
Meiosis: Division of a diploid cell to form two haploid daughter cells typically called the sperm and the egg.
Memory cell: Differentiated, specific B cells formed during the immune response that can convert to plasma cells when activated by the presence of a specific antigen.
Meningitis: An inflammation of the meninges following infection by any of a number of pathogenic bacteria and viruses.
Mesophile: Microorganisms that grow optimally at temperatures between 18°C and 40°C.
Mesosome: Cytoplasmic membrane invagination in bacteria.
Mesotrophic: A lake with moderate levels of nutrients.
Messenger RNA (mRNA): Single-stranded RNA complementary to template DNA formed via transcription. mRNA generally carries information for one polypeptide and is translated by ribosomes.
Metabolism: The sum of all biochemical events in a cell.
Metachromatic granules: Dark structures observed in EM thin sections of cells containing polyphosphate.
Metagenomic: A term that is used to describe the DNA of organisms in a community when subjected to molecular sequence analyses.
Metalimnion: The intermediate layer in a stratified lake, also called the thermocline.
Methanogens: Archaea that generate methane in anaerobic environments.
Methanotrophic bacteria: Organisms that oxidize methane.
Methylotrophic An organism that utilizes or "eats" compounds that contain methyl carbons bound to O, N, or S as substrates for growth.
Microaerophile: Microorganisms that require O2 but at lower levels than atmospheric pressure.
Microbial ecology: The study of the interactions among microorganisms and other organisms as well as the nonbiotic component of their habitat.
Microbial ecosystems: Communities composed largely of microorganisms.
Microbiota: Microscopic organisms collectively present in an environmental niche.
Microcyst: Resting spherical structures formed by some Cytophaga and Azotobacteria.
Microelectrodes: Fine probes used for measuring pH, oxygen concentration, and other factors in the microenvironment.
Microenvironment: The small area in which individual microorganisms grow and live in their habitat.
Microfilaments: Chains of actin arranged in two parallel helices. Constitutes an important part of the cytoskeleton.
Micropore: A coated pit for endocytosis found in Apicomplexa and other Alveolata.
Microtubules: Fibrous protein elements that give structure to eukaryotes.
Mineral scales: Mineral deposited in an organic matrix in the form of a scale, and secreted from the Golgi apparatus to cover the cell membrane.
Mineral skeleton: Deposition of minerals, often in an organic matrix, from the Golgi apparatus, that forms an elaborate system of spines to support the cell.
Mineralization: Complete biodegradation of organic matter to CO2 and other inorganic substances.
Minimum inhibitory concentration (MIC): Smallest amount of an antimicrobial agent that inhibits growth of microorganisms.
Mismatch repair system: A system that corrects mismatches in base pairing created during copying of DNA strands.
Mitochondrion: The organelle of eukarotic cells that is responsible for respiration and is descended from the Alphaproteobacteria.
Mitosis: The division of nuclear material in a eukaryote, yielding two nuclei of identical chromosomal composition.
Mitosome: A degenerate mitochondrion found in Giardia.
Mitotic spindle: Microtubular structure that attaches to chromosomes during mitosis to separate the chromosomes.
Mixed acid fermentation: One that generates mixed organic acids (lactic, acetic, etc.) as products.
Mixed flagellation: An organism that produces two types of flagella.
Mixotroph: A microorganism that assimilates organic carbon sources while using inorganic energy sources.
Modification enzymes: Enzymes that modify (usually methylate) DNA sequences that would otherwise be recognized by an organism's own restriction enzymes.
Mol % G + C: The proportion of guanine and cytosine to total DNA bases in an organism's DNA, also termed GC ratio.
Molecular mimicry: Production of molecules by pathogens that resemble components of the human tissue, thus minimizing recognition by the host immune system.
Molecular pattern receptors: These are also known as pathogen pattern receptors and interact with surface molecules on pathogens known as pathogen-associated molecular patterns.
Monoclonal antibody: An antibody of a specific type produced by a clone of identical plasma cells.
Monocyte: A type of white blood cell that is phagocytic and can migrate to host tissues, where it differentiates into a macrophage. These cells present antigen to T lymphocytes.
Monomer: A low-molecular-weight intermediate utilized in the synthesis of cellular macromolecules.
Monophyletic: A cluster of organisms that are most closely related to one another.
Monotrichous: A bacterium with a single flagellum.
Morbidity rate: Incidence of a particular disease in a population during a specified time period.
Mordant: A substance that increases the affinity of a cell for a dye.
Morphogenesis: Developmental process whereby an organism forms different cell types in its life cycle.
Morphology: The shape of an organism or part of it.
Mortality rate: Ratio of deaths from a particular disease relative to the total number infected.
Most probable number (MPN): Measure of the number of microorganisms by dilution. End point is highest dilution yielding growth.
Mot proteins: The two membrane-embedded components of the flagellum (MotA, MotB) that form the motor of the apparatus and drive flagellar rotation.
Motility: Purposeful movement of a microorganism.
mRNA: A ribonucleic acid copy of a gene encoded in DNA. Also referred to as a transcript.
Mucociliary escalator: Ciliary action that moves mucus towards the pharynx.
Murein: See peptidoglycan.
Murine typhus: Infection caused by Rickettsia typhi. The name refers to rats and squirrels that serve as the reservoir of this organism. Also called endemic typhus.
Mushrooms: Filamentous fungi that produce large fruiting structures. Selected species are edible.
Must: Crushed fruit, especially grapes, that can be fermented to produce an alcoholic product.
Mutagen: A physical agent (radiation) or chemical that induces mutation.
Mutation: Heritable change in the genetic makeup of a species.
Mutualism: A symbiotic association where both partners will gain.
Mycelium: A three-dimensional colony formed from the repeated branching of growing hyphae. Typical of some fungi and members of the Actinobacteria.
Mycoplasmas: A group of mostly pathogenic bacteria related to the Firmicutes.
Mycorrhiza: Fungal-plant root associations.
Myxobacteria: Bacteria that have a complex developmental cycle.
N-acetylglucosamine: An amino sugar found in peptidoglycan.
N-acetylmuramic acid: An amino sugar found in peptidoglycan.
Natural competence: The ability of bacteria to take up DNA from their environment.
Natural killer cells (NK): Lymphocytes that are part of the innate immune response and destroy aberrant host cells, such as tumor cells and virus-infected cells, using pattern recognition. They also produce cytokines that influence the responses by other cells, including interferon-gamma.
Near point: The closest position an object can be brought to the eye and still be resolved.
ncRNAs: Small noncoding regulatory RNAs.
Necrotizing fasciitis: A disease characterized by massive destruction of skin and soft tissues following infection by S. pyogenes.
Negative chemotaxis: Movement of a cell away from a nutrient.
Negative regulation: Regulation of gene expression through the action of repressors that interfere with initiation of transcription.
Negative stains: Staining procedures that use acidic dyes such as nigrosin which stain the background to distinguish it from the cell.
Negri bodies: Viral masses that form in the brain of rabies-infected animals.
Neurotoxin: One that harms nerve tissue.
Neutrophils: Short-lived leukocytes that are specialized for rapid recruitment from the blood into inflamed tissues, where they phagocytose and destroy pathogens.
N-formylated methionine (fMet): A modified methionine that is the first amino acid incorporated into a polypeptide chain during protein synthesis.
Niche: A habitat with all factors necessary for growth of a species.
Nitrification: Oxidation of ammonia to nitrate in the environment.
Nitrifiers: Members of the Bacteria and Archaea involved in oxidation of the reduced nitrogen compounds ammonia and nitrite.
Nitrogen fixation: Reduction of atmospheric nitrogen to ammonia. A property present in some Bacteria and Archaea. The enzyme involved is nitrogenase.
Nitrogenase: The enzyme that catalyzes nitrogen fixation in microorganisms.
Nodule: A structure formed in the roots or stems of symbiotic nitrogen-fixing plants. Filled with the nitrogen-fixing microorganisms.
Nomenclature: The aspect of taxonomy that treats the naming of organisms.
Nonprofessional phagocytes: Host cells that can be induced to phagocytose microbial organisms. These cells are then colonized by the microbe.
Nonreplicative transposition: A mechanism of transposition where the transposon is cut out from the donor site and inserted in the target sequence.
Nonsense codon: One that does not code for an amino acid but has a signal to terminate protein synthesis.
Northern blot: A technique of hybridization of single-stranded RNA or DNA probes to RNA fragments attached to a matrix.
Nosocomial infection: An infection acquired in a health-care facility or hospital.
Nuclear area: The area in a bacterium or archaeon that contains DNA.
Nuclear envelope: A double membrane surrounding the nucleus and traversed by protein-containing pores.
Nuclear fusion: Merging of two haploid nuclei into a single diploid nucleus.
Nucleic acid: Polymer composed of nucleotides.
Nucleic acid probe: A labeled single strand of nucleic acid that can hybridize with a complementary strand in a crude mixture. Employed in pathogen identification.
Nucleocapsid: The basic unit of a virion; nucleic acid surrounded by protein capsid.
Nucleolus: Site of transcription of DNA coding for ribosomes (rDNA) to ribosomal RNA (rRNA). Chromosome regions with ribosomal genes aggregated at the nucleolus.
Nucleotide: A monomeric unit that can polymerize to form nucleic acid. Composed of sugar (ribose or deoxyribose), phosphate, and a purine or pyrimidine base.
Nucleus: The double membrane-enclosed organelle in eukaryotes that contains the genetic material (DNA).
Nuisance blooms: Algal blooms that produce odors on the beach and may contain toxic cyanobacteria.
Numerical taxonomy: The use of a large number of strains and phenotypic tests to classify organisms.
Nutrient: Any substance that is assimilated by a microorganism during growth.
Obligate: A term used by microbiologists to indicate an absolute requirement: obligate aerobe, obligate autotroph, obligate intracellular pathogen, etc.
Occam's razor: A premise that the simplest explanation is most likely to be the correct explanation.
Okazaki fragments: Short fragments of DNA involved in discontinuous replication of DNA on the lagging strand.
Oligotroph: A microorganism that can live under low nutrient conditions.
Oligotrophic: Term used to describe aquatic habitats that contain very low concentrations of nutrients.
Oncogene: A gene that when expressed can convert a normal cell to a tumor cell.
Oocysts: Eggs.
Open reading frame (ORF): A contiguous coding sequence between initiation and termination codons.
Operator: A specific segment of DNA at the start of a gene where a protein (repressor) can bind to control mRNA synthesis.
Operon: A group of adjacent genes organized in such a way that they are transcribed from a single promoter, giving rise to polycistronic mRNA.
Opines: Derivatives of the amino acid arginine or sugars that are synthesized in plants transformed by Agrobacterium tumefaciens. Utilization of these compounds is restricted to the crown gall-inducing pathogenic agrobacteria.
Opportunist: A microorganism that is generally harmless but can cause disease under certain conditions or in an immunocompromised host.
Opsonins: Proteins that promote phagocytosis.
Opsonization: The process of coating a substance with an opsonin to facilitate phagocytosis.
Oral candidiasis (thrush): Infection of mucous membranes of the mouth by Candida albicans.
Organelle: A membrane-bound functional structure in a cell.
Organic scales: Scales formed inside the Golgi apparatus and secreted to the outside of the cell, usually made of polysaccharides or proteins.
Origin of replication: Site of initiation of DNA replication.
oriV: Site of origin of replication of plasmids.
oriT: Origin of transfer of conjugative plasmids.
Osmophiles: Microorganisms that grow best in media of high solute concentration.
Osmosis: Movement of water through a membrane from a low solute concentration to one of a higher concentration.
Osmotic balancers: Ions or soluble molecules that increase the cytoplasm osmotic potential.
Osmotrophy: The uptake of dissolved organic and inorganic nutrients, including minerals, through the cell membrane. This is the only form of nutrient uptake in prokaryotes, and it occurs in many protists.
Outbreak: Sudden high incidence of disease in a given population.
Overoxidizer: A vinegar bacterium that oxidizes acetic acid to carbon dioxide and water.
Oxidase positive: An organism that possesses cytochrome oxidase.
Oxidation: Loss of electrons.
Oxidation-reduction (redox) reaction: Coupled reaction where one partner donates electrons and the other accepts them. One is oxidized, the other reduced.
Oxidative phosphorylation: Employment of the electron transport system to generate a proton motive force that provides energy for ATP synthesis.
Oxygenic photosynthesis: Cyanobacterial or plant-type photosynthesis where water serves as the electron donor, resulting in oxygen production.
Pandemic: An epidemic worldwide. HIV is now a pandemic.
Paralysis: Complete or partial loss of motor function.
Parasite: A symbiotic association where one organism benefits and the other is harmed. Used to describe protozoa and worms.
Paraxonemal rod: A rod of proteins adjacent to the axoneme inside the cilium.
Paryphoplasm: The outlying cytoplasm of a member of the Planctomycetes that is devoid of ribosomes.
Passive diffusion: Movement of a molecule from an area of high concentration to one of lower concentration.
Passive immunity: A short-lived immunity gained by transferring specific immune antibodies to a nonimmune individual.
Pasteurization: Heating a fluid to temperatures that destroy spoilage- or disease-causing organisms.
Pathogen: A disease-causing organism.
Pathogenicity: A relative term indicating the disease-causing potential of a micro-organism.
Pathology: A generic term for tissue damage.
Pathovars: Pathogenic varieties of species.
Penicillins: Antibiotics that have a β-lactam ring and inhibit bacterial cell wall synthesis by blocking crosslinking of peptide chains in newly synthesized peptidoglycan.
Pennate diatoms: Diatoms with a bilateral symmetry.
Pentose phosphate pathway: A pathway that oxidizes glucose-6-phosphate to ribulose-5-phosphate. A source of 5-carbon sugars for DNA and RNA synthesis.
Peptic ulcers: Lesions of the stomach lining.
Peptide: A short linear sequence of amino acids.
Peptide bond: A covalent bond, formed by dehydration, between the carboxyl group of one amino acid and the amine of another.
Peptidoglycan (murein): The polymeric cell wall structure present in most Bacteria. It is formed by alternating units of N-acetylglucosamine and N-acetylmuramic acid. The N-acetylmuramic acids are cross-linked by amino acids.
Peptones: Enzymatically digested proteins that are used in preparation of culture media.
Pericarditis: Inflammation of lining that surrounds the heart.
Periplasm (periplasmic space): A space between the cytoplasmic membrane and peptidoglycan layer (gram-positives) and the outer envelope (gram-negative).
Periplasmic flagella: Flagella that are located in the periplasm as found in the spirochetes; also called endoflagella.
Perithecium: A flask-shaped ascocarp found in some Ascomycetes (Fungi).
Peritrichous: Having flagella distributed over the surface of a bacterium.
Permease: A protein in the cytoplasmic membrane that transports material inward.
Peroxisomes: Vesicles that contain oxidative enzymes.
Pertactin: One of several Bordetella pertussis surface adhesins.
Pertussis toxin: A toxin produced by Bordetella pertussis; modifies regulators of cyclic AMP synthesis in target cells.
Phagocyte: A cell that can capture and digest foreign material, generally macrophages, monocytes, and neutrophils.
Phagocytosis: A form of endocytosis where cell membrane invagination engulfs particles such as organic material, bacteria, or protists into phagosomes.
Phagolysosome: An intracellular membrane-bound compartment that results from fusion of a phagosome and a lysosome.
Phagosomes: Also called food vacuoles, they contain ingested material such as protists or bacteria.
Phagosome (immunology): A membrane-bound vacuole formed in phagocytes by invagination of the cell membrane about a foreign particle.
Phagotrophic: Eukaryotic cells that can engulf particulate food and cells.
Pharyngitis: Inflammation of the pharynx.
Phase variation: A reversible change in the expression of surface molecules on bacteria, particularly fimbriae.
Phenol coefficient: Relative strength of a disinfectant compared with phenol.
Phenotype: Expressed properties of a microorganism.
Pheromones: Molecules secreted to attract individuals of complementary mating types for the purpose of conjugation.
Phosphodiester linkage: A bond between 5′-phosphoric acid and 3′-hydroxyl group on neighboring nucleosides in DNA or RNA.
Phospholipid: The component part of a cytoplasmic membrane composed of fatty acids, glycerol phosphate, and generally with a polar molecule linked to the phosphate.
Photoautotroph: An organism that can utilize light as an energy source and CO2 as a carbon source.
Photoheterotroph: A microorganism that utilizes light energy while assimilating organic compounds as a carbon source.
Photophosphorylation: Generation of a proton motive force by use of light energy. This energy drives ATP synthesis from ADP and inorganic phosphate by ATP synthase.
Photoreactivation: A process of repair of dimerized pyrimidines by the action of the enzyme photolyase, which is activated by DNA-damaging ultraviolet light.
Photosynthesis: Use of light energy to generate chemical energy for cell maintenance and CO2 assimilation.
Phototaxis: Purposeful movement of an organism toward favorable wavelengths of light.
Phototroph: Organism that utilizes light as a source of energy.
Phragmoplast: Occurs in Charales (Chloroplastida) and higher plants, between the dividing cells at the site of cell wall deposition during cytokinesis.
Phycobiliproteins: Phycoerythrin (red) and phycocyanin (blue) pigments that trap light in phycobilisomes.
Phycobilisomes: Specialized structures on cyanobacterial membranes involved in light harvesting.
Phylogenetic classifications: A classification system based on analysis of sequences of macromolecules, in particular DNA, RNA, and protein.
Phylogenetic trees: Figural representations of phylogenetic classifications.
Phylogeny: The evolutionary history and genetic relationships between organisms.
Piezophilic: Organisms that can grow at high hydrostatic pressure, also called barophilic.
Pili: Protein filaments, the most common of which are fimbriae, present on bacterial cells that are involved in conjugation.
Pinocytosis: A form of endocytosis where invagination of the cell membrane results in external fluid being internalized in small 50-500 nm vesicles.
Pioneer: An initial organism in a succession.
Planctomycetes: A major phylum of the Bacteria.
Plague: A disease caused by Y. pestis infections.
Plaque: A clear area in a lawn of cells on an agar surface resulting from lysis of cells by a virus; or a microbial colony attached to and growing on a tooth.
Plasma: The fluid, noncellular portion of blood.
Plasma cell: A short-lived differentiated B cell that synthesizes and secretes large quantities of specific antibody.
Plasmid: A double strand of circularized DNA that exists and replicates independently in a cell; may integrate into the chromosome. Can carry information for specialized catabolic enzymes or drug resistance.
Plasmodesmata: Channels found in higher plants and in Charales (Chloroplastida) that allow communication between the cytoplasm of adjacent cells.
Plasmolysis: Loss of water by a bacterial cell placed in high solute concentration, causing shrinkage of the cytoplasmic membrane and potential death.
Platelets: Formed elements in blood that are pieces of megakariocytes without any nuclear material and are important for blood clotting.
Pleomorphic: Bacteria that are variable in shape.
Plus strand: Viral nucleic acid that is of a base sequence that can serve as mRNA.
Pneumococcus: A common name for Streptococcus pneumoniae.
Pneumonia: Infection and inflammation of the lungs.
Pneumonic plague: A severe form of infection by Yersinia pestis.
Point mutation: Defect in a single base pair in a specific location of a genome.
Polar flagellum: The end or both ends of a bacillary bacterium.
Polar mutations: Mutations in one gene that affect the expression of an adjacent gene.
Polycistronic mRNA: An mRNA molecule containing a number of genes that was transcribed from a single promoter.
Polyclonal B-cell activator: A molecule or substance that activates many different populations of B cells.
Poly-β-hydroxybutyrate (PHB): A linear polymer of β-hydroxybutyrate that serves as a storage material or granule in many bacteria.
Poly-hydroxyalkanoates (PHA): Polymers of hydroxy acids such as β-hydroxybutyrate that serve as a storage material in many bacteria.
Polymerase chain reaction (PCR): Amplification of DNA in vitro by synthesis of specific nucleotide sequences from a small amount of template DNA. This technique employs oligonucleotide primers complementary to sequences in the DNA and heat-stable DNA polymerases.
Polymeric substances: High-molecular-weight compounds such as DNA, RNA, protein, and polysaccharides found in cells.
Polymorphonuclear leukocyte (PMN): Motile white blood cells that specialize in phagocytosis.
Polyphosphate: A storage polymer of phosphate that may serve as a phosphorus or energy source for some bacteria.
Population: Mass of cells of the same species.
Porin: Proteins that form channels in the outer membrane of gram-negative bacteria for transport of nutrients to the bacteria.
Porters: Membrane proteins involved in transport, both inward and outward.
Positive chemotaxis: A phenomenon in which bacteria move toward a nutrient.
Positive selection: A process that immature T cells undergo in the thymus and which preserves their life.
Posttranslational modification: Covalent modification (e.g., phosphorylation or glycosylation) of a protein after its synthesis is complete. May or may not be reversible.
Posttranslational protein translocation: A protein secretion pathway where the secreted proteins are first synthesized by ribosomes and then interact with the Sec or Tat secretion machinery.
Potable: Water that is safe for drinking.
Prebiotics: Food substances that promote the growth of "good bacteria" in the gut.
Precursor metabolites: Twelve intermediates that originate in glycolysis, pentose phosphate pathway, or tricarboxylic acid cycle from which all cellular constituents are synthesized.
Presumptive test: First test used in identification of coliform bacteria.
Prevalence: Total percent of the population infected with a disease at a given time.
Pribnow box: A base sequence located about 10 base pairs upstream from the transcription start site. It is the binding site for RNA polymerase.
Primary consumers: The first level of consumers in a food chain.
Primary lymphoid organs: Those in which lymphoid cells mature, including the bone marrow and thymus in mammals.
Primary metabolites: Products secreted during the growth phase. Lactic acid and ethanol are examples.
Primary producer: Autotrophic organisms that fix atmospheric CO2, thus providing sustenance for the ecosystem.
Primary sludge: The settleable material in the initial stage of wastewater treatment.
Primary structure of a protein: Sequence of amino acids joined in a polypeptide chain.
Primary treatment: The first stage in wastewater (sewage) treatment.
Primer: A polynucleotide to which the DNA polymerase attaches during DNA replication.
Primordial soup: The hypothetical mixture of materials that could have served as the building blocks for the first forms of life.
Prion: An infectious proteinaceous particle in which no nucleic acid has been detected.
Probiotics: Dietary supplements containing potentially beneficial bacteria.
Prochlorophytes: An important group of photosynthetic cyanobacteria found in oceans.
Prokaryote: A name applied to all microorganisms that lack a nuclear membrane. Now replaced by Archaea and Bacteria.
Promiscuous plasmid: A plasmid capable of transferring between a wide range of bacterial species.
Promoter: The region on DNA at the start of a gene where RNA polymerase binds to initiate transcription.
Proofreading: Correction of errors created in DNA during replication.
Prophage: State in which a temperate viral genome is integrated into and replicates in concert with the host genome.
Prostaglandin E2: One of the prostaglandins, a group of hormone-like substances that participate in a wide range of body functions, including the contraction and relaxation of smooth muscle, the dilation and constriction of blood vessels, control of blood pressure, and modulation of inflammation.
Prostheca: Extension of the wall and cytoplasmic membrane to form hyphae, stalks, or unusual-shaped bacteria.
Protease: An enzyme that cleaves amino acids from a protein.
Protease inhibitor: A compound that inhibits a protease by binding to its active site. Certain protease inhibitors are used in the treatment of HIV infections.
Protein: A polymer composed of amino acids.
Protein jackets or S-layers: External cell layers produced by some bacteria and archaea.
Proteobacteria: A major phylum of the Bacteria.
Proteomics: The study of the types and functions of groups of proteins in a cell.
Proteorhodopsin: Light-absorbing, retinal-containing protein present in certain bacteria that can effect ATP synthesis.
Proteosome: A complex of enzymes in the cytoplasm of host cells that degrades proteins into peptides, some of which are suitable for presentation to T cells as antigens.
Protomer: Subunit of a viral capsid.
Proton motive force (pmf): An energized state of a membrane created when an electron transport system transports protons from one side of the membrane to the other. The resulting chemical and electrical gradient can be used to drive ATP synthesis.
Protoplast: An osmotically sensitive bacte