Term
|
Definition
| Close association between two different types of organisms |
|
|
Term
|
Definition
| Relationship in which members of two different species benefit and neither suffers from association |
|
|
Term
|
Definition
| Relationship in which one species gains some benefit while the other species has no advantage |
|
|
Term
| Saprobes, Saprobic, Saphrobic |
|
Definition
| term for organism that feeds on dead organic matter; most of fungi are saprobic |
|
|
Term
|
Definition
| One species of the association benefits while the other is harmed |
|
|
Term
|
Definition
| with flattened cristae; oomycetes have mitochondria with chloroplasts |
|
|
Term
|
Definition
| hollow tube hairs on the ends of flagella on oomycetes |
|
|
Term
|
Definition
| are fungi with small "f" but because of retronemes and they have ameboid pseudopodial stage; they are also social like protozoa; heterotrophic |
|
|
Term
|
Definition
|
|
Term
|
Definition
| encapsulated and unicellular |
|
|
Term
|
Definition
| filamentous and multicellular |
|
|
Term
|
Definition
| chitin & beta-glucans; chlorophytes and other fungus-like but not Fungi orgs have cellulose |
|
|
Term
|
Definition
| absorptive - because of chitin in cell wall, cannot phagocytize; plants are photosynthetic, animals are phagotrophic |
|
|
Term
| How are fungi main players? |
|
Definition
| they are the main contributors of carbon to terrestrial environment. w/o Carbon, it would be 100 years left of photosynthesis |
|
|
Term
| Four Fungi Phylum (based on reproduction stage) |
|
Definition
| Ascomycetes, Basidiomycetes, Zygomycetes, Chytridiomycetes |
|
|
Term
|
Definition
| The fungi is directed by the environment - choose best mode for survival; bad environment would direct sexual; good environment would direct asexual. Both stages morphologically distinct. |
|
|
Term
|
Definition
| Fungi still eukaryote but because they live w/i host & absorb nutrients, they are Fungi Kingdom. |
|
|
Term
|
Definition
| Cavelier-Smith found that Fungi have chitinous cell wall and absorb nutrients. Originally thought they were pre-ancestral flagellates that phagocytized w/ loricae made of chitin. |
|
|
Term
|
Definition
| allows for searching of nutrients in other areas if current environment lacking; filaments are very robust (unlike bacteria); can go through substrate. |
|
|
Term
|
Definition
| one-sided attraction to food source (no gradient like chemotaxis) |
|
|
Term
|
Definition
| Zygomycetes (derived from Chytrids) Coenocytic hyphae with septa only where reproductive cells are formed; form asexual sporangiospores; Zygosporangium is one big structure, like a sac, holding zygospores |
|
|
Term
|
Definition
| Ascomycetes; sac fungi; septic hyphae in mycelium; asexual reproduction leads to formation of conidiospores; ascospores on inside of sac but outside of fungi; even number of spores because meiosis; sexual & asexual (holomorphs) |
|
|
Term
|
Definition
| Basidiomycetes; Have a basidium & basidiospores; spores on outside; sexual & asexual (holomorphs) |
|
|
Term
|
Definition
| Oldest known fungi; "chytrids"; zoospores; flagella w/o retronemes |
|
|
Term
|
Definition
| saclike reproductive structure |
|
|
Term
|
Definition
| reproductive structure on which sexual spores are produced after hyphal fusion; spores don't mature inside mushroom - they do it outside in the gills |
|
|
Term
|
Definition
| "Chytrids"; only fungi w/ flagella but no retronemes |
|
|
Term
|
Definition
| anamorphic because no known sexual stage; might never have had it or lost it along the way; "mitosporic fungi" |
|
|
Term
|
Definition
| Hyphomycetes, Agonomycetes, Coelomycetes - no known sexual stage; asexual state; parasexuality; some of most frequently encountered fungi; ascomycetes & basidiomycetes; produce conidia - identified by development, morphology & conidiogenous cell & conidia |
|
|
Term
|
Definition
| oomycetes, not true Fungi; zoospores allow them to live in wet environment; fungi with small "f" |
|
|
Term
|
Definition
fungi-like protozoans that are motile; only resemble fungus in morphology
Acellular slime molds: like separated slugs; form structures to protect selves when nutrients limited; were myxomycetes; one big cell w/ millions of nuclei
cellular slime molds: amoeba joined together to form one signal to sporylate
protozoa |
|
|
Term
|
Definition
| plants w/o stems, roots or leaves; very filamentous and simple (like algae) |
|
|
Term
|
Definition
| vegetative body of thallophyte; used to designate somatic organization of fungus |
|
|
Term
|
Definition
| long branched filaments used by mold |
|
|
Term
|
Definition
| thick mass of intertwined hyphae |
|
|
Term
|
Definition
| term for diseases caused by fungi |
|
|
Term
|
Definition
| plant-pathogenic specialized hyphae that invade plant cell walls |
|
|
Term
|
Definition
| Basidiomycetes & Ascomycetes; have crosswalls; control of water balance so live in dry conditions. 2-4 microns |
|
|
Term
|
Definition
| Zygomycetes; no crosswalls; no control of water balance; live in damp conditions bcz of lack of water control; Can be up to 10 microns |
|
|
Term
|
Definition
|
|
Term
|
Definition
| alternate between unicellular and multicellular |
|
|
Term
|
Definition
| go on path of least resistance in search of nutrients; can spread out through substrate to look for food; macroscopic - mushroom like |
|
|
Term
|
Definition
| protection to spore-producing part of fungi; balled up mycelium (tissue) to elevate fungi to spread spores better; macroscopic; only part of fungi that can be grown in lab with right conditions (cannot do plants/animals) |
|
|
Term
|
Definition
Requires microscope to view;
Molds & Yeast |
|
|
Term
|
Definition
| Mushrooms, toadstools, basidiomycetes & ascomycetes; visible to naked eye |
|
|
Term
|
Definition
|
|
Term
|
Definition
| asexual stage - form asexual spores |
|
|
Term
|
Definition
| Teleomorph & Perfect Stage; can be used for protection & survival. Only one stage |
|
|
Term
|
Definition
| Anamorph & Imperfect Stage; zillions of spores can be released. This classification is used in biomedical mycology; can have several dozen asexual stages but still same organism. |
|
|
Term
|
Definition
| fungi can switch between sexual and asexual stages based on the need and environment; morphologically different and occur at different times and places (rarely at same time); one species can form several types of spores |
|
|
Term
|
Definition
| Because fungi doesn't have 1 specific sexual state; cannot determine naming convention |
|
|
Term
|
Definition
| Whole fungus - sexual & asexual states |
|
|
Term
|
Definition
| sexual state "perfect state" |
|
|
Term
|
Definition
| asexual state "imperfect state"; also mitosporic state |
|
|
Term
|
Definition
| union of two protoplasts (cells w/o cell walls) |
|
|
Term
|
Definition
| fusion of two nuclei --> diploid stage |
|
|
Term
|
Definition
| two cells that have fused with their own nuclei to create one cell with two nuclei |
|
|
Term
|
Definition
| meiosis occurs after reproduction stages to restore haploid stage |
|
|
Term
|
Definition
|
|
Term
|
Definition
Heterokaryosis; expression of multiple phenotypes; a lot of asexual fungi can have this (plasmogamy); appearance of sexuality - rearranged phenotype
Expression of different types of nuclei at same time w/i mycelium mass |
|
|
Term
|
Definition
fungal structure of tissue; naked asci; Cleistothecia is closed, hollow sphere
Perithecia: flask-like
Apothecia: cup or disk-like with stalk |
|
|
Term
|
Definition
spores are released from gills under caps; these can be very lethal to small animals
colors of spores can determine species and genera (white, lilac, pink, black, etc); dead air w/i crevices where spores stored until released by wind, water, etc |
|
|
Term
|
Definition
Red ball structures with zygospores inside
two mating types (+, -) with suspensors that are held up by stalks; they come together and reproduce |
|
|
Term
|
Definition
| depending on stage or situation, suspensors can have different morphologies |
|
|
Term
|
Definition
| asexual spores from mitosporic fungi (conidium singular); almost always ascomycetes or basidiomycetes; long chains allow for conidia to be dispersed by wind; hyphae are under surface medium or host |
|
|
Term
|
Definition
| Mitosporic fungi; most common; conidia produced on exposed conidiophores |
|
|
Term
|
Definition
| Mitosporic fungi; mycelial forms that are sterile but produce differentiated vegetative structures; cannot germinate or produce spores so unidentified; not morphologically distinct; 2 types: chlamydospores, sclerotia |
|
|
Term
|
Definition
| large, round cell w/ thick wall; survival stage w/o sexual stage |
|
|
Term
|
Definition
| dense, compact masses of hyphae & mycelium that survive in very low temps and are hard, dark pigmented structure; some form on wheat w/ alkaloids |
|
|
Term
|
Definition
| Mitosporic fungi; produce conidia in conidiomata; mainly in plants, plant pathogens; spores not out in open; plant-related saprotrophs |
|
|
Term
|
Definition
| asexual cavities w/ conidiospores lining w/i; not out in open; grow on plants or plants on dead wood |
|
|
Term
|
Definition
| part of hyphae on conidiophore that is above substrate or surface and extends up to allow better spreading of conidia (spores) |
|
|
Term
|
Definition
| AKA Chytrids; have zoospores (motile); single flagella; zygote as resting spore resembles zygomycetes; in moist environment - aquatic or terrestrial; saprotrophs or parasites; coencytic thallus |
|
|
Term
|
Definition
| Chemoorganotrophs; osmotrophic; parasites use exoenzymes to attack & break down substrates & also help metabolize |
|
|
Term
|
Definition
| used to attack & break down substrate when cannot get things into cell wall; yeast does not need because they reside in rotting foods with simple sugars that quickly absorb |
|
|
Term
|
Definition
| compound with known metabolic function; biproducts produced |
|
|
Term
|
Definition
| compound w/o known function; most medically necessary things from secondary; growth stopped but can still produce compounds for medical or industrial purposes; waste products produced |
|
|
Term
| Major Secondary Metabolites |
|
Definition
| Terpenes, Carotenoids, Steroids, Antibiotics |
|
|
Term
|
Definition
| Waste products, reserve storage food, safety-valve shunts, specialized functions: chelators, hormones, antibiotics; carbon-nitrogen ratio can be balanced out with this |
|
|
Term
|
Definition
| Major moderators of carbon cycle; have to degrade lignin to get to cellulose (more complex) so CO2 can be released; most organisms cannot break lignin; brown wood rotting fungi |
|
|
Term
|
Definition
| protects polysaccharides from enzymatic digestion; oxidative process; not primary carbon source |
|
|
Term
|
Definition
| Complex; needed for primary carbon source |
|
|
Term
|
Definition
| association of fungus and algae - two organisms intertwined to form what looks like individual organism; fungus responsible for nutrients, algae has photosynthesis and returns other nutrients to fungus |
|
|
Term
|
Definition
| association between hyphae of certain fungi & absorptive organs of plants; spread out into substrate or soil & bring in nutrients; fungus makes plants more competitive; 30% of plants have association |
|
|
Term
|
Definition
| Lichens; can live where others cannot; they start process of soil formation & produce acids that decompose minerals of rocks, allow for other organisms can come in; has maculae, medulla, upper/lower cortex, algal layer, rhizine |
|
|
Term
|
Definition
|
|
Term
|
Definition
| primary or secondary metabolites |
|
|
Term
|
Definition
| known function = biproducts that are made and can be used for later chemical functions |
|
|
Term
|
Definition
| no known function = waste products not needed but can be used by other organisms (antibiotics, steroids) |
|
|
Term
| Why are exoenzymes needed? |
|
Definition
| from outside cell to help fungi absorb nutrients |
|
|
Term
|
Definition
|
|
Term
| vegetative state of fungi |
|
Definition
|
|
Term
| phylogenetically heterogenous to Fungi but similar in characteristics |
|
Definition
|
|
Term
| one-sided attraction to nutrients |
|
Definition
|
|
Term
| Properties of medical microbiology |
|
Definition
| human-microbe interactions: parasites, pathogens, virulence, host resistance, infection, disease, normal flora |
|
|
Term
|
Definition
| organism living in or on host & causes damage; diagnostic micro: parasitic worms & protozoa (stool samples) |
|
|
Term
|
Definition
| necessary to keep pathogens or competing bacteria away; intimately intertwined in physiology; w/o it, we wouldn't last a week |
|
|
Term
|
Definition
| dry & acidic (from amino acids on surface & need water) - tough place to live; most w/I sweat glands & hair follicles, Gram (+) because more resistant to UV light |
|
|
Term
|
Definition
| never stays in same place - transiently colonizing; can cause pathogenicity |
|
|
Term
|
Definition
| always stays in same place |
|
|
Term
|
Definition
| Saliva is hard place to live because lack of nutrients & lysozymes/lactoperoxidase destroy bacteria; |
|
|
Term
|
Definition
| Teeth & gumline have most flora; most anaerobic or strict anaerobes; plaque buildup is biofilm & traps oral strep or bacilli; when eating, sugars attach & ferment acid on biofilm, eventually eroding teeth; not as diverse as other biofilms but not monotypic |
|
|
Term
| Intestinal tract gradient |
|
Definition
| gradient of pH increases & O2 decrease moving down tract; very complicated ecosystem; organisms stretch out on flora based on physiology (anaerobic bacteria closer to colon; more aerobic closer to esophagus); archaea bacteria in GIT; gas production (H2, CO2, CH4) |
|
|
Term
|
Definition
| B12 & K production, steroid mods; they create vitamins we can't but need; they modify basal compound steroids we made; process carbs first that we can't; they metabolize first then we absorb to digest; detoxify foreign chemicals |
|
|
Term
| Sloughing of epithelial cells |
|
Definition
| Gram (-) help to slough epithelial cells to inhibit growth of pathogens |
|
|
Term
| Disruption of normal flora (lower tract) |
|
Definition
| antimicrobials disrupt normal flora, especially in lower tract, which affects chemostat; need to limit antimicrobials |
|
|
Term
|
Definition
| mucous membranes - do most work, keep inhaled particles from entering lower tract |
|
|
Term
|
Definition
| lungs have normal flora; ciliated epi cells keep out particles; 15% have pneumocystis controlled by macrophages but can cause disease; normal flora can cause disease if immune system defective |
|
|
Term
| Urogenital Tract - Bladder |
|
Definition
| Bladder is sterile - urine great medium for culturing; can get cystitis |
|
|
Term
|
Definition
| facultative (-) rods & (+) cocci; can become opportunistic pathogens; nosocomial is infection from hospital from catheter |
|
|
Term
|
Definition
| Pre-puberty & post-menopause: no glycogen & alkalinic, Gram (-); Adults have glycogen & acidic, Gram (+) |
|
|
Term
|
Definition
| creation of disease; bacteria has to enter, adhere, invade tissues, colonize & have virulence factors; w/o adherence, nothing will occur |
|
|
Term
|
Definition
| Bacteria can adhere & not cause problems but must adhere if they are going to become pathogenic |
|
|
Term
|
Definition
| bacteria can colonize w/o causing problems; just growth doesn't mean pathogenic yet; mycobacteria can off and on colonize but not cause harm |
|
|
Term
|
Definition
| exposure, adherence, invasion of tissues, further exposure, colonization/growth, production of virulence factors = pathogen; either toxicosis or invasiveness causes pathogenicity |
|
|
Term
|
Definition
| spreads all over to cause tissue damage; ability to gain access to & invade, colonize & become pathogenic |
|
|
Term
|
Definition
| release of toxins to local or systemic areas to damage tissues |
|
|
Term
|
Definition
| breaks in skin or mucous membranes (wounds, trauma) allow easy entry but some can implant w/o aggressive entry (gonorrhea) |
|
|
Term
|
Definition
| glycocalyx (capsule, slime layer), fimbrae (many small rods) & pili (few) allow bacteria to adhere like glue to tissues or cells; E. coli mainly causes pathogenicity from fimbrae in upper UT; pili are like grappling hooks |
|
|
Term
| Fimbrae response to antibiotics |
|
Definition
| some antibiotics can strip pathogenic flora of its fimbrae, making it inactive & losing pathogenic status |
|
|
Term
|
Definition
| penetration of epithelium, initiation of pathogenicity, growth on altered normal surfaces (burned skin, cuts); need plenty of bacterial cells to invade; can leave local sites & grow distantly (blood, lymph) |
|
|
Term
|
Definition
| immune system tries to keep bacterial infection local so it does not become systemic |
|
|
Term
|
Definition
| physical (37oC), nutritional & trace elements (iron) needed; iron can be drawn in by acidophores from bacteria, allowing them to become pathogenic |
|
|
Term
|
Definition
| swollen lymph nodes signalling infection sites, inflammation causes sentinels to be called in to respond (WBC's, etc) |
|
|
Term
|
Definition
| viable or living bacterial cells in blood, but not growing |
|
|
Term
|
Definition
| pathogenic bacterial cells from blood that have invaded & grown - can cause death |
|
|
Term
|
Definition
| measure of how pathogenic a bacteria is or relative ability of parasite to cause disease; physiological factors allow them to be competitive in their environments helps to dominate body |
|
|
Term
|
Definition
| extracellular proteins help establish & maintain disease; enzymes aid colonization & growth; fibrin clots allow pathogens to live in body and not get attacked; have to be effective because of energy cost or will be cut lose |
|
|
Term
|
Definition
| continuous re-growth of pathogen eventually loses pathogenicity |
|
|
Term
| Virulence factors - toxicity |
|
Definition
| how much toxins are needed to cause pathogenicity |
|
|
Term
|
Definition
| extracellular proteins; cause damage far from infection site; botulinum loose - most virulent toxin; tetanus toxin clenched |
|
|
Term
|
Definition
| intestines; organ system failure; from food poisoning; massive secretion of fluid; E. coli and Shigella are same bug phylogenetically (shig has 4 diff species derived from non-pathogenic E. coli); shiga toxin causes more severe Shigellosis |
|
|
Term
|
Definition
| Gram (-) lipopolysaccharide; release of endogenous pyrenogens; usually have low levels in circulation; causes fever, diarrhea, decrease in lymphocytes & leukocytes & platelets, inflammation; severe is septic shock; test levels with Limulus (horseshoe crabs) |
|
|
Term
|
Definition
| Nonspecific, Specific, Natural Resistance; amplitude of reaction for response rate: nonspecific attack anything (weak rate), specific only attacks one kind (strong rate) |
|
|
Term
|
Definition
| always turned on, no prior stimulus from particular pathogen; can react towards anything (primary immune response) |
|
|
Term
|
Definition
| prior infection, body already built-up immune response for specific pathogen to be turned on (needs priming from repeated exposure to be more efficient) (secondary immune response) |
|
|
Term
|
Definition
| certain populations have resistance to diseases because they lack receptors for those pathogenic cells (bacteria, virus) |
|
|
Term
|
Definition
| can allow normal flora to become pathogenic, it harms immune system if too high |
|
|
Term
| Physical & Chemical defenses |
|
Definition
| these are independent of immune system; secretions, blood, cilia, mucous, normal flora, skin, acidity, flushing, pH |
|
|
Term
|
Definition
| body's response to infection - low amounts can be good to rid bacteria; high or chronic amounts are bad; swollen, red & warm when fluid released & blood (RBC, WBC) at site of infection; fever either kills or stimulates blood to kill pathogen (pyrogenic compounds) |
|
|
Term
|
Definition
| chemical messengers produced by leukocytes to send signals & bring in reinforcement |
|
|
Term
| Process of Clinical Microbiology |
|
Definition
| detection & ID of pathogens, antimicrobial susceptibility testing - determine if pathogen suspectible to what antibiotic; more important to figure out antimicrobial susceptibility than the ID of pathogen; can start broad spectrum AB's & switch once ID determined |
|
|
Term
| Clinical Microbiology Testing Routes |
|
Definition
| Microbiological route is Classical: collect specimen; Conventional: culture & isolate specimen; Molecular: immunological or molecular; Immunological |
|
|
Term
|
Definition
| detect genetics, molecules or Ag's specific to that bug; can also do Ag-Ab test (PCR most common); amplification of nucleic acids |
|
|
Term
| Conventional Microbiology route |
|
Definition
| enrich, select or differentiate culture & isolate to identify & determine Antibiotic susceptibility |
|
|
Term
| Molecular Microbiology route |
|
Definition
| search for genome of pathogen (nucleic acid hybridization or PCR) |
|
|
Term
| Molecular Immunology route |
|
Definition
| search for pathogen's microbial cells or virus particles using fluorescent Ab test or ELISA |
|
|
Term
|
Definition
| blood sample - search for Ab against suspected pathogens Ag; Ab assay (agglutination, RIA, ELISA, etc) |
|
|
Term
|
Definition
| most important step in clinical micro; asceptic collection; can get contamination or not enough of sample; transport |
|
|
Term
|
Definition
| general purpose (NA), enriched (BA), selective (EMB Gm -) or differential (EMB Lac +) |
|
|
Term
|
Definition
| rule out bacteremia vs. septicemia; aerobic & anaerobic vials; amt/vol of sample VERY important (can increase or decrease sensitivity) incubate 5 days |
|
|
Term
|
Definition
| very common & from normal flora, most common is nosocomial infection (from hospital); (-) rods or (+) cocci |
|
|
Term
|
Definition
bacturia - infection 105; culture on blood agar or MacConkey agar; MA selective gram (-) & differential for Lac (+); Blood is both Gram (+) & Gram (-)
Also blood specimen for nitrite production, or high WBC; dipstick |
|
|
Term
|
Definition
| preservation necessary; Selective & Differential media required; Campylobacter most common cause of GTI's; H10157 big outbreak from variation of Enterohemorrhagic E. coli (cause shiga toxins); Parasites (worms, protozoa) |
|
|
Term
|
Definition
| worms like tapeworms or protozoa like nematodes |
|
|
Term
|
Definition
wound - superficial, deep; specimens - tissue, fluid aspirate, swab; anaerobes
tissue sample or fluid aspirate from outside of wound (not swab of tissue); "jelly donut story"; most likely polymicrobic infection (do anaerobic & aerobic cultures) |
|
|
Term
|
Definition
| antimicrobials hard to disseminate abscesses so masses have to be excised |
|
|
Term
|
Definition
| STD's; some hard to culture, Neisseria, Chlamydia, Treponema pallidum (syphillis) & HIV |
|
|
Term
|
Definition
| STD; enriched, selective agar w/ increased CO2 & humidity |
|
|
Term
|
Definition
#1 STD; very hard to culture; cell culture & Ag detection or nucleic acid sequencing tests (can also determine if other infections)
***for sexually abused - cannot run nucleic test bcz false (+); only cell culture for legal purposes |
|
|
Term
|
Definition
| Gram (-) diplococci Neisseria - can see only one form for males but different morphology for females |
|
|
Term
| Growth-dependent ID methods |
|
Definition
| selective & differential media; conventional biochemical tests; rapid biochemical tests; automated biochemical tests |
|
|
Term
| Antimicrobial susceptibility testing |
|
Definition
| disk diffusion methods & liquid dilution methods |
|
|
Term
| Disk diffusion methods (antimicrobial susceptibility testing) |
|
Definition
| Kirby-Bauer, Zones of inhibition, interpretation: sensitive, intermediate |
|
|
Term
| Liquid dilution methods (antimicrobial susceptibility testing) |
|
Definition
| minimum inhibitory concentration (MIC) |
|
|
Term
| Immunological ID methods (blood) |
|
Definition
| serology: Ag-Ab reactions, IgM, IgG, agglutination, fluorescent Ab's, ELISA (enzyme-linked immunosorbant assay) |
|
|
Term
|
Definition
| IgM key because it's quickly increased during infection (current or recent infection); IgG harder to test for |
|
|
Term
|
Definition
| Ag-Ab binding to form lattice = + result |
|
|
Term
|
Definition
| tag Ab's w/ fluorescent dye & wash; see binding with color |
|
|
Term
| ELISA (don't focus on - might not be on test) |
|
Definition
| direct enzyme-linked immunosorbant assay; Ab's to virus on plate; add patient sample (serum, etc) which possible virus particles or Ag's; Add antivirus Ab with conjugated enzyme; wash w/ buffer; add substrate for enzyme; + results are colored; quantitation proportional to Ag |
|
|
Term
| Molecular diagnostic methods* |
|
Definition
| based on analysis of pathogen-specific nucleic acid (NA); can use PCR's or other technology to amplify sequences; because complimentary DNA is stable |
|
|
Term
| Benefits of molecular diagnostic methods |
|
Definition
| readily extracted, visualized & detected; sequences unique to each pathogen & can be amplified; DNA stable |
|
|
Term
| Mol diagnostic methods: NA (nucleic acid) probes & PCR* |
|
Definition
NA probes: ssDNA, specific to particular pathogen, hybridization reactions
PCR: amplify NA targets, increasity sensitivity, qualitative PCR, quantitative PCR (viral load), reverse transcriptase PCR (RT-PCR); PCR uses two NA primers, one is cell & one is ssDNA |
|
|
Term
|
Definition
| place specimen cells on filter; lyse cells & generate ss target DNA; add reporter-labeled probe; allow for reannealing to target; measure hybridization directly if reporter radioactive or fluorescent; add enzyme substrate if reporter enzyme; detect using radioactive detector, fluorimeter or colorimeter/visual inspection |
|
|
Term
| NA probes - Measure Reporter* |
|
Definition
| lyse & denature sample in NaOH; region complementary to target DNA with reporter probe & capture probe; hybridize sample DNA to probes in solution; nucleases destroy unhybridized probe; target DNA against complementary DNA - capture w/ dipstick; measure reporter. |
|
|
Term
|
Definition
| Used for mycobacterium TB |
|
|
Term
|
Definition
| HIV is RNA virus so RT needed, then do PCR |
|
|
Term
| clinical micro - diagnostic virology* |
|
Definition
| cytopathogenic effect on cell lines; electron microscopy; ELISA, virus-specific PCR |
|
|
Term
| clinical micro - diagnostic virology* |
|
Definition
| selective media, non-selective media, direct microscopic observation |
|
|
Term
| Exotoxins - Gram (+) or (-)? |
|
Definition
|
|
Term
| Endotoxins - Gram (+) or (-)? |
|
Definition
|
|
Term
|
Definition
| study of biodiversity of microbes in nature; measure of activities & effects on microbes |
|
|
Term
| Microbial Ecology Organization Levels |
|
Definition
| Populations, Guilds, Communities, Ecosystems |
|
|
Term
|
Definition
| Most elemental cycles run, controlled & moderated by microbes so not just geochemical cycles |
|
|
Term
|
Definition
| Not just relying on med microbiology - study microbes out in environment; enrichment highly selective & appropriate inoculum used - can add Organic N, atmospheric N, heterotrophic populations grow, nitrogen-fixing bacteria appear & not overgrown |
|
|
Term
|
Definition
| separation of individual organisms from the mixed community |
|
|
Term
|
Definition
| select for desired organisms through manipulation of medium and incubation conditions; easy to tell bacteria is there, hard to prove that it's not there |
|
|
Term
|
Definition
| miniature ecosystem w/o homogenous mixture; serves as long-term source of bacteria for enrichment cultures; soil, water & light; each tube has different environment for different activities |
|
|
Term
|
Definition
Microorganisms cultured in lab are frequently only minor components of the natural microbial ecosystem
in lab only able to provide beneficial environments for a few types of microorganims, therefore only these species are benefit |
|
|
Term
|
Definition
w/ enrichment & isolation & manipulation; contain a single kind of microorganism (can be obtained by streak plate, agar dilution or liquid dilution)
they are clones of cells started from an individual cell |
|
|
Term
|
Definition
| Used for enumeration & mainly for nucleic acids or DNA; view w/ fluorescent microscope; Might have some UV damage; 3 Types: DNA-binding stains, Acridine Orange (orange or green), DAPI |
|
|
Term
| DAPI & Acridine Orange (AO) |
|
Definition
Different staining methods:
DAPI and AO fluoresce under UV light, are nonspecific and stain nucleic acids
DAPI stains bright blue; AO stains orange or greenish-orange
*cannot differentiate between live and cells |
|
|
Term
| Viability Stains (viable counting) |
|
Definition
| can differentiate between live and dead cells bcz two dyes are used; based on integrity cell membrane (not intact in dead cells); green cells alive & red dead |
|
|
Term
| Fluorescent Antibody (Ab) Staining |
|
Definition
| Monochrome staining; can be used as a cell tag; highly specific for the molecule recognized by Ab; used to identify any type of cell for specific Ab; making antibodies is time consuming and expensive |
|
|
Term
| Green Fluorescent Protein (GFP) |
|
Definition
| genetically engineered into cells to track bacteria, if always expressed; can act as a reporter gene, if fused to a promoter of interest; can use fluorescence to see how much bacteria still living |
|
|
Term
|
Definition
| DNA or RNA complimentary to a sequence in a target gene or RNA molecule |
|
|
Term
| Fluorescent in situ hybridization (FISH) |
|
Definition
| phylogenetic probes to find species-specific oligonucleotide signature sequences; highly specific & simple; multiple probing of single sample; culture not needed when this performed |
|
|
Term
|
Definition
| study unculturable organisms, determine morphology, abundance, microbial associations; probes allow for determination of species that couldn't be differentiated with just simple staining |
|
|
Term
|
Definition
| Not based on 16s taxonomy; based on physiology & nitrogen cycle; can view different activities of different organisms with supporting metabolisms with different color probes for that specific sig sequence ("Multiplexing"); activities can work off of or support each other in "Consortium" |
|
|
Term
| FISH Chromosomal Painting |
|
Definition
| locate, count specific metabolic populations; can search for whatever gene you require; physiology & neighboring organisms |
|
|
Term
| In situ reverse transcriptase (RT) FISH |
|
Definition
| Locates specific genes & detects expression & transcription for those genes; needed when RNA is present, not DNA, so RT needed for complementary DNA; can run multiple tests - see specific genes turned on/off |
|
|
Term
| PCR & Microbial Community Analysis |
|
Definition
Can determine candidate name for unknown genes until bug isolated & description correlated
Path 1: Extract total community DNA, amplify with PCR & fluorescent tagged primers; put on T-RFLP gel; excise bands & clone 16s rRNA genes; sequence; generate tree; Path 2: extract, amplify with general/restrictive primers (bacteria or endospore-specific); use DGGE gel, excise bands; sequence; generate tree |
|
|
Term
| Polymerase Chain Reaction (PCR) |
|
Definition
| new process allows for no TAC polymerase inhibitors of PCR in community; able to amplify PCR |
|
|
Term
|
Definition
| Phylogenetic Tree for single genes or total gene pool of community; can identify & link to phenotypes; Path 1: amplify single gene & sequence, generate tree; Path 2: restriction enzymes digest all DNA then shotgun sequence or seq directly (w/o cloning); get partial genomes & can discover new genes, link to phylotypes |
|
|
Term
| Microbial Activity Measurements |
|
Definition
| Microcosms - take sample of soil to lab w/o disturbing environment; label w/ different macromolecules based on metabolic processes wanted; track where things are going, what happens to substrate; Two Types: Radioisotopes & Microelectrodes |
|
|
Term
| Microbial Activity Measurement Types |
|
Definition
| Radioisotopes: high sensitivity, turnover rates, fate of substrate & killed cell control; Microelectrodes: micromanipulator, microbial mats & multiple electrodes; can look at physical aspects like O2 tension, pH, H2S concentration; can multiplex and look at multiple states at once |
|
|
Term
| FISH Microautoradiography (MAR) |
|
Definition
| 14C or 35S used for short term; labeled sugars put on photographic plate; wherever radioactivity is concentrated shows what populations metabolizing |
|
|
Term
|
Definition
| Test physical parameters & compounds for specific metabolic activities; can tell where no O2 - orgs fermentative or anaerobic; can do w/o disturbing population |
|
|
Term
| Microbial Activity Measurements - stable isotopes |
|
Definition
| Biogeochemical cycles & food chains: 12C, 13C, etc - stable isotopes that hang around for awhile - used for biological processes; enzymes very selective and will favor one isotope over another; fractionates isotopes by selectively enriching 12CO2 to 12C and diminishes 13CO2 to 13C; shows how much enzymes moderate organisms & fixes carbon |
|
|
Term
| Carbon Isotopic Compositions |
|
Definition
| Different substrates & their organic processes & result - how much carbon; CO2 fixed and fungi breaks down to release carbon into ecosystem |
|
|
Term
| Populations, Guilds & Communities |
|
Definition
| Community 1: photic zone (oxygenic phototrophs), Comm 2: oxic (O2 loving & facultative); Comm 3 (sediments): Anoxic (ferm, anaerobic); Guild 1: methanogenic or homoacetogenic bacteria; Guild 2: sulfate- or sulfur-reducing bacteria; Guild 3: denitrifying or ferric iron-reducing bacteria: Guild 4: ferm bacteria (ferm sugars, acids, etc) |
|
|
Term
|
Definition
| Metabolically related populations of microbes that work together to ferment, depending on environment; each guild makes similar product in own process; each element has own guild to perform their own process; unique to microbial ecology |
|
|
Term
|
Definition
| Prime niche; spatially very small; physical or chemical conditions change rapidly; heterogenous; environments change physiology & can change (increase/low pH, etc) from physical or chemical; different numbers show levels of O2 for each niche |
|
|
Term
| Nutrient Levels & Growth Rate |
|
Definition
| Feast or famine - when things get bad, organisms sacrifice self to help rest of population; happens when nutrients low or distribution not uniform; competition; no periods of optimal growth; when nutrients high, metabolism increases exponentially; organisms grow quickly & die quickly |
|
|
Term
|
Definition
| neighbor gains access to nutrients faster, killing off competition; can also inhibit growth of others by releasing compounds as antibiotics (fungi) or bacteriosis |
|
|
Term
|
Definition
| work together instead of fighting; "Syntrophy"; close associations |
|
|
Term
|
Definition
| cooperation, eating together ("commensal") & working together ("Consortium") |
|
|
Term
|
Definition
| everyone works together metabolically so can share to attack particular substrate together, better |
|
|
Term
| Terrestrial Environments (soil) |
|
Definition
| Different horizons (layers of environments or microniches); most complex for microbes; each horizon has different nutrients, temps |
|
|
Term
|
Definition
O: undecomposed plant materials
A: surface soil (high in organic, dark, tilled for agriculture; plants & large #'s microbes grow)
B: subsoil (minerals, humus, leached from soil; little organic; low microbial activity)
C: soil base (directly from underlying bedrock; microbial very, very low) |
|
|
Term
|
Definition
| Microcolonies form on different soil particulates held together by minerals from organisms or fungi w/ EC polysacch "glue"; each mineral (clay, water, quartz) has different surface properties for different microcolonies to grow & flourish |
|
|
Term
| Terrestrial Environments (deep subsurface) |
|
Definition
| Several to 1000+M; anaerobes that are sluggish chemoorganotrophs & chemolithotrophs (not a lot of organic available); no photosynthesis; divide only once every 100 years |
|
|
Term
|
Definition
| Diverse (oceans, marshes, rivers etc); phototrophic microorganisms are primary producers & drive carbon into ecosystem; phytoplankton bottom dwellers; benthic algae; biologic activity depends on rate of primary production. |
|
|
Term
|
Definition
| O2 limited solubility in H2O; O2 depletion when heterotrophs use up oxygen; Stratification of deep lakes: epilimnion & hypolimnion; when frozen, hypo no longer supports water so crashes down below for nutrients & support; might have high levels of organic matter from leaves falling, etc |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Lower layer of water - provides nutrients |
|
|
Term
|
Definition
| highly mixed & high organic levels possible so lower O2 levels |
|
|
Term
| Biological Oxygen Demand (BOD) |
|
Definition
| O2 consuming property of water; measures amt of organic material that can oxidize by microorgs; > BOD = > pollution & > org level; > carbon = < O2 |
|
|
Term
| Effect of high organic levels |
|
Definition
| when point source hits, organic carbon and BOD increases while O2 greatly decreases; eventually, carbon taken up and BOD decreases or bacteria moves; levels normalize, move up and down |
|
|
Term
|
Definition
| Inshore - higher nutrient levels, high primary production, high heterotrophic activity, potentially low O2; inorganic materials allow heterotrophs to be vast |
|
|
Term
|
Definition
| open ocean depleted of photosynthesizers; high chlorophyll content inland, rivers |
|
|
Term
|
Definition
| limited inorganic nutrients, limited primary production; limited heterotrophs; O2 levels high. Cyanobacteria primary producers O2; 1/2 O2 we breathe from cyanobacteria |
|
|
Term
|
Definition
| Photic zone 0-300M; biologically active lower; Deep >1000M; water relatively inactive biologically; low temp & nutrients, high pressure; physiologically separated microbes based on pressure (baro) |
|
|
Term
|
Definition
| down to 3000M, no growth above 5000M |
|
|
Term
|
Definition
| 4000-6000m, optimum at 4000M |
|
|
Term
|
Definition
| 10000M, opt 7000-8000M, no growth <4000M |
|
|
Term
| Molecular effects of high pressure |
|
Definition
| decrease binding capacity of enzymes, membrane process, use outer membrane porins to bind substrates; limited gene expression |
|
|
Term
|
Definition
| volcanic environment at ocean bottom (deep sea vents); black smoker chimneys very hot, metal sulfides & hydrothermal gradients; metabolism occurs in surrounding areas of sea mounts |
|
|
Term
| What do the vents release? |
|
Definition
| H2S, CO2, NH4+ (no organic material) |
|
|
Term
| Vent invertebrate communities |
|
Definition
| Sessile tubeworms and mollusks that live close to the vent; Receive C source (chemotrophic dependent), few predators; red parts (hemoglobin like) to attract nutrients |
|
|
Term
| Chemolithotrophs of deep sea |
|
Definition
| CO2 fixation from nutrients out of vents, tube worms have trophosomes that live inside tissue of worm; giant clams & methanotrophs that release CO2 |
|
|
Term
|
Definition
| prokaryotic cell symbionts in tube worms that use hemoglobins to bind O2 and H2S; Houses and delivers H2S and CO2 to chemoautotrophs |
|
|
Term
| Black smoker chimney worms |
|
Definition
| chemolithotrophic bacteria grown on surface of worm bodies to hold nutrients; worms graze hairs & eat; not one homogenous population of bacteria |
|
|
Term
| Higher temps for microbes |
|
Definition
| in situ evidence for colonization, growth at 125-140oC; biological sulfate reduction at 130oC; ATP unstable at 150oC |
|
|
Term
|
Definition
| carbon reservoirs in land/living plants; carbon in humus; CO2 transfers; photosynthesis (terrestrial, aquatic); |
|
|
Term
|
Definition
Main 2 types: CO2 fixation; Carbon mineralization (decomposition)
Other: Methanogenic archaea; Methylotrophs; Carbon monoxide metabolism |
|
|
Term
|
Definition
| mix of phenolic compounds that enzymatically bind together, like a sponge in soil - it holds majority of carbon; microbes must go through humus to get carbon |
|
|
Term
|
Definition
| swamps, marshes, soils, protozoan endosymbionts, rumen, cows (burp 50L/day) |
|
|
Term
|
Definition
| digestive area of cow: find bacteria, protozoa, anaerobic fungi, microbial cells digested, microbial protein recovered; strict anaerobic fungi digests cellulose |
|
|
Term
| Chemoautotrophic benefits |
|
Definition
| Maintain access to H2S and CO2 |
|
|
Term
|
Definition
| Presence of specific enzymes dictate metabolic capabilities/habitat distributions |
|
|
Term
|
Definition
| Chemical transformations by biological organisms; every element has own cycle, almost always moderated by microbes |
|
|
Term
| Purposes of biogeochemical cycles |
|
Definition
| Converts one chemical form to another, maintains essential compounds in biosphere; leaching of ores (copper, gold); heavy metal transforms, biodegrade/biomediate toxins, etc |
|
|
Term
| Biogeochemical Cycles & Pseudomonas |
|
Definition
| pseudomonas altered metabolically and put in toxic environment for cleanup; they don’t compete so eventually die out; fluorescence used to view colonies. |
|
|
Term
| Plant-Microorganism Interactions |
|
Definition
| Ways to put Nitrogen into ecosystem; plants (legumes/nonlegumes), Gram (-), N2 fixing bacteria, root/stem nodule bacteria; Plants reliable - bacteria nutrient rich & gets N2 from plant; high species specificity (only 1 species per plant) |
|
|
Term
|
Definition
| Protein synthesis; Nucleic acid synthesis; other cell components; Major reservoir of N2 is atmostphere |
|
|
Term
|
Definition
| CO2 -> Organic carbon; CO2 is a major reservoir of carbon; CO2 fixation is done by Primary Producers (autotrophs) |
|
|
Term
| Carbon Cycle - Decomposition |
|
Definition
| decomp produces methane (CH4) & CO2; both organic aerobic & anaerobic ferments to release carbon back into atmosphere |
|
|
Term
|
Definition
| Anaerobic process done by methanogenic Archaea |
|
|
Term
| The sulfur cycle (2 types) |
|
Definition
| Sulfur oxidation (elemental sulfur) & reduction (dissimilatory sulfate reduc) |
|
|
Term
|
Definition
| sum total of all organisms in specified environment |
|
|
Term
|
Definition
| portion of ecosystem suited to a specific population |
|
|
Term
| Eutrophic lake, eutrophication |
|
Definition
| buildup of inorganic/organic material (nutrients) = eutrophication = fish die |
|
|
Term
|
Definition
| different oxygen levels, physical & chemical changes can change environment rapidly |
|
|
Term
| Aquatic habitats depend on what? |
|
Definition
| rate of primary production (carbon) |
|
|
Term
| Primary producers of aquatic? |
|
Definition
| phytoplankton & benthic algae |
|
|
Term
|
Definition
| restriction enzymes cut DNA at specific sequences; identifies higher level of phylogenetic tree (more general) |
|
|
Term
|
Definition
| separates down to the molecules of DNA, even if 1 base pair differs; identifies lower levels of tree (more specific) |
|
|
Term
|
Definition
| it is selective for isolation & different gradients; microbial diversity in artificial environments |
|
|
Term
|
Definition
ISRT: dyes nucleic acids; gene expression
FISH: dyes DNA, gene transcription |
|
|
Term
|
Definition
| experiment that uses intact tissue (no harm to sample bcz not individual cells) |
|
|
Term
|
Definition
| DNA staining, also use DAPI |
|
|
Term
|
Definition
|
|
Term
| gene transcription staining |
|
Definition
| FISH chromosomal painting |
|
|
Term
| Why are Gram (-) more dangerous as endotoxin? |
|
Definition
| because Lipid A layer of LPS has toxins |
|
|
Term
|
Definition
| closed, hollow sphere ascocarp |
|
|
Term
|
Definition
|
|
Term
|
Definition
| cup, or disk-like ascocarp |
|
|
