MIMG 100 NOTES

1/10 (Lecture 1: Brief History) Microbiology - the study of microbes Dominant & diverse life forms Dry biomass - sucking all of the water out of microbes/bacteria FUN FACT: prions do not have genetic material Prokaryotes NO nucleus & membrane organelles Archaea: live in extreme environments Bacteria: can cause disease but MOST are gooood Eukaryotes YES nucleus & membrane organelles WAYYYY larger than prokaryotes Fungi: decomposers Algae: photosynthetic Protozoan: Ameba: Tapeworm: These are the only ones that do endosymbiosis Viruses NO cells making it very simple NOT living Need to latch onto a host mechanism in order to replicate Similarities & differences in the 3 categories: All have genetic material All can cause diseases Viruses need hosts to replicate, other 2 can on their own Robert Hooke discovered that all living things are composed of cells Evidence against spontaneous generation? Meat in glass test Pasteur’s experiment Displayed that contamination comes from microbes in the air DISPROVING SPON. GEN. Discovered fermentation of alcohol Yeast converts sugar -> alcohol w/o air Discovered pasteurization Heating food then cooling it quickly to avoid spoiling FUN FACT: cyanobacteria were internalized (AKA endosymbiosis bc it means inner) 1/15 (Lecture 2: ) Germ theory of disease - specific microbes cause specific diseases Robert Koch demonstrated this direct link Koch’s Postulates 1. Has to be in abundance and absent from healthy specimen 2. Isolated & grown in pure culture; causative agent is not in healthy animal 3. Inject cultured agent in host & it causes disease 4. The newly diseased host’s microbe strain is extracted & has the same characteristics as the 1st Koch limitations Some microbes can’t be grown in a pure culture (b/c some need help from other microbes) Not all exposed organisms will get infected A host could be infected but the microbes are dormant so you wouldn’t be able to tell Some causal agents only work w/ specific hosts Pathogen - bacterial agent that caused both infection & disease in a human host Parasite vs pathogen Parasite is a pathogen that is not a bacteria, virus, or fungi Virulence - severity of a disease Virulence factors (REMEMBER FOR CASE STUDY) Ivasion Invasiveness Primary pathogens - MORE likely to cause disease in healthy host b/c of high virulence & rapid reproduction Opportunistic pathogens - LESS likely to cause disease in healthy hosy b/c of low virulence Nonsocomial infections - infection contracted by receiving treatment in a facility EX: C-diff Common in healthcare settings b/c of… the high volume of antibiotics staff may not wash hands properly lots of bacteria in setting bad immune systems due to already diseased hosts combines with the antibiotics makes one very susceptible What do pathogens need in order to be successful? Space, nutrients & other resources If antibiotics caused a problem, how can we treat somebody w/o giving them more? Fecal transplant - taking health microbiota & putting it into the infected host so the healthy microbiomes take over and overpower the unhealthy ones Commensalism - type of symbiosis when 1 organism benefits but the other isn’t affected Lecture 3: 1/17 Endosymbiotic origin of eukaryotes Had own genetic material, but once were absorber, they not can’t live outside the cell because they have evolved to stay true to its inner form https://www.bing.com/videos/search?q=endosymbiotic+origin+of+eukaryotic+cells&&view=detail&mid=B657E5D5C0D83B6EB6C0B657E5D5C0D83B6EB6C0&&FORM=VRDGAR Symbiosis 1 org. lives in or on another Prokaryotes from SYMBIOTIC relationships w/ eukaryotes Classified based on how the other species it links to reacts Mutualism Commensalism Parasitism Pathogenesis Communicable pathogens are passed to others Non-communicable pathogens stay w/ host (very rare; can’t cause disease) NEEDS 1. Enter host 2. Stick to tissues Adhesin on pathogen binds w/ receptor on host tissue that matches 3. Overcome host defense [[[COMMENT BY Keiarah Mitchell (2019-01-17T21:29:00Z)]]] Green: signs & symptoms occur here [[[---]]] Attacking host Disguising itself Hiding 4. Damage host tissue Cellular lysis = cell broken down by pathogen reproduction Enzymes and/or toxins can be released by pathogen itself (EX: CDiff) 5. Exit host *do it all over again* What’s needed for infection?? Agent Reservoir Host portal of exit Microbial reservoir Habitat where host lives until transferred Humans Animals Environment Reservoir vs vector Reservoir has to be living but vectors can be nonliving Transmission types Contact - pathogen has direct contact w/ person (EX: STI) Vector-borne - vector introduces pathogen to tissue (EX: insect -> human) Vehicle - vehicle that carries pathogen to host (EX: food, air, water, blood) Can lead to rapid spread Vertical - mother to child Congenital infection - affects unborn fetus Perinatal infection - infection from 22 weeks in belly -> 7 days out of belly Horizontal - host to another human using contact, vehicle or vector types Immunopathology - disease symptoms from immune system that happen while responding to pathogens Lecture 4: 1/22 Direct vs indirect modes of transmission & contact EX: inhaling droplets from a sneeze would be direct transmission through indirect contact Factors influencing disease outcome # of microbes needed to cause disease, immune system, nutrition, exercise, age, environment, severity of agent (virulence), ability of microbe to cause disease (pathogenicity) Microbial factors Entry at appropriate site Microbial genetic factors Fewer microbes to cause disease = MORE lethal ID vs. LD The smaller the infectious dose/lethal dose, the more virulent it is How to determine which microbes cause disease? Morphology (what they look like) Koch’s postulate Gram staining Bacteria characteristics Size from 1.2-2.0 Cell wall determines shape Shapes Coccus/cocci (round) Bacillus/bacilli (rod) Spiral *varying* Arrangements Pairs (diplo-) Chains (strepto-) Clusters (staphylo-) tetrads/sarcinae (3D type) Can be species specific Gram staining procedure 1. Put fresh, new, actively growing liquid culture on slide in thin layer & let dry 2. Fix cells to slide using heat/chemicals 3. Add crystal violet dye (positive), let sit for a min. then rinse Cells w/ peptidoglycan will turn purple Soluble so can get into cells freely 4. Add gram iodine Forms complex so the crystal violet is sealed (gets insoluble) in & can’t get out 5. Add ethanol to strip outer layer of cells Thick peptidoglycan layers retain the trapped dyes w/o ethanol, they’d all stay purple 6. Safranin colors DNA in cells that have lost purple dye GOAL??? Bacteria cell wall Cell lysis is when cell BURSTS Cells begin as isotonic, then go into hypotonic/hypertonic environment, & w/o a wall it bursts Atypical walls Acid-fast bacteria - peptidoglycan too thick for chemicals to pass thru Wall-less bacteria - no cell wall so need to ALWAYS be in isotonic solution (or lysis happens) 1/24 Gram positive The peptidoglycan has 6-12 glycan sheets w/ teichoic acid (lil sticks) that regulate ion flow, attachment & growth Why are these easier to kill? b/c they don’t have a membrane around it, so its exposed! b/c there’s more peptidoglycan to attack! Gram negative 3 glycan layers & membranes on both sides Less layers = why the purple dye done get stuck well Outer membrane plays a role in pathogenicity Glycocalyx - simple polysaccharide chains layered outside cell wall Capsule = gel like & firmly attached Slime layer = fluid & loosely attached Biofilm = group of microbes attached to surface *GOAL* protect from drying out & phagocytosis Fimbria - straight, stiff, short Pilia - short, for adhering to stuff Flagella - stiff, helical protein filament for mvmt. = ^ virulence Counterclockwise mvmt. can form propeller Clockwise mvmt. moves however Flagella stain - thickens structures Animal vs plant cells Plant cell have cell wall Prokaryotes AND eukaryotes have ribosomes Endomembrane system - direct proteins to their right location Golgi apparatus, nucleus & smooth/rough ER WHO MAKE ENERGY Chloroplasts: make atp from water, CO2 & light energy Mitochondria: make atp from glucose breakdown 1/31 Culturing samples on various solid media determines what growth factors/requirements a sample has Medium types Agar plates w/ RBC’s Medium w/ heated RBC’s (aka chocolate media bc when heated it turned brown) If we want to attack gram-negative bacteria, DO NOT use substance that attacks cell walls b/c they don’t have any (no peptidoglycan) FUN FACT: Only 1% of microbes can be grown in a lab Culture - cultivating microbes in an artificial medium w/ nutrients How to get a pure culture Isolate from other microbes Make a colony Colony forming units can signify one bacteria or a chain of bacterias Colonies - millions of cells that can be seen by eye =pure cultures bc they are derived from a single cell Streak plate method Bacteria cells make colonies on solid media w/ agar added to make firm surface You use streaking to obtain ONE CELL from all the bacteria & replicate that one cell to then make a colony Bacteria needs to grow synthesize/get all components of the new cell GROW MOST pathogen are organotrophs All biological mols. have C Growth media Broth media - water based w/ nutrients In tubes or flasks Semisolid media - broth w/ solidifying agent added Agar is most common solidifying agent Solid media - use agar & nutrients Goes into a petri dish Use differential & selective medias to isolate pathogens from a flora Differential - makes it possible to distinguish b/w 2 bacteria types Selective - inhibits growth of unwanted orgs. in a mixed culture Enhancing microbial growth Fastidious microbes - need growth factors not usually found in media Enrichment media - has nutrients to enhance growth of ONE microbe can’t distinguish b/w this & Binary fission Asexual process 1. Replication of chromosome 2. Parting chromosome into daughter cells 3. …… Direct cell count methods Petroff-Hauser counting chamber Put bacteria in chamber Cover with lens Look at thru microscope Fluorescence staining Some dye can only link w/ alive cells & some only for dead cells Indirect cell count method Fluorescence activated cell sorter Optical density/turbidity measurements Spectrophotometry Optical density (turbidity) measurement at certain wavelength Viable count dilution Dilute OG sample them pour into plate or spread layer onto plate Both ways the bacteria will show 2/5 Tardigrades can survive in extreme conditions How to quantify bacterial growth Microscopic counting chamber Requires direct counting so it’s very time consuming Spectrophotometry turbidity/optical density Quick & easy Don’t know if alive or dead Can’t get EXACT #’s Fluorescence dye Dilution plating for viable counts Count colonies not exact bacterias Phases of growth (only good for liquid/broth culture in lab) Lag Cells alter metabolism to adapt to new envir. Exponential growth/log Growth rate reaches a max. value It grows quickly b/c they continuously replicate until all the nutrients are used up ANTIBIOTICS MOST EFFECTIVE HERE b/c this is where peptidoglycan is being made & antibiotics has to target this Stationary Pop. consumes nutrients & excretes waste Growth machinery shuts down Stress response occurs!! When cell replication rate = death rate START SYNTHESIZING ANTIBIOTICS Bacteria that makes antibiotics are not harmed by the antibiotics they make Death Cells go thru morph changes or lysis Can be exponential (sharp) too Physical requirements for growth (4) Temp Have a certain temp. they need to survive Minimum Optimum (best) Maximum Microorganisms are divided by temp (C* in order from least to most hot) Psychrophiles Grow in cold temps & spoil food in fridge Mesophiles Most pathogens are this Thermophiles Hyperthermophiles pH Most orgs. Live in 6.5-7.5 pH Higher or lower stops growth Pumps, proteins & enzymes are all helpers when pH changes Osmolarity Most orgs. Prefer isotonic Halophiles (salt lovers) prefer hypertonic Cell wall protects against hypotonic envir. Oxygen Some need oxygen, some get killed by it Obligate aerophile - need high O Microaerophile - needs O but not as much as the air supplies Only small amounts! Facultative anaerobe - don’t need oxygen but is good w/ it Aerotolerant - doesn’t use O, but doesn’t hurt it either Obligate anaerobe - NO OXYGEN Strict anaerobes vs strict aerobes FUN FACT: In electron transport chain, O is the acceptor Endospore formers Endospores - dormant cells resistant to harsh environments Their resistance makes it difficult to remove or be treated w/ antibiotics Gram POSITIVE bacteria only! Bacillus Clostridium Endospore Formation Steps??????? How is C. difficile spread? Opportunistically thru endospore formation in a hospital setting How to prevent disease transmission Washing hands