-alive & teeming w/ organisms

-affected by pH, moisture, weather, climate, nutrient input, & physical disturbance

-imp. for C & N cycling

-diversity of microbes greatest near soil's surface

-microbial activity affects soil characteristics such as porosity, aggregation

-no till increases microbial activity & decreases nutrient run-off

wetlands: high productivity, low rate of mineralization in anoxic environment

drained wetlands: low productivity, high rate of mineralization in oxic environment

biodiversity analysis of microbial community (steps)

1) extract DNA from community

2) amplify by PCR 16S rRNA genes using general or specific PCR primers

3) analyze diversity

4) sequence determined for unique genes

5) phylogenetic relationship determined & sequence placed in tree

6) FISH

phyllosphere: above-soil part of plant

rhizosphere: zone around roots below soil

rhizoplane: surface of root

epiphytes: microbes inhabiting plant are colonizing plant surface

endophytes: microbes inhabiting plants are colonizing inside plant

-legumes associate w/ rhizobia bacteria to fix nitrogen & add it to soil

-nodule: specialized structures of plant roots that contain nitrogen-fixing rhizobia

development of rhizobia-legume mutualism

1) plant roots secrete flavanoid compounds

2) rhizobia sense flavonoid signal

3) rhizobia make & secrete nodulation factor in response to flavonoid sensing

4) plants respond to nod factor by curling root hair time & begin nodule formation

-prevalence: essentially every organism is symbiotic

-function: symbiotic bacteria provide imp. novel functions to host

-new frontier: much remains to be learned about symbiosis

-ourselves & plants & animals we consume are symbiotic

-15% of insects contain endosymbionts, often multiple types

-vertically transmitted (mother to offspring; transovarian) & often can be strictly coevolved w/ hosts

-can have severely reduced genomes w/ high GC%

-primary endosymbionts have essential function for host; secondary symbionts have benefits that are facultative

-symbiosis results in bioluminescence --> obvious phenotype easy to detect in luminometer or modified scintillation counter

-monoxenic --> squid light organ colonized by only V. fischeri

-adult squids are collected & mated to yield symbiont-free (aposymbiotic) offspring

mucous secretion --> peptidoglycan

reactive oxygen species --> catalase, luciferase

cell swelling --> luciferase

hemocyte trafficing/apoptosis --> LPS/TCT

capsule, LPS --> initiation of symbiosis

1) opportunistic: infection immunocompromised host

2) accidental: accidental infection of host

3) obligate: can't exist outside of host organism

4) facultative: exists outside of host

1) exposure

2) adherence

3) invasion

4) colonization & growth

5) toxicity & invasiveness

6) tissue damage & disease

-often mediated by adhesins, which are proteins that recognize receptors on host cells, often glycoproteins or glycolipids & may be attached to fimbriae

-capsule slime layers can allow attachment by binding to host cell lectins, which are sugar binding proteins

-flagella & lipotechoic acids can also mediate attachment for some bacteria

toxic proteins (usually) released from pathogen cells

3 types:

1) cytolytic: lyse host cells

2) AB exotoxins--2 subunits: 1 binds, 1 is toxic

3) superantigens: hyperstimulate immune cells leading to inflammation & tissue damage

1) B subunit binds to host receptor

2) A subunit cleaved & inserted into host cell

3) A subunit inactivates elongation factor 2 (EF-2) by attaching ADP-ribose to it

4) EF-2 no longer aids entry of charged tRNA in ribosome stopping translation

Clostridia botulinum & tetani are strict anaerobes, spore forming inhabitants of soil, but not invasive to humans

-pathogenicity due to toxicemia, toxin production

-death due to flaccid muscle paralysis & respiratory failure

-tetanus toxin acts by blocking glycine release by inhibitory interneurons

-this causes continuous release of acetylcholine & muscle constriction also referred to as 'lockjaw'

toxins whose activity affects small intestine cholera toxin, results in massive water loss from intestinal lumen, resulting in severe diarrhea

-ion replacement & rehydration are effective cholera treatments

LPS produced by many Gram neg bacteria

-can contaminate food in absence of viable bacteria

-toxicity due to its effectiveness for stimulation of innate immune system, including inflammation

endemic: 'normal' or background incidence of disease in population

epidemic: high incidence of disease in population

pandemic: widespread, often worldwide, epidemic

1) infection--initial exposure & entry

2) incubation--period where agent multiplies before disease shows itself

3) acute--disease symptoms are evident

4) decline--survival or host & often acquired resistance to infectious agents

-reservoir control: monitor disease prevalence in animals, immunize uninfected animals, & euthanize infected animals

-transmission control: eliminate or modify insect vectors, improve water quality

-immunizations: successful in elimination of small pox, diptheria, etc.

-quarantine: restricted movements of infected individuals, required for small pox, cholera, etc.

-surveillance: monitor disease spread

-tracking infectious diseases: involves required reporting of certain infectious diseases

-ecological/environmental changes

-human demographics--pop growth, drug use, etc.

-international travel

-microbial adaptation

-poor public health

-easily transmitted/person-to-person transmission

-high mortality rate & potential for major health impact

-might cause panic or social disruption

-require special attention for public prepardness

-microbes cannot grow in air, so microbes in air are results of environment: soil, water, plants, animals, humans

-indoor air has diff. microbes than outdoor air

-air is dry & inhospitable to infectious disease agents: moisture droplets quickly evaporate, enveloped viruses & Gram neg bacteria easily dry out, Gram positives w/ thick cell walls are more resistant, spores are resistant, but few diseases are transmitted by spores

-Streptococcalpharyngitis (Strep throat)

-Scarlet fever: red rash

-delayed sequelae: reoccurrance of Scarlet fever

-Rheumatic fever: streptococcal surface antigen resembling human antigen & body attacks itself

-necrotizing fascititis: flesh-eating bacteria that cause rapid damage to skin, muscle, caused by superantigens

caused by negative sense single-stranded orthomyxovirus

antigenic drift: minor antigenic changes due to point mutations in coding sequences that alter 1+ proteins

antigenic shift: reassortment of 2 diff virus types (this is how new pandemic strains evolve)

measles, mumps, & rubella

measles: causes cough, fever, & eventual skin rash

mumps: inflammation of salivary glands

rubella: disease less severe than measles, infection of fetus can damage heart, brain, & eyes

-caused by varicella-zoster virus, highly contagious & infects respiratory tract

-characteristics: lesions on skin that fill w/ pus, rupture, & scab

-latent virus in nuclei of sensory neurons, can be activated later in life to cause shingles

hepatitis A: person to person, or by digesting fecally-contained food or water; usually mild

hepatitis B: causes acute & often severe disease, chronic infections lead to cirrhosis & liver cancer; transmitted genetically or by exchange of fluids

hepatitis C: initially mild, but can develop chronic infections & lead to liver cancer & cirrhosis

hepatitis D: defective, lacks coat proteins, transmitted only w/ HBV

hepatitis E: fecal contaminating water

characteristics of gonorrhea

-STD caused by Neisseria gonorrhoeae

-Gram neg, non-motile aerobic diplococci

-males: painful infection of urinary tract

-females: weak or symptomatic vaginitis can lead to pelvis inflammatory disease, which can lead to sterility

-can cause eye infections in newborns, washing newborns w/ ointment is mandatory

-penicillin is NO LONGER effective due to widespread resistance

-STD caused by Trepanema pallidum

-cogenital syphilis --> transmitted from mother to infant

-requires skin breaks to infect

-localized infection called primary syphilis

-hypersensitivity to treponemes, resulting in skin rash is secondary syphilis

-tertiary syphilis is widespread infection that ranges from mild to lethal

penicillin is effective treatment!

-STD caused by Chlamydia trachomatis

-obligate intracellular bacterium

-most prevalent STD in U.S.

treatment of AIDS

chemotherapeutic drugs

1) AZT--base analog w/ -OH, prevents polymerization of DNA by reverse transcriptase when incorporated

2) nevirapine--binds to reverse transcriptase catalytic site & prevents DNA polymerization, although NOT base analog

3) sequinavier--peptide analog that blocks HIV protease & prevents processes of HIV polyproteins

4) evfuvirtide--36 amino acid synthetic peptide fusion inhibitor

5) integrase inhibitors--experimental drugs to inhibit integration of HIV DNA into host genome

zoonosis: animal disease that's transmissable to humans

enzootic: zoonosis that's present endemically in population

epizootic: zoonosis that has reached epidemic proportion

rabies

-agent: rhabdovirus

-transmission: bites from infected animals, but respiratory transmission also survival

-infects: CNS

-incubation period: 1-2 weeks in animals; up to 9 months in humans

-fatality rate: nearly 100% fatal if not treated

-symptoms: fever, excitation, dilation of pupils, excessive salivation, uncontrollable spasms, death from respiratory paralysis

-treatment: post-exposure vaccines + anti-rabies immunoglobulin

-prevention: vaccination of domestic animals & control of disease in wild animals

hantaviruses

-agent: enveloped, segmented, negative strand RNA virus; related to hemorrhagic fever viruses such as Ebola & Lassa fever viruses

-diseases: hantavirus pulmonary syndrome (fever, muscle pain, decreased blood platelets, lungs fill w/ fluid) & hemorrhagic fever w/ renal syndrome (acute kidney failure)

-transmission: inhalation of dried, airborne fecal material from infected animals

-carriers: rodents, humans

-incubation: possibly 1-5 weeks, once symptoms appear, more severe complications arise in 2-3 days

-fatality rate: 36% in U.S.

-treatment: no vaccines available!

-prevention: avoid contact w/ rodents

-Rickettsias: small bacteria that are obligate intracellular parasites, mainly infecting mammals

-hosts: animals, humans

-transmission: bite from blood-sucking insects

-treatment: antibiotics

Lyme disease (most prevalent tick-borne disease in U.S.)

-infectious agent: bacterium, Borrelia burgdorferi

-transmission: bites from infected deer ticks, rodents

-stages: 1) first 3-30 days--expanding circular rash around bite lesions 2) dissemination of symptoms--several weeks to months of neurological problems, heart inflammation, arthritis 3) years later--demyelination of neurons with symptoms resembling MS & Alzheimer's

-treatment: antibiotics AFTER infection

1) sporozites released into blood by infected mosquito

2) sporozites removed in liver & form schizont (enlarged cell)

3) schizonts segment into merozoites

4) merozoites infect red blood cells

5) 48 hours of blood cell lysis manifest in clinical symptoms (chills then fever)

6) gametocytes also made that infect mosquitoes

7) zygote formed in intestine, migrates to salivary gland where sporozoites are again generated

-infectious agent: flavivirus, positive-strand RNA virus

-transmission: mosquitoes

-reservoirs: birds are major reservoirs

-origin: Uganda

-symptoms: flu-like symptoms plus swelling of lymph nodes & nausea

-treatment: no drugs known

-mortality rates: 4% in humans, most infections are asymptomatic

-prevention: protection again mosquito bites

-agent: Gram neg, facultative aerobic bacterium Yersinia pestis

-transmission: flea bites

-reservoir: natural disease of rodents (rats)

-spreading: when disease spreads & rat mortality becomes too great, fleas seek new hosts, including humans

-mortality rate: 14% in U.S.

pneumonic: bacterium grows in lungs, almost no symptoms till patient coughs up large amounts of bloody septum, highly contagious

septicemic: bacterium spreads throughout bloodstream w/o forming buboes; usually death occurs before diagnosis can be made

-soilborne pathogens are accidental agents of infection

-soil is unlimited source of pathogens, so soilborne pathogens can't be eliminated

causes diseases through 3 mechanisms:

1) some fungal antigens trigger immune responses that result in allergic reactions

2) some fungi produce toxins called myxotoxins

3) fungal infections = mycoses

-infectious agent: Clostridium tetani

-transmission: deep wounds contaminated by soil

-disease mechanism: non-invasive, caused by potent toxisn (tetanus toxin), incubation period of 4 days to several weeks, death is by respiratory failure

-prevention: tetanus vaccine

infections in animals or humans that are caused by multiple bacteria, viruses, fungi, or parasitic organisms, or combinations of these

-can be induced or enhanced by:

weaked or immuno-compromised host, initial infection that creates new pathways for secondary pathogens, pathogens sharing properties that, when they work together, favour infections more readily than each does separately

1) perishable: meats, fish, poultry, eggs, milk, produce

2) semiperishable: potatoes, apples, nuts

3) nonperishable: sugar, flour, rice, dry beans

food preservation methods

1) refrigeration: inhibits growth of most microbes due to lower temps

2) acidity: acidic pHs (below 5) inhibits growth of most pathogens

3) drying: reducing water content inhibits growth

4) chemical preservatives: sodium benzoate, sodium nitrate, sorbic acid, sodium propionate act as growth inhibitors & are GRAS (generally recognized as safe) by FDA

5) radiation: ionizing radiation kills microbes

6) heat: pasteurization (short-term heating to reduce # of microbes in food w/o significant reduction in food quality) & canning (heating in sealed container, often complete sterility isn't achieved

-yeast bread: yeast ferments sugars in flour & produces carbon dioxide, which raises dough & makes holes in finished product

-dairy products: developed to preserve milk; lactose is hydrolyzed into glucose plus galactose, which are fermented by lactic acid bacteria into lactic acid

-meat: most dry & semi-dry sausages; meat is fermented using lactic acid bacteria to pH below 5

-vegetables: often fermented in salt brine to enhance preservation & flavour & prevent contamination by unwanted microbes (cabbage & cucumbers // sauerkraut & pickles)

-transmission: undercooked foods containing fecal contamination

-disease: colonizing of small & large intestines, causes headaches, chills, vomiting, diarrhea, followed by fever

foodborne pathogens: E. coli

-transmission: undercooked foods

-disease: grows in small intestine & produces verotoxin which causes bloody diarrhea & kidney failure

-transmission: found in cooling towers & condensers of air conditioning units; spread by inhalation of contaminated water droplets

-disease: parasite invades macrophages in lungs; most cases are mild

anitbodies (characteristics & types)

-epitope: specific part of antigen recognized by antibodies

-antigens: often proteins

-cross reactivity: when antibody binds to similar epitope of another protein

-antibodies can be very selective in recognizing antigen & useful for diagnosing infectious diseases

-antibodies can be directly or indirectly labeled w/ enzymes, fluorescent dyes, & radioactivity to facilitate their detection

polyclonal antibodies

monoclonal antibodies

-neutralization: antibodies against toxin inhibits toxic activity

-precipitation: caused by networks of antibody-antigen binding

-agglutination: use of antibodies to bind to antigens on large particles

-fluorescently-labeled: antibodies w/ fluorescent molecules attached, usually made by chemical modification of purified antibodies

-indirect ELISA: uses enzyme-linked secondary antibodies to detect primary antibodies, which are bound to antigen on surface of plate

-radioimmune assays: antibodies/antigens labeled w/ radioactive isotope

-western blots: proteins can be separated by size by gel electrophoresis, then transferred (blotted) onto membrane where they stick; antibodies then bind to antigen present in protein band

2 types of fluorescently-labeled antibodies

1) direct labeling: where antibody to antigen is labeled

2) indirect labeling: where secondary antibody is labeled that recognizes antibody to antigen