chapter 1

disease: abnormal, bodily, impairs functioning, has signs and symptoms (seen/feelings)

• infectious disease: disease caused by a host organism with pathogenetic microbes (make suffering; prions, viruses, bacteria, protozoa)
  EID: emerging infectious disease → disease that "emerged" in the past 20-30 years; re-emerging infectious diseases decreased in prevalence at one time and have reappeared recently
• antibiotic-resistant pathogens can cause EIDs (staphylococcus aureus, tuberculosis)
  parasite: organism that feeds on other life (host)
• macroscopic parasite: can be seen without magnification; ectoparasites feed outside, like blood feeders; endoparasites live within (worms)
  • arthropod vector: transfers microbial pathogens, often ectoparasite
    pathogen: organism that harms another organism
• opportunistic pathogen: will not normally cause disease unless in special circumstances (e. coli, pneumocystis jirovecii)
• microbial pathogen: too small to be seen without magnification (see path. microbes)
  ecology: the study of organisms and their interactions with the environment
• infectious disease medical ecology studies host pathogens and environment → infectious disease
• symbiosis: the living together of two or more different organisms. mutualism both partners benefit, commensalism one benefits and one is neutral, parasitism see parasite
• symbiotic relationships can change
  agents of infectious diseases: prions, viruses, prokaryotes, eukaryotes, fungi, macroparasites, ectoparasites
• mad cow disease, creutzfeldt-jakobs
• hiv, ebola, polio, rabies
• bacteria, e. coli, salmonella, std
• protozoa, malaria, sleeping sickness
• yeast, coccidioides
• worms
• vectors
  agents must cause an infectious disease by

1. transportation to host
2. colonization or invasion of host
3. grow/fulfill life cycle
4. evade host defense mechanisms
5. damage the host thru mech. chem or molec. means
6. leave and invade another host

• infectious diseases cause diseases within a host organism through pathogenetic microbes like viruses, prions, protozoa
• eids are infectious diseases which recently appeared/infected the given population, or diseases which receded in prevalence but reappeared within the community recently: ebola, covid-19
• symbiosis: the relationship between two or more different organisms which live with another. there are mutualistic, commensalistic, and parasitic relationships: a parasitic relationship is e. coli in your bladder, which benefits the pathogen but harms you
• parasitism: see above, a symbiotic relatonship where one organism benefits by harming another
• parasite: an organism that feeds on other life; blood-feeders like mosquitoes are ectoparasites, which feed outside of the organism
• host: an organism which another lives on or off of and develops a symbiotic relationship with. humans are host to a range of symbiotic relationships; in a parasitic relationship like pathogenetic e. coli, they are the host being harmed at the benefit of the organism
• pathogen: an organism that harms another organism in any way
• the political ecology of infectious disease: infectious diseases can be influenced by environmental changes, and political decisions and globalization can influence these changes in turn. our governments' political decisions and how they influence the environment causes changes which give rise to eids and other diseases found in nonhuman hosts, which may spread to humans through evolution. swine flu rose in prevalence due to factory use in the livestock industry: the unhealthy nature of these factories increases the virulence rate of swine flu, as does the mortality

chapter 2

• prokaryotes and eukaryotes, cells
  • cell theory: all organisms are made of 1+ cells; cells are the smallest living things; cells arise through division of previously existing cells
  • cells have plasma membrane, cytosol, chromosomes, and ribosomes
    • prokaryotes have no nucleus or membrane bound organelles, includes bacteria and archaea
      • external, cell envelope, and internal sections
      • cell membrane, cytoplasm, ribosome, chromosomes, cell wall
      • some bacteria have: flagella, pili, fimbriae, capsules, slime layers, inclusions, actin cytoskleton, endospores
      • glycocalyx coating on cell wall: slime layer loosely org/attached, capsule heavily
    • eukaryotes have membrane bound organelles, double membrane bound nucleus with chromosomes; includes algae, protozoa, fungi, orgs
      • external structures, cell boundary, organelles inside cell membrane (includes cytoplasm, nucleus, organelles, locomotor organelles, ribosomes, and cytoskeleton)
• bacteria:
  • glycocalyx inhibits phagocytosis of wbc, which adds to pathogenicity; the capsule coating blocks phagocytes from finding bacteria, so bacteria can multiply and infect
  • glycocalyx also helps form biofilms and protects from dehydration
  • biofilms: layered groups of microorgs enclosed in a polymeric matrix; highly adherent. 99% of bacteria live in biofilms
  • biofilms accumulate on damaged tissues; they are very resistant to antiseptics and antibiotics and help increase sharing of genetic material. they are key in infections and diseases
  • fimbriae and pili are appendags; pili is longer, sex pilus is used to transfer dna
    cell shapes: monomorphic or pleomorphic
  • mono is one shape: coccus, bacillus, vibrio, spirillum or spirochete (round, oblong, curved oblong, spiral)
  • pleo varies in shape and size, and numbers: diplo- or strepto (two or a chain)
  • coccus: tetrads, sarcinae, staphylo (sarc. eight cube, a bunch; also has diplo and strepto)
  • bacilli are v shaped or palisades; v shape or side by side wall
• cell envelope either gram positive or gram negative
  • thick cell wall made of peptidoglycan, cell membrane
  • negative: outer cell membrane, thin layer (cell wall), inner cell wall
  • animals do not have cell walls; bacteria and archaea cell walls diff
  • gram-positive walls: acid-fast bacteria chemicals, mycolic acid helps survive desiccation and staining, acid-fast stain
  • gram-negative walls have phospholipids, proteins, and lipopolysaccharide
    • lipid A can be toxic and impede disease treatment
• gram stain: a stain that distinguishes cell wall types
  • crystal violet dye
  • gram-positive keeps cv and is purple stain; negative loses and stains red
  • gram stain diagnoses and helps with treatment
• archaea
  • archaea: archaea domain; closer related to eukarya as they share ribosomal rna and similar synthesis / subunit structures; unique membrane lipids and cell walls (no peptidoglycan)
  • live in extreme habitats (extremophiles) adapted to the specific environment
  • includes: methanogens, hyperthermophiles, extreme halophiles, and sulfur reducers
• cyanobacteria
  • "bluegreen algae" causes harmful bloom
  • oxygenic phototrophic bacteria
    • gram negative cell wall, any shape, 1-100 micm, many fimbriae and trichomes with akinetes (intermediate cyst/spores)
  • bacteria domain and kingdom
  • genus: anabaena, oscillatoria (moving), nostoc, spirulina
• fungi
  • mycelia or single-celled yeast
  • saprophytes, decomposers, some can be parasitic
  • a/sexual reproduction: latter makes spores that can grow into either; pathogenetic fungi enter as spores and cause disease; can cause allergies
  • clinically important fungus: mycosis and disease caused by mycotoxins is mycotoxicosis ie coccidioides immits (valley fever)
  • three groups: molds, flesh, unicellular (mold, mushroom, yeast)
  • eukarya domain, fungi kingdom
  • examples: albugo bliti (white rust), rhizpopus stolonifer (bread mold), saccharomyces cerevisiae (brewer's yeast, benefits in alcohol and food), penicillium chrysogenum (antibiotic penicillum), aspergillus niger, claviceps purpurea
• protists
  • protista kingdom, eukarya domain
  • algae, protozoa
  • algae are photoautotrophic, unicellular, sometimes chemoheterotrophic; classified by differences in pigments, food preserve, structures and types
  • protozoa: animal like; single celled, always chemoheterotrophic (can be predatory, saphrophytic, or parasitic) mobile
  • plant-like protists can be fungus-like: caused potato famine (phytophthora infestans) cellulose cell walls, motile spores, plant parasites like downy mildews
  • protozoa are diverse, include amoebae, flagellates, ciliates, sporozoa
    • flagellates: mastigophora
      • entamoeba histolytica: amoebic dysentery
      • giardia intestinalis: causes diarrheal disease after drinking contaminated water
      • trypanosoma brucei: sleeping sickness
      • t. cruzi: chagas disease
    • ciliophora: ciliates
      • cilia projections spread around cell
      • balantidium coli: gastrointestinal infection, diarrhea or perforated colon
    • apicomplexa: sporozoa
      • obligate endoparasites without flagella or cilia; move by gliding on tissues
      • plasmodium falciparum: malaria
      • toxoplasma gondii: human brain infection; possible cause of schizophrenia
• algae protists
  • chlorophyta and bacillariophyta phylums: shellfish poisoning
  • amnestic
  • diarrheal
  • neurotoxic
  • paralytic
  • often neurological diseases
• multicellular parasites: helminths
  • sometimes macro, sometimes micro
  • chemoheterotrophs, adapted to life, poor digestive systems (absorb nutrition from host), poor muscular and nervous system (don't hunt; ring or worm structure, no skeleton) complex reproductive system, always need new hosts, many offsprings
    • trematoda-fluke: trematodes, flukes
    • schistosoma mansoni: snail fever
    • cestoda: tapeworm, including taenia solium (pork tapeworm, undercooked pork), planaria
• nematoda phylum: ascaris, pinworms, hookworms, heartworms
  • soil and water, microscopic stages ineffective, can be attached to host directly or transported by vectors
    • ascaris lumbricoides, dracunculus medinesis
    • enterobius vrmicularis (pinworm)
    • wuchereria bancrofti (elephantiasis or enterobius vermicularis)
• arthropoda phylum: small arthropods in fresh water
  • vector ectoparasites: transmission agents
  • sarcoptes scabiei, pediculus humanus capitus, dermacentor andersoni, iodex dammini
• virus
  • acellular, small, may be double or single stranded dna or rna; infects humans, animals, plants, bacteria; lacking enzymes, no metabolic pathway
  • cannot reproduce independently; control host cell material and synthesize/assemble new viruses
  • no cytoplasmic membrane, cytosol, organelles
  • Viral genome is either DNA or RNA but NEVER both
  • extracellular virion: capsid coat, nucleocapsid (acid and capsid), sometimes phospholipid envelope
  • intracellular: no capsid, virus is nucleic acid
    • viral capsid: on every virus; protein coat protects nucleic acid, uses capsomers (protein subunits); may be helical or icosahedral (helix or 3d with various number of capsomers) nucleic acid is at the center always
    • naked and enveloped virus: icosahedral viruses may be naked, ie rotavirus
      • capsid and envelope protect, bind to cell surface and penetrate into host cell
    • examples: poxvirus (smallpox) no capsid, covered by lipoproteins
    • enzymes for viral replication: polymerases, replicases, reverse transcriptase
    • viral structure is not resembling cell: no protein synthesis, only parts to invade and control host cell; divided into covering and central core
  • viral envelope: phospholipid bilayer and proteins made from cell membrane of host
    • types of protein structures: nucleocapsid, spike, envelope, membrane
  • viruses in cancer
    • viruses cause 20-25% of human cancers: burkitt's lymphona, hodgkin's disease, kaposi's sarcoma, cervical cancer
  • viroids
    • small, single strand rna (ssrna) infectious and pathogenic in plants; no capsid, rna viruses
    • no protein codes, adheres to plant rna, makes disease state of plant
  • prions
    • proteinaceous infectious agent; piece of protein
      • cellular prp: all mammals make it, alpha helices
      • prion prp: beta pleated sheets, prion prp causes cellular prp to refold into prion prp
    • prions cause transmissible spongiform encephalopathy (TSE) a brain disease; bovine spongiform encephalopathy (mad cow disease), creutzfeld-jakob disease, kuru, chronic wasting disease
      • no cure and minor treatment

chapter 3

• history of infectious disease
  • "food fight"; humans are fast food of pathogens
  • pathogens on top of food chain; predators
  • "ancient diseases" shared by close relatives, great apes
• hunter-gatherer lifestyles constantly moved, minimized transmission of pathogens; "sedentary" growth through agriculture led to livestock, leading to zoonoses → animal pathogens transferring to humans in close contact
• early cities: feces and fecal-oral transmission became problem, rodent vectors, close contact human transmission
• era of spectulation: unknown microbes, unknown epidemics, ie black death
  • believed to be miasma
  • microbial pathogens unseen
  • "wee animalcules": 1600s: anton van leeuwenhoek → bacteria and protozoa
  • 1700s: smallpox vaccine: edward jenner: triggered cross-reactive antibodies that helped boy survive smallpox → vaccinia virus, first disease successfully eradicatd
  • ignas semmelweiss: attempted handwashing to decrease spread of disease
    • nosocomial infection: infection acquired in healthcare
    • joseph lister: carbolic acid disinfectant/antiseptic, wash hands, patients dying from infections decreased
• pasteur and koch: golden age of microbiology
  • louis pasteur: proved microbes were everywhere, fermentation studies, foundation of germ theory of disease, rabies vaccine
  • robert koch: 4 steps to prove microbe caused disease: koch's postulates → proves germ theory of disease (specific microbe can invade another organism and cause a specific disease
    1. causative agent must be isolated and absent of healthy hosts
    2. microbe must be grown in pure culture
    3. if introduced into healthy host, the host must receive this disease
    4. the microbe must be reisolated from the host
• ehrlich, domagk, fleming: age of chemotherapy
  • 1940: dna genetic info; 1953: dna revealed
    • paul erhlich: selective toxicity
    • gerhard domagk: sulfa drugs as antibacterial chemotherapeutic agents
    • alexander fleming and howard florey: production and spread of penicillin as an antibiotic (fleming: lysozyme discovery)
  • issues
    • antibiotic resistance
    • population explosion
    • hunger
    • war
    • migration to megacities
    • multiple partner, anonymous sex
    • drug abuse
    • rapid transport
    • destruction of wildlife habitats
    • inadequate health care
    • climate changes
  • other epidemiologists
    • john snow: "father of epidemiology" → determined source of cholera epidemic, contained → epidemiological study, first public health response
      • common source spread illustration: csingle source
        • point source spread: short time period of operation (single food)
        • continuous ccs: lasts longer than incubation period (water)
        • intermittent css: periodic infection (well only contaminated in certain conditions)
      • propagated spread: direct or indirect person to person contact; no single source, always continuous unless stopped early
    • florence nightingale: recordkeeping and analysis

chapter 4

chapter 5

chapter 6

chapter 7

chapter 8