Mod 6 - Microbiology
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| Microbiology | The study of microorganisms (microbes):
- Viruses
- Bacteria
- Parasites
- Fungi
- Others
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| Prokaryotes vs Eukaryotes | PROKARYOTES DO NOT HAVE:
- membrane bound nucleus
- membrane bound organelles
- DNA that is organized into chromosomes.
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| Prokaryotes Classification | - All living cells are either prokaryotes or eukayotes
- All bacteria are prokaryotic cells
- Divided into (5) classes
- Prokaryons in Kingdom Monera
- Many classes
- Earth's most abundant form
- 0.5-2UM in size
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| Prokaryotic Cell Structures | - Cytoplasm
- Ribosomes
- Nucleoid (chromosome)
- Inclusion Bodies
- Some prokaryotes secrete a capsule & have plasmids.
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| Prokaryotic Cytoplasm | - Semi-fluid substance that fills inner cellular space
- Primarily water with carbohydrates, lipids, and various enzymes.
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| Prokaryotic Ribosomes | - Consists of RNA and protein
- Used in protein synthesis
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| Prokaryotic Nucleoid | - Chromosomes
- No real nucleus
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| Prokaryote Inclusion Bodies | Stores molecules essential to cell function.
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| Capsule | A protective structure that serves as a defense mechanism in some prokaryotes consisting of:
- Tightly bound wall with complex polysaccharide molecules that form a gel-like covering that surrounds the bacterial cell.
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| Plasmids | Some prokayrotes contain a self-replicating extrachromosomal DNA that carry 1 or more pieces of genetic information, not required to sustain life.
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| Prokaryote Cell Structure | Cell Wall:
- Shape & stability
- Contain peptidoglycan, large polymer resembling a "chain link fence"
- Antibiotics target cell wall (i.e penicillin)
"Eukaryotes do not have cell wall"
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| Prokaryote Cell Membrane (aka plasma membrane) | - Regulates transport of material in and out of the cell
- Made of phospholipids
- Long-chain fatty acids and proteins
- Selectively permeable
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| Peptiglycan | Large polymer which makes up a prokaryote cell membrane with an immense, covalently-linked molecule linked in multi-layers resembling a "chain-link" fence
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| Flagellum (singular); Flagella (plural) | Filamentous organelles of locomotion found on half all known bacteria
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| Motile | Various degrees of movement
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| Pili (singular: pilus) | Tiny, tube-like projections from the cell's surface associated with adherence
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| Prokaryotic Bacterial Cells: (Shape & Arrangement) | - characterized by shape & size
- before culture information is available, location and appearance characteristics were used
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| Cocci (singular: coccus) | Spherical bacterial cells
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| Bacilli (singular: bacillus) | Rod-shaped bacterial cell resembling a hot dog
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| Vibrios | Comma shaped bacterial cell
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| Coccobacillus | Bacterial cell shaped between cocci & bacilli
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| Spirillia | Bacterial cell which appears loosely-coiled or wavy
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| Spirochetes | Bacterial cell which appear tightly coiled, corkscrew-shaped rods.
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| Gram Stain | Method used to group bacteria into 2 different catagories:
- Gram positive bacteria (purple)
- Gram negative bacteria (pink)
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| Gram-Positive Bacteria | - Thick layer of peptidoglycan (thick cell wall)
- Teichoic acid causes retention of crystal violet (blue) dye
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| Gram-Negative Bacteria | - Thin layer of peptidoglycan (thin cell wall)
- High lipoprotein content which releases crystal violet dye when rinsed with alcohol
- The safranin (pink) counterstain is retained
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| Gram Stain Method | 1-Sample smeared on slide & fixed with heat
2-Slide stained with crystal violet (purple)@ 1-2 mins.
3-Gram's iodine used to "fix" the crystal violet (help retain stain)
4-Acetone used to decolorize slide
5-Stain slide w/safranin (pink)
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| Diplococci | - Cocci in pairs
- Ex.: Gonorrhea
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| Streptococci | - Cocci in chains
- Ex.: Aureus, Boils
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| Staphylococci | - Cocci in grape like pairs
- Ex.: Staphylo (irregular clusters)
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| Culture Media - Identifing Specific Bacteria | - Can be liquid or semi-solid
- 3 Different Types:
< Enriched Media
< Selective Media
< Differential Media
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| Tetrad | - Group of four
- Micrococcus
- Rarely pathogenic
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| Enriched Media | encourages the growth of most bacteria (Sheep's blood "Agar plate")
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| Selective Media | Encourages the growth of some bacteria which inhibiting others ("MacConkey" Agar)
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| Differential Media | Groups bacteria based on the fermentation of carbohydrates ("MacConkey" Agar)
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| MacConkey Agar | Used in both Selective and Differential Media
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| Aerobes | - Require atmospheric oxygen
- Ex.: Staphylococcus, Streptococcus, E. coli
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| Anaerobes | - Require no oxygen
- Ex.: Colstridium species, Gangrene
- Used to put candle in the container until it burns out
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| Microaerophilis | - Require reduced oxygen & increased CO2
- Ex.: Campylobacter
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| Binary Fission | - Term used to describe cell division
- Aka "Transverse Fission"
- Do not have a cell cycle replicating their DNA
- Continuosly dividing &
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| Lag Phase | - Gear up phase
- Organisms not greatly increasing in #, but metabolically active
< Growing, synthesizing enzymes, & producing lrg. amounts of ATP
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| Log Phase | - Once bacteria have adapted to nutrient-rich environment, growth is exponential (Logarithmic)
- Generation time: genetically determined period of log. growth
- Varies by species (min to hr)
- Ex.: generation = 20 min
< 1000 org/ml - initial
<
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| Stationary Phase | - When the # of new cells produced is the same as the # of cells dying
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| Decline (Death) Phase | - # of cells dying is greater than the # of new cells arising from division
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| Symbiosis | - "Living together" in relation to bacteria
- 3 Different types:
< Mutualism
< Parasitism
< Commensalism
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| Mutualism | - Both the host & the microorganism benefit
< E. coli, a bacterium that lives in the large intestines
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| Parasitism | - One organism benefits, the other is harmed
< Tapeworm, Malaria
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| Commensalism | - One organism benefits, the other is neutral
< skin bacteria, normal flora
< majority of microbes
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| Normal Flora | - Organisms that live on or in the body but do not usually cause disease (commensals)
< skin, conjunctiva, mouth, nose, throat, urinary tract, reproductive, & GI tracts.
- Nutrients from oils & sweat facilitate colonization up to a dozen staph specie
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| Normal Flora in Infants | Infant have:
- not acquired normal flora
- less organic acid available to minimize growth
- ideal environment to grow pathogens
- Pathogens include: Grp B strep & Candida (yeast)
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| Resident Microflora | Organisms found on/in specific areas of the body
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| Transient Microflora | Organisms that "come and go" and exist in the same areas occupied by resident flora
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| Pathogenicity | Organism which benefits from its host and often lead to infection
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| Virulence | Term used to describe the intensity of bacterial & other microbial infections
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| Pathogenic Mechanisms of Bacteria | 3 Types:
- Adherence
- Colonization
- Formation of a capsule
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| Adherence | Bacteria use pili to cling to surface of host cells, multiply & form colonies
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| Colonization | Once in place within host tissue, bacterial replication forms colonies and may overcome host defenses.
< colonization in small #s of non-invasive organisms is normal in all animals
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| Formation of a Capsule | Capsule contributes to organism's virulence due to thick, polysaccharides structure - helps to resist host defense processes
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| Invasiveness | Ability of organisms to penetrate host tissue, usually by special enzyme
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| Enzymes contributing to Invasiveness | 3 Different Types:
- Hyaluronidase
- Coagulase
- Streptokinase and Staphylokinase
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| Hyaluronidase | Attacks hyaluronic acid, the ground substance of connective tissue
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| Coagulase | Breaks down collagen, the framework of muscles
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| Streptokinase & Staphylokinase | Digest fibrin & prevent the clotting of blood
< "flesh-eating bacteria" ex. of organism that produces streptokinase
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| Exotoxins | Secreted primarily by Gram-positive organisms
< Gram (+) = botulism, gas gangrene, tetanus, staphylococcal food poisoning
< Gram (-) = E. coli O157:H7 Shiga toxin
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| Endotoxins | - Release from Gram (-) bacteria when they die
- Non-specific gastrointestinal symptoms such as diarrhea, cramping, & generalized malaise
< Ex.: cholera, salmonella
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| Endospores | - Dormant form
- Form when conditions are unfavorable for growth
- Survive under harsh conditions
< excessive heat or cold
- Revert to active under favorable conditions
- Clostridia species that cause tetanus, botulism, & gas gangrene form endosp
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| Exchange of Genetic Material | Bacteria can exchange genetic material 3 different ways:
< Transformation
< Transduction
< Conjugation
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| Transformation | - DNA is acquired directly from the environment which was released from another cell through lysis etc.
- Fragments are then "spliced" into the host cell's DNA
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| Transduction | - An asexual genetic process
- Viruses (Bacteriophages or phages) transfer genes between mating bacteria
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| Conjugation | - Requires contact between 2 bacteria
- utilizes a plasmid
- transfers a greater amount of DNA than transformation or transduction
- DNA is to be transferred from a donor cell to a recipient cell
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| F-Pilus | - Sex pilus
- transfers DNA from one cell to another in conjugation
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| Plasmid | Extra-chromosomal DNA in the cytoplasm of some bacteria but not required by the bacterium
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| Resistance Transfer Factors | Bacteria which develop a drug resistance through plasmids
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| Genetic Recombination | By 3 different processes, transfers DNA leading to new strains of bacterium including antibiotic resistant strains
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| Antimicrobial Agents | Substances used to specifically treat infectious microbial diseases
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| Antibiotics | Antimicrobial agent containing substances derived from other organisms
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| Spectrum of Activity | Antimicrobial classifications:
< Broad Spectrum
< Narrow Spectrum
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| Broad Spectrum | Antimicrobials which are effective against a wide range of microorganisms including both gram (+) & gram (-) bacteria
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| Narrow Spectrum | Antibiotics are effective against a limited # of microorganism or single taxonomic group
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| Bacteriocidal Drug | Kills the organism
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| Bacteriostatic Drug | Inhibit the organism growth & allows immune defenses to act against the invader
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| Resistance Factors (Causes of) | Occurs through:
- overuse of antibiotics
- plasmids
- genetic transfer mechanisms
- development of neutralizing enzymes
- alteration of pathways used by antibiotics
- altering cell membrane permeability
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| Agar Disc Diffusion (Kirby Bauer Method) | - Uses paper discs impregnated with specific concentration of the antimicrobial to be tested
- Result reported as either:
< Sensitive: stays away from seed; inhibiting
< Intermediate
< Resistant: grows up to seed
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| Upper Respiratory Tract Infections | Pharyngitis
- infections of upper tract:
< pharynx
< ears
< eyes
< sinuses
< upper bronchioles
- e.g. Strep throat caused by Streptococcus pyogenes
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| Lower Respirator Tract Infections | - Pneumonias
- Casulated organisms that cause pneumonias include:
< haemophilus influenza
< Klebsiella pheumoniae
< Streptococcus pneumoniae
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| Gastrointestinal Bacterial Infections | - Gastrointestinal
- Contaminated food or water
< Salmonella (raw eggs)
< Shigella
< Staphylococcus aureus
< E. coli O157:H7 (raw hamburger, contaminated fecal material)
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| Nervous System Infections | - Meningitis
< haemophilus influenzae (children)
< Neisseria meningitidis
< Vaccines available for both
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| Toxin-Induced Infections | - Botulism (Colstridium botulinum)
- Tetanus (Colstridium tetani)
- Toxic Shock Syndrome (Staphylococcus aureus)
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| Intracellular Bacteria | 2 Different Classes:
- Chlamydia
- Rickettsias
- To a lesser extent: Mycoplasmas
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| Chlamydia Trachomatis | - intracellular organisms
- require eukaryotic cell to replicate
- causes variety of human infections including:
< Trachoma (eye infection)
< Sexually-transmitted disease causeing pelvic inflammatory dise.
< Conjunctivitis in newborns
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| Richettsias | - Obligate intracellular parasite
- Transmitted by a vector (ex. ticks & lice)
- Rocky Mountain Spotted Fever (RMSF)
- To human transmitted through the bite of the vector
- Rocky Mountian spotted fever, Lyme Disease
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| Mycoplasma Pneumoniae | Primary atypical pneumonia "walking pneumonia"
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| Mycoplasmas | - Tiniest free-living organisms
- Do not have a cell wall
- Mycoplasma pneumoniae (walking pneumonia)
< causes primary atypical pneumonia
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| Viruses | - Obligate Intracellular Parasite
- Replicates w/n host cell
- virus provides RNA or DNA to replicate
- Host cell provides energy & resource
- Contain RNA or DNA (not both)
< RNA viruses contain code for reverse transcriptase, enzyme which makes D
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| Viral Structure | - Nucleic Acid (RNA or DNA)
- Capsid: protective coat enveloping nucleic acid
- Envelope
< present in some viruses
< May have glycoprotein spikes
* determine specificity
* hide virus from immune system
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| Nucleic Acid | Either a single or double strand of DNA or RNA, differing among viral groups
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| Capsids | - Enclosed within a protective coat
- Determines the shape of the virus
- Composed of individual protein subunits (capsomeres)
- Can be helical, polyhedral (multi-sided) or bullet-shaped
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| Capsomeres | Individual protein subunits found in a capsid
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| Nucleocapsid | Combined capsid/nucleic acid arrangement
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| Viral Envelope | - External to the capsid
- Acquired from combo of proteins, lipids & carbohydrates found in host cell
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| Spikes | A projection, usually glycoprotein molecules, that attach to specific sites on host cell wall
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| Viral Replication | Five Steps:
- Adsorbtion
- Penetration
- Synthesis
- Maturation
- Release
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| Adsorption (Viral Replication - Step 1) | Attachment of virus to host cell
< specificity to certain cells
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| Penetration (Viral Replication - Step 2) | Virus enters host cell (endocytosis or fusion) and "uncoats" (takes off envelope and capsid)
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| Synthesis (Viral Replication - Step 3) | Utilizes host nucleus to make new genetic material
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| Maturation (Viral Replication - Step 4) | Virus is packaged into new complete virons
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| Release (Viral Replication - Step 5) | Departure of new virons from host cell
< host cell may rupture OR
< host cell remains intact & releases the virus
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| Uncoating | Process of a virus loosing the envelope & capsid
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| Viral Pathogenicity | Two Main Catagories:
- Acute Infections
- Latent/Persistent Infections
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| Acute Infections | - Disease cycle is relatively short
- Host cell ruptures; virus spreads to neighboring cells
< Common cold (rhinovirus), influenza, some hepatitis viruses
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| Latent/Persistent Infections | - Virus becomes relatively inactive by reemerges
- Provirus remains in host cells
- Replicates new virions when triggered by some external event (stress, fever, etc)
< Herpes Virus, Epstein-Barr Virus, Human Immunodeficiency Virus (HIV); T-Helper Ce
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| Immune System Viruses | Epstein-Barr Virus (infectious mononucleosis) & Human Immunodeficiency Virus (HIV)
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| Oncogenic Viruses | - Possess oncongenes (cancer causing genes) that cause uncontrolled & abnormal division of host cells by altering cell cycle "checkpoints"
< Hepatitis B, Hepatitis C
< Human Papilloma Virus (cause of cerical cancer)
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| Oncogenes | Uncontrolled and abnormal division of host cells
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| Interferon | Antiviral therapy which inhibits viral activity
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| Prions | - Infectious proteins w/o genetic material
- Come in contact w/normal proteins and transform them into infectious
- Affects cells of the brain
- Creutzfeldt-Jakob disease ("mad cow")
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| Infectious Particle | Infectious protein which affects the cells of the brain
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| Transmissible Spongiform Encephalopathies | - "Spongiform" = cytopathic effect on brain tissue
- "Infection" = produces microscopic holes in brain resembling a sponge
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| Prion Characteristics | - Generally resistant to inactivation by heating to 90*
- Resistant to radiation treatments
- Not susceptible to enzymes that inactivate RNA & DNA
- Susceptible to protein denaturing agents
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| Fungi | - Important for decomposition & recycling
- Divided into 2 different groups:
< Yeasts = unicellular
< Molds = multicellular
- Ex.: Candida Albicans (yeast infection) & Tinea Corporis (ringworm, mold)
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| Spores | Small deposits from the enviroment
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| Molds | - Multicellular fungi
- One or more spores grows into filamentous, thread-like mass called "mycelium"
- Ex.: Athlete's foot, jock itch & ringworm
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| Yeasts | - Unicellular fungi
- important in beer, bread, and alcohol production
- most common yeast infection: Candida albicans (infections: mouth & pharynx = thrush); vaginitis
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| Protozoa | - Parasites except Helminths (worms)
- found in the Kingdom Protista
- single-celled organism
2 Different Stages:
- Motile trophozoite
> infective stage
- Cyst stage
> dormant state
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| Parasitic Organisms (Protozoa & Helminths) | - Live at expense of host
- Transmitted to humans by vectors
> Biological = mosquito transmitting malaria
> Mechanical = transmission of parasite eggs to food by flies & other insects
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| Helminths | - Known as "worms"
- multicellular
- found in Kingdom Animalia
- 4 Different Groups:
> Flukes
> Tapeworms
> Roundworms
> Tissue Parasites
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| Trophozoite Stage | Stage of the protozoa which is the motile, invasive form of the organism
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| Cyst Stage | Stage of the protozoa which allows the organism to survive in a dormant state in the external enviroment
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| Common Pathogenic Protozoans | - Giardia Lamblia:
> ingesting cysts from animal contaminated water
> intense gastrointestinal (GI) distress & diarrhea
- Cryptosporidium:
> self-limiting GI symptoms
> if infected, can become carrier
> recently associated w/recreati
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| Anopheles | Mosquito which serves as the definitive host in Malaria
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| Helminths (Parasitic Worms) | - Hosts are definitive or intermediate
> Definitive: harbor parasite when it reproduces
> Intermediate: harbor parasite during a developmental stage in the parasite's life cycle
> Accidental: not part of the normal cycle; "dead end" hosts
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| Tapeworms | - Segmented worms that contain a head (scolex) and many segments call "proglottids"
- Hermaphrodites
- Infective stage is larvae found in cattle & swine
- Most prevalent in
> Beef & Pork (taenia)
> Fish (Dibothrocephalus)
- Several cm to meter
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| Roundworms (intestinal) | - Live in lumen of intestinal tract
- Infection occurs by ingestion of egg or penetration of the skin by larvae
> Pinworms (Enterobius)
> Ascarids (Giant intestinal worms)
> Hookworms
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