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121 Cards in this Set
- Front
- Back
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taxonomy
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the science of classification of organisms
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taxa( or taxonomic categories)
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subdivisions used to classify organisms - usually based on similarities
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phylogeny
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the study of the evolutionary history of organisms
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Domains
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eukarya, bacteria, and archeae
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domain
Eukarya |
animals, plants, fungi, and protozoa
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domain
Bacteria |
includes prokaryotes:
pathogens (disease-causing) non-pathogens (organisms found in water and soil) other bacteria |
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domain
Archeae |
prokaryotes that don't have peptidoglycan in their cell walls
live in extreme environments and carry out unusual metabolic processes - extreme halophiles extreme thermophiles methanogens |
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classification of prokaryotes
2 domains |
bacteria and archeae
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eukaryotes
kingdom protista |
simple eukaryotic organisms, mostly unicellular, approx 200,000 species
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eukaryotes
kingdom fungi |
more complex eukaryotes, including molds, yeasts and mushrooms
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euakaryotes
kingdom plantae |
includes some algae, mosses, ferns, conifers, flowering plants
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eukaryotes
kingdom animalia |
includes sponges, worms, insects, vertebrates
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morphological(structural) characeristics
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examples of morphology include:
shape presence of flagella presence of a capsule or slime layer arrangement of the organisms |
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biochemical tests
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metabolic activity may provide clues for identification
examples include: fermentation of different sugars production of various enzymes- oxidase, catalase, coagulase, API strips |
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serology
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anitgen-antibody complexes
differentiates strains by sterotype or biovars known antibody you can test it on an unknown organism, if a complex forms then they match |
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other methods for identification and classification
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-phage typing - highly specific viruses that infect and
lyse bacteria -fatty acid profiles -flow cytometry |
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molecular subtyping capabilities
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PCR
Real time PCR Mircosphere array PFGE gene sequencing fragment analysis- VNTR |
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master mix
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cocktail of reagents
components: water forward primer reverse primer MgCl2 Taq polymerase dNTPs ( A, T, G, C) doesn't include DNA master mix made for multiple samples then aliquoted into tubes - 1 tube per sample DNA from each sample is added to the corresponding tube |
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PCR on RNA
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RNA must be converted into DNA
RNA uses the Reverse Transcriptase enzyme to make a complementary strand of DNA which can then be copied in a PCR reaction |
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Real Time PCR
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fluorescence probes are used to detect amplicon (FAM, TAMRA, SYBR Green)
PCR product detected by lasers during annealing or extension stage results 30 mins to 2 hours after extraction hand held or transportable models available faster and more sensitive than gel based PCR |
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Real Time PCR applications
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multiplexing-Up to 4 assays can occur simultaneously in well or tube
viral screening and subtyping (H1, H3, H5, H7) bioterrorism agents agents identified from environmental and clinical samples US Postal Service Biological Detection System (BDS) |
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Biological Detection System
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Northrop Grumman/Cepheid
automated air sampling real-time PCR Monitor B. anthracis Y. pestis, F. tularensis and Brucella in development USPS in use 2002 national network notification LRN lab confirms positive samples |
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mircosphere Assay
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PCR or ELISA based
antigen coated beads red and green laser detection methodology allows detection of 100 targets/well next generation will allow detection up to 1000 targets/well |
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Microspehere assay
BT screening |
BioWatch LRN
screens B. anthracis, Y.pestis and F. tularensis, SEB and Ricin toxin |
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mircosphere assay
RVP |
17 respiratory viruses
results < 8h |
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microsphere assay
Salmonella Serology |
detects approximately 95% of common serotypes
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sequencing applications
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pathogen identification
strain typing viral genotyping antimicrobial susceptibility partial or whole genome sequencing |
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VNTR
variable number tandem repeats |
PCR based
detects length variations in DNA fragments containing tandem repeats --5-CAATATCAACAA-3 variation in repeated region give strain unique pattern used to strain type origin of B. anthracis in mail |
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pathogen identification
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16s or 18s rRNA sequencing allows more discrimation identification of nonculturable nonviable, low copy number in inert fastidious organisms
compares sequence to known databases useful by Coroners in unexplained deaths when infectious agents suspected |
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domain bacteria
proteobacteria |
from Greek god, Proteus, who could assume many shapes
gram negative |
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proteobacteria
5 classes |
alpha
beta gamma delta epsilon |
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alphaproteobacteria
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human pathogen
obligate intracelluar parasites capable of growth at very low levels of nutrients Bartonella B. hensela: cat-scratch disease Brucella:brucellosis Ehrlichia:tickborne; ehrlichiosis arthropod-borne, spotted fevers, only infect mammalian cells, transmitted by insects R. tickettsii: rocky mountain spotted fever |
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Brucella mircoscopic
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gram negative coccobacillus
faintly staining appears like fine sand no bipolar staining |
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betaproteobacteria
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Neisseria : chemoheterotropic, cocci
N. meningitidis N. gonorrhoeae Spirillum : chemoheterotrophic, helical Bordetalla : chemphetertrophic, rods B. pertussis B. parapertussis Burkholderia : nosocomial infections can degrade > 100 organic molecules contaminates drugs and equipment, can live in disinfectant Zoogloea: slimy masses in aerobic sewage- treatment processes |
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gammaproteobacteria
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largest group of organisms
human pathogens include the genera: Francisella Pseudomonas Moraxella Legionella Coxiella Vibrio Pasteurella Haemophilus |
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gammaproteobacteria
Pseudomonadales |
Pseudomonas
opportunistic pathogens metabolically diverse polar flagella often pigmented Moraxella : conjunctivitis |
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gammaproteobacteria
Legionella |
legionella: found in stream, warm-water pipes, cooling
towers L. pneumophilia Coxiella: Q fever transmitted via aerosols or milk |
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gammaproteobacteria
Vibrionales |
found in coastal water
Vibrio cholera causes cholera V. parahaemolyticus means gastroenteritis |
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Francisella tularensis
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tiny gram negative coccobacillus
mostly single cell faintly staining grows poorly on SBA gray-white, non-hemolytic at 48-72hrs |
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gammaproteobacteria
enterobacteriales (enterics) |
found in inestines
peritichous flagella, facultatively anaerobic Enterobacter Erwinia Escherichia Klebsiella Proteus Salmonella Serratia Shigella Yerisinia |
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gammaproteobacteria
Pasteurellales |
Pasteurella : cause pneumonia and septicemia
Haemophilus : require X (heme) and V (NAD+, NADP+) factors |
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deltaproteobacteria
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members of this group include bacteria that prey on other bacteria..
no human pathogens |
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Epsilonproteobacteria
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include slender gram negative rods that are helical or vibriod ( without a complete turn)
human pathogens include : Campylobacter- dairy or poultry Helicobacter- ulcers or stomach cancer |
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Nonproteobacteria gram negative bacteria
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include photosynthesizing bacteria ( which we typically don't think of as pathogens)
Cyanobacteria : formerly known as the blue-green algae produce toxins as evidence by fish kill-offs purple and green photosynthetic bacteria |
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gram positive bacteria
2 groups |
high G+C ratio = actinobacter (highly pleomorphic)
low G+C+ ratio = firmicutes (endospore formers) |
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Firmicutes
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low G+C , gram- positive
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Firmicutes
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endospore-forming rod-shaped bacteria
Clostridium Bacillus Gram positive cocci gram negative rods Staphylococcus Lactobacillus Streptococcus Listeria Enterococcus |
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Mycoplasma
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wall-less pleomorphic
0.1-0.24 um M. pneumoniae |
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Actinobacteria
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high G+C , gram positive
organisms are varied in shape (pleomorphic) Include: Mycobacterium (fungus like, ie T.B.) Corynebacterium (club like, ie. diptheria) Proprionibacterium (acid former used in swiss cheese) Gardnerella ( causes vaginitis) Streptomyces (produces most of antibiotics) Actinomyces/Nocardia (causes pulmonary infections) |
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Chlamydias
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unique cell walls- don't contain peptidoglycan
unique development cycles- intracellular within host include 3 species : Chlamydia trachomatis- STD- urethritis Chlamydia psittaci Chlamydia pneumoniae |
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Spirochete
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coiled morphology - like a spring
motility by axial filaments (endoflagella) includes these species : Treponema Borrielia Leptospira |
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Phylum Bacteriodetes
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Anaerobic bacteria
include: Bacteriodes live in the intestinal tract, gingival crevices, and often found in deep wound infections Cytophaga : soil organisms that degrade cellulose and chitin |
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Fusobacterium
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spindle-shaped
anaerobic found in the gingival crevices may be responsible for some dental abscesses |
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fungi
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include mold, yeast, mushrooms
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mycology
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study of fungi
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hyphae
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body of mold consists of long filaments of cells joined together
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septate hypahae
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contain crosswalls (septa) and their hyphae
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non-septate or coenocytic hyphae
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without crosswalls
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vegetative hyphae
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the hyphae that grows into the media to obtain nutrients
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aerial hyphae
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reproductive hyphae
the portion extending above the surface of the media where the spores are located |
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mycelium
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a colony or body of mold
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mold macroscopic appearance
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rapid growers form mature colonies in 5 days
intermediate in 6-10 days slow growers > 10 days |
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mold mircoscopic appearance
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hyphae septate or coenocytic
color of the hyphae- dark (dermatiaeous) or light (hyaline) arrangements of spores |
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mycelium
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texture-cottony, velvety, powdery, smooth
shape- dome shaped, wrinkled, deep folds color- both top and undersurface |
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yeast
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single-celled fungi and appear microscopically as small round to ovoid bodies
reproduce by budding biochemical test most common pathogen is Candida albicans |
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pseudohyphae
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yeast produce buds that fail to detach themselves, forming a short chain of cells
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gram stain of yeast
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retain the crystal violet on gram-staining - in fact appear very dark blue to black rather than purple
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dimorphic fungi
2 different forms of growth |
either as mold or yeast
thermal dimorphism: room temp mold body temp yeast primarily fungi that cause the systemic mycoses Histoplasma capsulatum Coccidioides immitis |
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molds
asexual |
hyphae fragmentation
spores- formed on the hyphae of 1 organism |
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molds
sexual |
spores result from the fusion of 2 stains of the same species
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mold nutrition
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ph of 5 or less
high sugar and salt concentration (osmotic pressure) low moisture content capable of metabolizing complex carbohydrates such as lignin |
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fungal disease
mycosis |
mycoses are classifies by
degree of tissue involvement mode of entry into the host fungal infection are chronic- fungi grow slowly in body |
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types of fungal infections
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systemic
subcutaneous cutaneous superficial opportunistic infections |
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lichens
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combination of a green alga ( cyanobacteria) and a fungus
inhabit areas in which neither fungi nor algae could survive alone lichens or their acids cause allergic contact dermititis in humans |
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thallus
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body of a multicellular algae
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algin
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food thickener extracted from their cell walls
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protozoa
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unicellular, eukaryotic chemoheterotrophic organisms
20,000 species but few human pathogens inhabit soil and water-require moisture for survival |
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protozoa
trophozoite |
feeding and growth stage
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protozoa
cyst |
the environmentally resistant stage
( not all protozoa have a cyst stage) |
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protozoa
Archaezoa/flagellates |
medically important
typically spindle-shaped with flagella projecting from the front end 2 or more flagella which move in a whiplike manner that pulls the cell thru their environment Examples : Trichomonas vaginalis no cyst stage as it dries out, it dies an undulating membrane and flagella Giardia lamblia has both cyst and trophozite stages |
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protozoa
flagellates |
found in small intestine of humans and mammals and passed in the feces into the environment where it is ingested by the susceptible host
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protozoa
amoebozoa/amoeba |
move by pseudopods: blunt, lobe-like projections of
the cytoplasm ex: Entamoeba histolytica causes amoebic dysentery Acanthamoeba sp. can infect the cornea and causes blindness |
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protozoa
apicomplexa |
not motile in their mature form
obligate intracellular parasites complex life cycle that involves transmission between several hosts Ex : Toxoplasma gondii Plasmodium sp. causative agent of malaria |
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protozoa
Malaria |
transmitted by bite of infected mosquitoes
complex life cycle diagnosis by observing the parasite inside the host's red blood cells |
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protozoa
Ciliophora / ciliates |
use cilia for movement and to bring food particles into
their mouth similar to, but shorter than flagella generally cover entire surface ex: Balantidium coli- causes a severe type of dysentery |
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Helminths/ worms
2 phyla |
platyhelminthes = flatworms
Cestodes = tapeworm Trematodes = flukes Nematodes = roundworms multicellular eukaryotic animals are highly specialized to live inside their hosts their eggs are mircoscopic and diagnosis of helminthic infections are often made by visually indentifying these eggs |
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trematodes / flukes
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complex life cycles with intermediate hosts
named for the tissue in the definitive host in which the adult parasite lives flat, leaf-shaped body with a ventral sucker and an oral sucker; identify eggs in appropriate sample lung flukes = sputum and feces |
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Cestodes / tapeworms
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intestinal parasite
complex life cycle with intermediate hosts head (scolex) has suckers for attaching to the intestinal mucosa body consists of segments called proglottids proglottids furthest from the head are the mature ones containing eggs these proglottids break off and are passed with the feces into the environment |
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Nematodes
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cylindrical and tapered at each end
some are free-living in soil and water; others are parasites of plants and animals nematode infections of humans can be divided into 2 categories: egg is infective larva is infective |
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Pinworms / Enterobius vermicularis
egg infective |
adult found in large intestine; female migrates to anus to deposit eggs; eggs ingested by contamination with fingers, clothing, or bedding
diagnosed using Graham sticky tape method |
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Hookworms / Necator americanus
larvae infective |
live in small intestine in humans
eggs are excreted in the feces larvae hatch from the eggs larvae enter host by penetrating host's skin migrates thru body diagnosis based on presence of eggs in feces |
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arthropods
vectors |
carry pathogenic mircoorganisms
mechanical vectors = carry mircobes on feet or bodies such as house fly biological vectors = multiple/ reproduce in vector a and then accumulate in the vector's feces or saliva, suck as tick |
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Arachuida (8 legs)
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spider, mites, ticks
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arthropods (4 antennae)
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crabs, crayfish
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arthropods (6 legs)
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bees, flies, lice
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virus
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viro in latin = poison
obligate intracellular parasite consists of non-living particles they are all infectious |
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virus
capsid |
outer most part of a virus
composed of : proteins |
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virus
core |
consists of nucleic acids are either DNA or RNA but not both
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virus
envelop |
NOT found in all viruses usually a piece of the host plasma membrane
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classification of virus
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based on:
type of nucleic size and shape presence or absence of outer envelop are obligate intracellular parasites CANNOT multiply outside a living cell |
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virus
general morphology |
capsid architecture
helical polyhedral enveloped complex viruses, including bacteriophages |
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bacteriophages
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infect bacteria
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growing animal viruses
3 methods |
living animals
embryonated eggs cell cultures |
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embryonated egg
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hole is drilled in egg and virus is injected
viral growth is indicated by : death of embryo cell damage lesion formation |
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cyropathic effect
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mircoscopic changes in the monolayer
CPEa include: destruction of cells if the monlayer formation of giant cells detachment of the monolayer changes to the monolayer cells |
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cell lines
primary cell lines |
derived from animal tissues
die out after a few generations |
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cell lines
diploid cell lines |
derived from human embryos
can be maintained for 100 generations |
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cell lines
continuous / immortal cell lines |
uses transformed or cancerous cells
can be maintained thru an indefinite number of generations ex : HeLa cells |
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viral multiplication
5 major steps |
attachment
penetration biosynthesis maturation release |
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viral multiplication
lytic cycle |
ends in lysis and death of the host cell
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viral multiplication
lysogenic cycle |
host stays alive
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viral multiplication
animal viruses steps |
attachment
penetration uncoating biosynthesis maturation release |
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pinocytosis or fusion
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entry into the host cell
with enveloped viruses following attachment, host cell's plasma membrane folds inward creating a vesicle that includes virus |
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virus multiplication
budding |
as virus particle pushes thru the plasma membrane, part of membrane adheres to virus forming the envelope
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virus multiplication
rupture |
non-enveloped viruses are released thru ruptures in host plasma membrane - usually causing death of the host cell
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burst time
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time from attachment until release
varies depending on the viral species averages from 20-40 minutes |
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burst size
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number of viral particles released from each cell
averages from 50-200 particles |
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oncogenes
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genes that cause malignant transformations - cancer
activated by viruses oncoviruses can induce tumors in animals |
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latent viral infections
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HSV-1 cold sores
HSV-2 genital herpes Varicella- Zoster Virus causes chickenpox and shingles |
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persistent viral infections
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occur gradually over a long period and are usually fatal
Hep B = liver cancer HPV or Human Papilloma Virus = cervical cancer |
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prions
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proteinaceous infectious particle
neurological diseases called spongiform encephalopathies because large holes/vacuoles from in the brain Ex : mad cow disease Creutzfeldt-Jakob disease altered protein = prion diseases |
