Flashcards About Test on Micro Final
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| Symbiosis |
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| Close association between two different types of organisms |
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| Mutualism |
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| Relationship in which members of two different species benefit and neither suffers from association |
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| Commensalism |
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| Relationship in which one species gains some benefit while the other species has no advantage |
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| Saprobes, Saprobic, Saphrobic |
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| term for organism that feeds on dead organic matter; most of fungi are saprobic |
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| Parasitism |
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| One species of the association benefits while the other is harmed |
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| Mitochondria |
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| with flattened cristae; oomycetes have mitochondria with chloroplasts |
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| retronemes |
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| hollow tube hairs on the ends of flagella on oomycetes |
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| oomycetes |
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| are fungi with small "f" but because of retronemes and they have ameboid pseudopodial stage; they are also social like protozoa; heterotrophic |
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| achlorophyllous |
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| cannot photosynthesize |
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| yeasts |
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| encapsulated and unicellular |
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| molds |
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| filamentous and multicellular |
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| cell wall properties |
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| chitin & beta-glucans; chlorophytes and other fungus-like but not Fungi orgs have cellulose |
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| osmotrophic |
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| absorptive - because of chitin in cell wall, cannot phagocytize; plants are photosynthetic, animals are phagotrophic |
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| How are fungi main players? |
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| they are the main contributors of carbon to terrestrial environment. w/o Carbon, it would be 100 years left of photosynthesis |
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| Four Fungi Phylum (based on reproduction stage) |
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| Ascomycetes, Basidiomycetes, Zygomycetes, Chytridiomycetes |
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| facultative lifecycle |
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| 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. |
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| Eukaryote Phylogeny |
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| Fungi still eukaryote but because they live w/i host & absorb nutrients, they are Fungi Kingdom. |
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| Radical Invention |
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| 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. |
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| Translocation |
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| allows for searching of nutrients in other areas if current environment lacking; filaments are very robust (unlike bacteria); can go through substrate. |
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| Chemotropism |
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| one-sided attraction to food source (no gradient like chemotaxis) |
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| Zygomycota |
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| 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 |
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| Ascomycota |
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| 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) |
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| Basidiomycota |
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| Basidiomycetes; Have a basidium & basidiospores; spores on outside; sexual & asexual (holomorphs) |
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| Chytridiomycota |
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| Oldest known fungi; "chytrids"; zoospores; flagella w/o retronemes |
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| Ascus |
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| saclike reproductive structure |
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| Basidium |
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| reproductive structure on which sexual spores are produced after hyphal fusion; spores don't mature inside mushroom - they do it outside in the gills |
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| Chytridiomycetes |
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| "Chytrids"; only fungi w/ flagella but no retronemes |
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| Deuteromycetes |
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| anamorphic because no known sexual stage; might never have had it or lost it along the way; "mitosporic fungi" |
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| Mitosporic fungi |
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| 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 |
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| Zoospores |
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| oomycetes, not true Fungi; zoospores allow them to live in wet environment; fungi with small "f" |
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| Mycetozoans |
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| 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 |
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| Thallophytes |
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| plants w/o stems, roots or leaves; very filamentous and simple (like algae) |
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| Thallus |
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| vegetative body of thallophyte; used to designate somatic organization of fungus |
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| Hyphae |
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| long branched filaments used by mold |
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| Mycelium |
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| thick mass of intertwined hyphae |
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| Mycoses |
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| term for diseases caused by fungi |
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| Haustoria |
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| plant-pathogenic specialized hyphae that invade plant cell walls |
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| Septic Hyphae |
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| Basidiomycetes & Ascomycetes; have crosswalls; control of water balance so live in dry conditions. 2-4 microns |
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| Aseptic Hyphae |
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| Zygomycetes; no crosswalls; no control of water balance; live in damp conditions bcz of lack of water control; Can be up to 10 microns |
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| mycology |
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| study of fungi |
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| dimorphic |
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| alternate between unicellular and multicellular |
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| Rhizomorph |
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| go on path of least resistance in search of nutrients; can spread out through substrate to look for food; macroscopic - mushroom like |
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| Stroma |
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| 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) |
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| Microfungi |
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| Requires microscope to view; Molds & Yeast |
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| Macrofungi |
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| Mushrooms, toadstools, basidiomycetes & ascomycetes; visible to naked eye |
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| Meiosis |
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| sexual stage |
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| Mitosis |
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| asexual stage - form asexual spores |
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| Sexual Stage |
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| Teleomorph & Perfect Stage; can be used for protection & survival. Only one stage |
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| Asexual Stage |
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| 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. |
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| Pleomorphic |
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| 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 |
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| Nomenclature problems |
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| Because fungi doesn't have 1 specific sexual state; cannot determine naming convention |
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| Holomorph |
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| Whole fungus - sexual & asexual states |
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| Teleomorph |
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| sexual state "perfect state" |
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| Anamorph |
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| asexual state "imperfect state"; also mitosporic state |
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| Plasmogamy |
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| union of two protoplasts (cells w/o cell walls) |
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| Karyogamy |
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| fusion of two nuclei --> diploid stage |
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| Dikaryotic Stage |
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| two cells that have fused with their own nuclei to create one cell with two nuclei |
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| Haploid Restoration |
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| meiosis occurs after reproduction stages to restore haploid stage |
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| Nuclear Cycle |
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| haploid or diploid |
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| Parasexuality |
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| 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 |
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| Ascocarp |
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| fungal structure of tissue; naked asci; Cleistothecia is closed, hollow sphere Perithecia: flask-like Apothecia: cup or disk-like with stalk |
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| Basidiocarps |
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| 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 |
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| Zygosporangia |
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| Red ball structures with zygospores inside two mating types (+, -) with suspensors that are held up by stalks; they come together and reproduce |
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| Zygosporangia Suspensors |
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| depending on stage or situation, suspensors can have different morphologies |
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| Conidia |
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| 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 |
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| Hyphomycetes |
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| Mitosporic fungi; most common; conidia produced on exposed conidiophores |
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| Agonomycetes |
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| 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 |
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| chlamydospores |
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| large, round cell w/ thick wall; survival stage w/o sexual stage |
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| sclerotia |
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| dense, compact masses of hyphae & mycelium that survive in very low temps and are hard, dark pigmented structure; some form on wheat w/ alkaloids |
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| Coelomycetes |
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| Mitosporic fungi; produce conidia in conidiomata; mainly in plants, plant pathogens; spores not out in open; plant-related saprotrophs |
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| Conidiomata |
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| asexual cavities w/ conidiospores lining w/i; not out in open; grow on plants or plants on dead wood |
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| Aerial Hyphae |
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| part of hyphae on conidiophore that is above substrate or surface and extends up to allow better spreading of conidia (spores) |
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| Chytridiomycotina |
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| AKA Chytrids; have zoospores (motile); single flagella; zygote as resting spore resembles zygomycetes; in moist environment - aquatic or terrestrial; saprotrophs or parasites; coencytic thallus |
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| Fungi Characteristics |
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| Chemoorganotrophs; osmotrophic; parasites use exoenzymes to attack & break down substrates & also help metabolize |
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| Exoenzymes |
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| 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 |
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| Primary Metabolite |
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| compound with known metabolic function; biproducts produced |
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| Secondary Metabolite |
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| 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 |
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| Major Secondary Metabolites |
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| Terpenes, Carotenoids, Steroids, Antibiotics |
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| Secondary Metabolism |
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| Waste products, reserve storage food, safety-valve shunts, specialized functions: chelators, hormones, antibiotics; carbon-nitrogen ratio can be balanced out with this |
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| Fungi Ecology |
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| 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 |
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| Lignin |
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| protects polysaccharides from enzymatic digestion; oxidative process; not primary carbon source |
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| Cellulose |
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| Complex; needed for primary carbon source |
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| Lichen |
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| 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 |
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| Mycorrhiza, Mycorrhizae |
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| 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 |
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| Pioneer Organisms |
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| 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 |
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| Lichen |
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| always fungi & algae |
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| Metabolism |
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| primary or secondary metabolites |
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| primary metabolites |
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| known function = biproducts that are made and can be used for later chemical functions |
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| secondary metabolites |
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| no known function = waste products not needed but can be used by other organisms (antibiotics, steroids) |
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| Why are exoenzymes needed? |
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| from outside cell to help fungi absorb nutrients |
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| macroalgae |
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| thallophyte |
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| vegetative state of fungi |
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| thallus |
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| phylogenetically heterogenous to Fungi but similar in characteristics |
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| oomycetes & mycetozoans |
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| one-sided attraction to nutrients |
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| chemotropism |
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| Properties of medical microbiology |
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| human-microbe interactions: parasites, pathogens, virulence, host resistance, infection, disease, normal flora |
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| Parasites |
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| organism living in or on host & causes damage; diagnostic micro: parasitic worms & protozoa (stool samples) |
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| Normal flora |
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| necessary to keep pathogens or competing bacteria away; intimately intertwined in physiology; w/o it, we wouldn't last a week |
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| Skin |
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| 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 |
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| Transient Flora |
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| never stays in same place - transiently colonizing; can cause pathogenicity |
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| Resident Flora |
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| always stays in same place |
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| Oral Cavity - Saliva |
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| Saliva is hard place to live because lack of nutrients & lysozymes/lactoperoxidase destroy bacteria; |
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| Oral Cavity - Teeth |
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| 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 |
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| Intestinal tract gradient |
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| 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) |
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| Intestinal tract flora |
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| 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 |
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| Sloughing of epithelial cells |
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| Gram (-) help to slough epithelial cells to inhibit growth of pathogens |
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| Disruption of normal flora (lower tract) |
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| antimicrobials disrupt normal flora, especially in lower tract, which affects chemostat; need to limit antimicrobials |
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| Upper respiratory tract |
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| mucous membranes - do most work, keep inhaled particles from entering lower tract |
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| Lower respiratory tract |
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| 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 |
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| Urogenital Tract - Bladder |
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| Bladder is sterile - urine great medium for culturing; can get cystitis |
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| Urethra |
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| facultative (-) rods & (+) cocci; can become opportunistic pathogens; nosocomial is infection from hospital from catheter |
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| Vagina |
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| Pre-puberty & post-menopause: no glycogen & alkalinic, Gram (-); Adults have glycogen & acidic, Gram (+) |
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| Pathogenesis |
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| creation of disease; bacteria has to enter, adhere, invade tissues, colonize & have virulence factors; w/o adherence, nothing will occur |
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| Adherence |
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| Bacteria can adhere & not cause problems but must adhere if they are going to become pathogenic |
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| Colonization |
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| bacteria can colonize w/o causing problems; just growth doesn't mean pathogenic yet; mycobacteria can off and on colonize but not cause harm |
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| Harmful interactions |
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| exposure, adherence, invasion of tissues, further exposure, colonization/growth, production of virulence factors = pathogen; either toxicosis or invasiveness causes pathogenicity |
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| Invasiveness |
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| spreads all over to cause tissue damage; ability to gain access to & invade, colonize & become pathogenic |
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| Toxicity |
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| release of toxins to local or systemic areas to damage tissues |
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| Host entry - specific |
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| breaks in skin or mucous membranes (wounds, trauma) allow easy entry but some can implant w/o aggressive entry (gonorrhea) |
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| Specific adherence |
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| 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 |
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| Fimbrae response to antibiotics |
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| some antibiotics can strip pathogenic flora of its fimbrae, making it inactive & losing pathogenic status |
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| Host entry - invasion |
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| 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) |
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| Immune system & invasion |
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| immune system tries to keep bacterial infection local so it does not become systemic |
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| Growth limitations |
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| physical (37oC), nutritional & trace elements (iron) needed; iron can be drawn in by acidophores from bacteria, allowing them to become pathogenic |
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| Dissemination |
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| swollen lymph nodes signalling infection sites, inflammation causes sentinels to be called in to respond (WBC's, etc) |
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| Bacteremia |
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| viable or living bacterial cells in blood, but not growing |
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| Septicemia |
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| pathogenic bacterial cells from blood that have invaded & grown - can cause death |
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| Virulence |
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| 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 |
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| Virulence factors |
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| 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 |
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| Attenuation |
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| continuous re-growth of pathogen eventually loses pathogenicity |
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| Virulence factors - toxicity |
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| how much toxins are needed to cause pathogenicity |
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| Exotoxins |
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| extracellular proteins; cause damage far from infection site; botulinum loose - most virulent toxin; tetanus toxin clenched |
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| Enterotoxins |
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| 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 |
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| Endotoxin |
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| 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) |
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| Host defense mechanisms |
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| Nonspecific, Specific, Natural Resistance; amplitude of reaction for response rate: nonspecific attack anything (weak rate), specific only attacks one kind (strong rate) |
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| Nonspecific mechanism |
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| always turned on, no prior stimulus from particular pathogen; can react towards anything (primary immune response) |
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| Specific mechanism |
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| 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) |
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| Natural host resistance |
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| certain populations have resistance to diseases because they lack receptors for those pathogenic cells (bacteria, virus) |
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| Stress reactions |
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| can allow normal flora to become pathogenic, it harms immune system if too high |
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| Physical & Chemical defenses |
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| these are independent of immune system; secretions, blood, cilia, mucous, normal flora, skin, acidity, flushing, pH |
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| Inflammation & fever |
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| 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) |
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| Cytokines |
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| chemical messengers produced by leukocytes to send signals & bring in reinforcement |
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| Process of Clinical Microbiology |
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| 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 |
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| Clinical Microbiology Testing Routes |
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| Microbiological route is Classical: collect specimen; Conventional: culture & isolate specimen; Molecular: immunological or molecular; Immunological |
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| Molecular route |
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| detect genetics, molecules or Ag's specific to that bug; can also do Ag-Ab test (PCR most common); amplification of nucleic acids |
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| Conventional Microbiology route |
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| enrich, select or differentiate culture & isolate to identify & determine Antibiotic susceptibility |
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| Molecular Microbiology route |
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| search for genome of pathogen (nucleic acid hybridization or PCR) |
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| Molecular Immunology route |
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| search for pathogen's microbial cells or virus particles using fluorescent Ab test or ELISA |
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| Immunology route |
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| blood sample - search for Ab against suspected pathogens Ag; Ab assay (agglutination, RIA, ELISA, etc) |
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| Specimen collection |
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| most important step in clinical micro; asceptic collection; can get contamination or not enough of sample; transport |
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| Culture media |
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| general purpose (NA), enriched (BA), selective (EMB Gm -) or differential (EMB Lac +) |
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| Blood cultures |
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| rule out bacteremia vs. septicemia; aerobic & anaerobic vials; amt/vol of sample VERY important (can increase or decrease sensitivity) incubate 5 days |
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| UTI's |
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| very common & from normal flora, most common is nosocomial infection (from hospital); (-) rods or (+) cocci |
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| Urine specimens |
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| 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 |
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| Fecal specimens |
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| 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) |
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| Fecal Parasites |
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| worms like tapeworms or protozoa like nematodes |
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| Wound/Abscess cultures |
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| 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) |
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| Abscess treatment |
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| antimicrobials hard to disseminate abscesses so masses have to be excised |
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| Genital cultures |
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| STD's; some hard to culture, Neisseria, Chlamydia, Treponema pallidum (syphillis) & HIV |
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| Neisseria |
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| STD; enriched, selective agar w/ increased CO2 & humidity |
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| Chlamydia |
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| #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 |
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| Polymorphonuclear cells |
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| Gram (-) diplococci Neisseria - can see only one form for males but different morphology for females |
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| Growth-dependent ID methods |
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| selective & differential media; conventional biochemical tests; rapid biochemical tests; automated biochemical tests |
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| Antimicrobial susceptibility testing |
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| disk diffusion methods & liquid dilution methods |
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| Disk diffusion methods (antimicrobial susceptibility testing) |
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| Kirby-Bauer, Zones of inhibition, interpretation: sensitive, intermediate |
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| Liquid dilution methods (antimicrobial susceptibility testing) |
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| minimum inhibitory concentration (MIC) |
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| Immunological ID methods (blood) |
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| serology: Ag-Ab reactions, IgM, IgG, agglutination, fluorescent Ab's, ELISA (enzyme-linked immunosorbant assay) |
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| IgM, IgG Ab's |
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| IgM key because it's quickly increased during infection (current or recent infection); IgG harder to test for |
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| Agglutination of Ab's |
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| Ag-Ab binding to form lattice = + result |
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| Fluorescent Ab's |
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| tag Ab's w/ fluorescent dye & wash; see binding with color |
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| ELISA (don't focus on - might not be on test) |
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| 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 |
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| Molecular diagnostic methods* |
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| based on analysis of pathogen-specific nucleic acid (NA); can use PCR's or other technology to amplify sequences; because complimentary DNA is stable |
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| Benefits of molecular diagnostic methods |
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| readily extracted, visualized & detected; sequences unique to each pathogen & can be amplified; DNA stable |
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| Mol diagnostic methods: NA (nucleic acid) probes & PCR* |
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| 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 |
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| NA probes - Detection* |
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| 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 |
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| NA probes - Measure Reporter* |
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| 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. |
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| Qualitative PCR |
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| Used for mycobacterium TB |
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| RT-PCR* |
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| HIV is RNA virus so RT needed, then do PCR |
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| clinical micro - diagnostic virology* |
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| cytopathogenic effect on cell lines; electron microscopy; ELISA, virus-specific PCR |
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| clinical micro - diagnostic virology* |
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| selective media, non-selective media, direct microscopic observation |
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| Exotoxins - Gram (+) or (-)? |
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| Gram (+) |
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| Endotoxins - Gram (+) or (-)? |
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| Gram (-) |
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| Microbial Ecology |
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| study of biodiversity of microbes in nature; measure of activities & effects on microbes |
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| Microbial Ecology Organization Levels |
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| Populations, Guilds, Communities, Ecosystems |
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| Biogeochemical Cycles |
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| Most elemental cycles run, controlled & moderated by microbes so not just geochemical cycles |
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| Enrichment & Isolation |
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| 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 |
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| Isolation |
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| separation of individual organisms from the mixed community |
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| Enrichment cultures |
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| 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 |
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| Winogradsky column |
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| 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 |
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| Enrichment bias |
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| 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 |
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| Pure cultures |
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| 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 |
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| Fluorescent Staining |
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| 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 |
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| DAPI & Acridine Orange (AO) |
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| 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 |
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| Viability Stains (viable counting) |
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| 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 |
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| Fluorescent Antibody (Ab) Staining |
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| 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 |
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| Green Fluorescent Protein (GFP) |
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| 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 |
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| Nucleic acid probe |
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| DNA or RNA complimentary to a sequence in a target gene or RNA molecule |
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| Fluorescent in situ hybridization (FISH) |
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| phylogenetic probes to find species-specific oligonucleotide signature sequences; highly specific & simple; multiple probing of single sample; culture not needed when this performed |
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| FISH Community Analysis |
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| study unculturable organisms, determine morphology, abundance, microbial associations; probes allow for determination of species that couldn't be differentiated with just simple staining |
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| Multiple FISH Probes |
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| 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" |
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| FISH Chromosomal Painting |
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| locate, count specific metabolic populations; can search for whatever gene you require; physiology & neighboring organisms |
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| In situ reverse transcriptase (RT) FISH |
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| 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 |
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| PCR & Microbial Community Analysis |
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| 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 |
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| Polymerase Chain Reaction (PCR) |
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| new process allows for no TAC polymerase inhibitors of PCR in community; able to amplify PCR |
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| Environmental Genomics |
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| 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 |
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| Microbial Activity Measurements |
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| 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 |
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| Microbial Activity Measurement Types |
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| 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 |
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| FISH Microautoradiography (MAR) |
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| 14C or 35S used for short term; labeled sugars put on photographic plate; wherever radioactivity is concentrated shows what populations metabolizing |
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| Microelectrodes |
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| Test physical parameters & compounds for specific metabolic activities; can tell where no O2 - orgs fermentative or anaerobic; can do w/o disturbing population |
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| Microbial Activity Measurements - stable isotopes |
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| 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 |
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| Carbon Isotopic Compositions |
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| Different substrates & their organic processes & result - how much carbon; CO2 fixed and fungi breaks down to release carbon into ecosystem |
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| Populations, Guilds & Communities |
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| 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) |
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| Guilds |
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| 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 |
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| Microenvironments |
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| 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 |
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| Nutrient Levels & Growth Rate |
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| 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 |
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| Competition |
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| neighbor gains access to nutrients faster, killing off competition; can also inhibit growth of others by releasing compounds as antibiotics (fungi) or bacteriosis |
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| Cooperation |
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| work together instead of fighting; "Syntrophy"; close associations |
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| Syntrophy |
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| cooperation, eating together ("commensal") & working together ("Consortium") |
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| Consortium |
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| everyone works together metabolically so can share to attack particular substrate together, better |
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| Terrestrial Environments (soil) |
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| Different horizons (layers of environments or microniches); most complex for microbes; each horizon has different nutrients, temps |
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| Terrestrial Horizons |
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| 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) |
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| Soil Aggregate |
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| 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 |
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| Terrestrial Environments (deep subsurface) |
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| Several to 1000+M; anaerobes that are sluggish chemoorganotrophs & chemolithotrophs (not a lot of organic available); no photosynthesis; divide only once every 100 years |
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| Aquatic Habitats |
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| 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. |
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| Aquatic O2 Relationships |
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| 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 |
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| Epilimnion |
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| Upper layer of water |
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| Hypolimnion |
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| Lower layer of water - provides nutrients |
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| Aquatic - Rivers |
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| highly mixed & high organic levels possible so lower O2 levels |
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| Biological Oxygen Demand (BOD) |
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| O2 consuming property of water; measures amt of organic material that can oxidize by microorgs; > BOD = > pollution & > org level; > carbon = < O2 |
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| Effect of high organic levels |
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| 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 |
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| Marine Environment |
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| Inshore - higher nutrient levels, high primary production, high heterotrophic activity, potentially low O2; inorganic materials allow heterotrophs to be vast |
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| Chlorophyll Distribution |
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| open ocean depleted of photosynthesizers; high chlorophyll content inland, rivers |
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| Open Oceans |
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| limited inorganic nutrients, limited primary production; limited heterotrophs; O2 levels high. Cyanobacteria primary producers O2; 1/2 O2 we breathe from cyanobacteria |
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| Deep Sea |
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| 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) |
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| Barotolerant |
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| down to 3000M, no growth above 5000M |
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| Barophilic |
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| 4000-6000m, optimum at 4000M |
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| Extreme Barophiles |
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| 10000M, opt 7000-8000M, no growth <4000M |
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| Molecular effects of high pressure |
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| decrease binding capacity of enzymes, membrane process, use outer membrane porins to bind substrates; limited gene expression |
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| Hydrothermal vent |
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| 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 |
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| What do the vents release? |
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| H2S, CO2, NH4+ (no organic material) |
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| Vent invertebrate communities |
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| Sessile tubeworms and mollusks that live close to the vent; Receive C source (chemotrophic dependent), few predators; red parts (hemoglobin like) to attract nutrients |
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| Chemolithotrophs of deep sea |
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| CO2 fixation from nutrients out of vents, tube worms have trophosomes that live inside tissue of worm; giant clams & methanotrophs that release CO2 |
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| Trophosome |
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| prokaryotic cell symbionts in tube worms that use hemoglobins to bind O2 and H2S; Houses and delivers H2S and CO2 to chemoautotrophs |
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| Black smoker chimney worms |
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| chemolithotrophic bacteria grown on surface of worm bodies to hold nutrients; worms graze hairs & eat; not one homogenous population of bacteria |
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| Higher temps for microbes |
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| in situ evidence for colonization, growth at 125-140oC; biological sulfate reduction at 130oC; ATP unstable at 150oC |
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| Carbon cycle |
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| carbon reservoirs in land/living plants; carbon in humus; CO2 transfers; photosynthesis (terrestrial, aquatic); |
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| Carbon Cycle 2 types |
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| Main 2 types: CO2 fixation; Carbon mineralization (decomposition) Other: Methanogenic archaea; Methylotrophs; Carbon monoxide metabolism |
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| Humus |
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| 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 |
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| methanogenic habits |
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| swamps, marshes, soils, protozoan endosymbionts, rumen, cows (burp 50L/day) |
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| Rumen |
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| digestive area of cow: find bacteria, protozoa, anaerobic fungi, microbial cells digested, microbial protein recovered; strict anaerobic fungi digests cellulose |
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| Chemoautotrophic benefits |
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| Maintain access to H2S and CO2 |
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| Metabolic Diversity |
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| Presence of specific enzymes dictate metabolic capabilities/habitat distributions |
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| Biogeochemical cycles |
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| Chemical transformations by biological organisms; every element has own cycle, almost always moderated by microbes |
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| Purposes of biogeochemical cycles |
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| Converts one chemical form to another, maintains essential compounds in biosphere; leaching of ores (copper, gold); heavy metal transforms, biodegrade/biomediate toxins, etc |
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| Biogeochemical Cycles & Pseudomonas |
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| pseudomonas altered metabolically and put in toxic environment for cleanup; they don’t compete so eventually die out; fluorescence used to view colonies. |
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| Plant-Microorganism Interactions |
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| 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) |
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| Nitrogen Cycling |
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| Protein synthesis; Nucleic acid synthesis; other cell components; Major reservoir of N2 is atmostphere |
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| CO2 fixation |
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| CO2 -> Organic carbon; CO2 is a major reservoir of carbon; CO2 fixation is done by Primary Producers (autotrophs) |
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| Carbon Cycle - Decomposition |
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| decomp produces methane (CH4) & CO2; both organic aerobic & anaerobic ferments to release carbon back into atmosphere |
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| CH4 production from CO2 |
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| Anaerobic process done by methanogenic Archaea |
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| The sulfur cycle (2 types) |
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| Sulfur oxidation (elemental sulfur) & reduction (dissimilatory sulfate reduc) |
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| Ecosystem |
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| sum total of all organisms in specified environment |
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| Habitat |
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| portion of ecosystem suited to a specific population |
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| Eutrophic lake, eutrophication |
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| buildup of inorganic/organic material (nutrients) = eutrophication = fish die |
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| Microenvironments |
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| different oxygen levels, physical & chemical changes can change environment rapidly |
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| Aquatic habitats depend on what? |
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| rate of primary production (carbon) |
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| Primary producers of aquatic? |
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| phytoplankton & benthic algae |
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| PCR gel T-RLFP |
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| restriction enzymes cut DNA at specific sequences; identifies higher level of phylogenetic tree (more general) |
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| PCR gel DGGE |
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| separates down to the molecules of DNA, even if 1 base pair differs; identifies lower levels of tree (more specific) |
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| Winogradsky column |
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| it is selective for isolation & different gradients; microbial diversity in artificial environments |
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| Chromosomal staining |
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| ISRT: dyes nucleic acids; gene expression FISH: dyes DNA, gene transcription |
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| In situ? |
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| experiment that uses intact tissue (no harm to sample bcz not individual cells) |
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| Acridine Orange |
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| DNA staining, also use DAPI |
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| gene expression staining |
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| ISRT |
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| gene transcription staining |
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| FISH chromosomal painting |
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| Why are Gram (-) more dangerous as endotoxin? |
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| because Lipid A layer of LPS has toxins |
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| Cleistothecia |
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| closed, hollow sphere ascocarp |
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| Perithecia |
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| flask-like ascocarp |
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| Apothecia |
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| cup, or disk-like ascocarp |
