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Taxonomy

The classification of living organisms

Nomenclature

The kingdom system was orig set up (from most diverse to most specific)

Bergey's manual of Determinative Bacteriology

Classifies bacteria by


gMorphology, stanining, metabolism, oxygen requirements, nutrition, motility

Criteria for Identification

Morphology features, biochemical tests, serology, phage typing, base composition, nucleic acid hybridization, amino acid sequence



Class Epsilonproteobacteria

Have flagella for motility

Class Gammaproteobacteria

Pseudomonas


Adaptive and resistant to antibodies


can grow on a sterile enviornment

Class Alphaproteobacteria

Brucella


non motile


coccobacillus


causes undulant fever



Order Enterobacteriales

Enteric


Lives in intestinal tract


litmus milk test





Order Vibrionales

Vibrio


Motile with polar flagella


Causes cholera



Order Aeromonas

Aeromonas


Causes intesinal disorders, wound infection



Order Pasteruellaceae

Haemophilus


Arch formation


V, X factors diagnostic


causes meningitis



Gram neg Anaerobic bacteria


q

Bacteriodes


Causes peritonitits



Gram + cocci

Staphylococcus


Catalase positive (diagnostic)


causes skin infections, pneumonia, meningitis



S. epidermis

flora on our skin

S. aureus

deadly, causes wound and gut infection

Mycology

the study of fungi



Heterotrophic

Cant make its own food must eat by absorbtion

Eukaryotic

has a nucleus

hyphae

branching network, body

Coenocytic hyphae

not sep by inside crosswalls



Septated hyphae

sep by cross walls


Mycelium
A mass of intertwined and elongated hyphae.

VegetativeMycelium- growsbelow surface and functions like a plant root absorbing organicnutrients. Aerialmycelium- reproductive myceliumthat grows above the surface and usually holds reproductive spores Ex. Penicillin

Yeasts

Unicellular

Reproduceby budding (up to 24 daughter cells)Pseudohyphae: buds fail to detachthemselves, form short chain of cells (similar to Siamesetwins)


A few typeswill grow by fission.


Will re-formwith or without oxygen.

Dimorphism
Same species, two forms of growth. Fungal spores are reproductive structures. Fungalspore reproduction is dikaryotic (two nuclei)


Arthrospore
isformed by the fragmentation of septate hyphae into single slightly thick cells.

Ex. Coccidioides immitiscauses pneumonia

Chlamydospore
isa thick walled spore formed by segmentation within a hyphae.

Ex. Candidaalbicans causes yeast infections.

Sporangiospore

1. is a spore formed in a sac (sporangium-stalk) at the end of an aerial hyphae.



Ex.


Rhizopus produces such spores.
Conidiospore
1. is a multicellular or unicellular spore that is not enclosed in asac. They are produced in a chain at theend of a conidiophore.


Ex.



Peniciliumproduces such spores.


Blastospore
1. is a bud spore that comes from the parent cell, it can be found in someyeasts.

Sexual Spores

occur less frequently, the organism must be stressed toproduce them.


Zygospore

1. is a large spore enclosed in a thickwall.



The phylum Zygomycota produces suchspores



Ex.



Rhizopus


Ascospore

1. is produced as 2-8 ascospores in aascus (sac).



The Phylum Ascomycotaproduces such spores.



Ex.


Penicilium
Basidiospore

1. is a spore is formed externally on abase pedestal (basidium).



Only the PhylumBasidiomycota produces such spores.



Ex.


Basidiomycota-mushrooms
1. Zygomycota

Have coenocytic hyphae





Ex.



Rhizopus nigricans causespneumonia


1. Ascomycota

Have septated hyphae.



Have arrangements of conidiosporesin Penicilium.


1. Basidiomycota


Have septated hyphae.



Ex.



puffballsmushrooms, jelly fungus, shell fungus.




1. Deuteromycota


Division of molds not yet placed in a category, a.k.a. “imperfectfungi”. These are fungi that have notyet been found to produce sexual spores.



Have septated hyphae.



Reclassification of pathogenic fungiis fairly common today.



Ex.



Pneumocystis pneumoniahas been reclassified to Pneumocystis carinii. It causes the pneumoniathat kill AIDS patients.


1. Systemicmycoses-


Fungal infections deep within the body, spreads systematically.



Are not contagious from animal tohuman or from human to human.



Ex.



Histoplasmosis-lung infection



Coccidioidomycosis-encountered in areas with lots of wind, forms as a spore.


1. Subcutaneous mycoses-


Fungal infections beneath the skin that enterthrough a puncture wound in the skin
Cutaneous mycoses

Are called dermatophytes. They are fungi that infects onlythe epidermis, hair, and nails. The infection is called dermatomycosis orcutaneous mycosis. Keratinase is an enzyme secreted bydermatophytes which degrades the skin and destroys keratin (a protein found inhair, skin and nails). Infection istransmitted from humanto human or from animal to human by direct contact or by contact with infectedhairs and epidermal cells.



Ex.



Microsporum



Trichophyton



Epidermophytoncauses tinea (ring worm, athlete’s foot)


1. Superficialmycoses-


Are localized along hair shafts and in superficial epidermalcells. These infections are prevalent in thetropics.



Ex.



Tricosporium



Cladosporium


Viruses-

Are obligatory intracellular parasites- they must live withinliving cells



Contain asingle type of either RNA or DNA (ss = single strand, ds = double stranded).



Has aprotein coat and sometimes an envelope of lipids, proteins, and carbohydrates.



Multiplyinside living cells using the machinery of the host cell.



Causesynthesis of an element that can transfer viral nucleic acids to other cells.




Virion-
a “baby” virus. It is a completelyassembled and infective virus particle
Virus host range

Viruses, as a whole, have a wide variety of hosts they caninfect, but most individual viruses can infect only specificcells of a specific species.


Thereare certain factors required for multiplication and penetration of the hostcell
Viral size
Smallerthan bacteria, less than .2 micrometers.
Viral structure

Nucleic acids ofviruses are encapsulated by a capsid. A capsid is an envelope made of protein partscalled capsomeres. The number ofcapsomeres varies from 12 to 252 and can be used to classify viruses. Somecapsids are covered by envelopes made of lipids, proteins, and carbohydrates.



Nucleocapsid- is a viral head + DNA (nucleic acids +capsid)


Viroid- (NOT tobe confused with a virion)


Is naked virus RNA a virus withouta capsid. So far onlyidentified in plant diseases.


Helical capsid symmetry

Virus shapes-


TMV (tobacco mosaic virus), infects tobacco plants



Appearsas a long, slender rod.





Icosohedral capsid symmetry

Has twenty sides (looks like a space ship), spherical shape.



Ex.polio


Complex or Combined shape

ex. poxvirus



T-evenphage (bacteriophage) includes a head, collar, sheath, base plate andfibers. It attaches,the sheath contracts and sends the RNAor DNA into host cell.


Bacteriophage

1. is called the plaque method. It is a monolayer formation which causesplaque or “clearing of the lawn”because of destruction of bacteria. Clearing of the lawn is visible when bacteria is heavily grown on a plate. Then a virus is introduced to it, it is incubatedfor 24 hours. If the virus destroyed the bacteria there will be ringsaround the prong marks where you introducedthe virus.




Lytic cycle

Adsorption to death



Sequenceof events in viral multiplication



Previouslydescribed as the death of a cell


Lysogeny
In the lysogenic phase viral DNA is incorporatedinto the hosts DNA and is dormant until the optimum time to reproduce. Cell lysis is not immediate. The prophage (provirus) remains latent untilit exits the host DNA and cell lysis takes place.
Provirus

Viral DNA that is integrated onto the host cell’s DNA.


Latent Viral Infection-
- The virus remains in the host cell for a longperiod of time before producing disease.Ex. herpes simplex
Slow Viral Infection

There is a long timeperiod before symptoms appear. Bursttime is not long by implicationand the cause may be a viroid.


Inclusion Bodies
- are used for diagnosis. One type of CPE (cytopathogenic effect) mayresult from accumulation of assembled orunassembled viruses in a host cell, might also be in earlier viralsynthesis sites in the host cells. Canbe found in diseases such as rabies, smallpox, measles, and herpes.

Polykaryocyte-

Is anothertype of CPE. There is fusing of manyadjacent infected cells to form a giant cell.




Interferon
Is produced by infected cells to protectneighboring cells that are still uninfected. These areantiviral proteins and are host specific not virus specific.
Viruses and Cancer
A tumor is a group of cells multiplying without control (uncontrolledmitosis). Thosethat are cancerous are called malignant.
Metastasis

the spreading of cancer tovarious parts of the body.


Oncogenic virus

Any virus capable of producingtumors



Viralnucleic acids are incorporated in the DNA.



Somechemical and physical agents can also cause cancer.



Tumorcells contain antigens (virus specific) called tumor specific transplantationantigen (TSTA)on a cell surface or t-antigen in nucleus.


Chromosomalabnormalities:


Oncogenic virus could be DNA orRNA virus. Oncogenic viruses (retroviruses-operate using reversetranscriptase, are found in both groups.



DNA oncogenic viruses



Adenovirus



Herpes



Poxvirus



RNA oncogenic virus-



Retroviridae Aids is a retrovirus


Non specific defenses
skin , hair, mucous , pH Inflammatory response , interferon
Immune System-

- Is a specific defense. A resistance to disease by productionof specific antibodies and otherspecific defenses against microbial infections. The immune system has two major parts:


Various types of immunity

1. Natural-you are directly exposed to the pathogen.



2. Artificial- you are exposed artificially, as in avaccination.



3. Active-antibodies you make



4. Passive- you are exposed by antibodies already present(such as gamma globulin shots).


Types of immunity

1. Native-you areborn with immunity, present at birth.



Speciesand individual immunity. Canine distemper



2. Acquired- obtainedafter birth. Involves both immunesystems (humoral and cell mediated), could be acquired actively or passively, couldbe natural or artificial.



3. Naturallyacquired active immunity- This is individual, it is your antibodyresponse to antigens. Provides lifelongimmunity for diseases such as measles, yellow fever, and chicken pox. Works against bacteria, viruses, fungi.



4. Naturallyacquired passive immunity- Involves transfer of humoral antibodies froma donor to a successful recipient, such as from a mother to her fetus throughplacenta or through nursing.



5. Artificiallyacquired active immunity- Exposes an artificial immune response due tovaccination.



6. Artificiallyacquired passive immunity- the transfer of antibody from person to a susceptible person byinjection of antibody containing the serum. It is useful against venom, botulism, tetanus, rabies, toxins.


Antigens

does not imply disease- includes blood type, Rh type) Arechemical substances that cause production of specific antibodies(immunogenicity).





Reactivity:those antibodies will specifically react with the antigen.



Antigens couldbe protein produced, nucleoprotein, lipoprotein, glycoprotein, or polysaccharides. Ex. a bacteria could also have severalantigens (whole, proteins, or toxins)




Hapten-
is an incomplete or partial antigen that could be madecomplete by combining with a carrier. Hasreactivity (can react with antibody) but not immunogenicity-less than 10,000 daltonsso no production ofantibodies. Allergies

Antibodies-


Do not ingest, they neutralize.



Workin blood stream – plasma



Cannotgo inside the cell



Couldbe a protein produced by the body in response to an antigen.



Capableof combining with antigens that induce its production.



Mostantibodies are bivalent (two places for attachment) at a minimum.



Immunoglobulinor gamma globulin.


Mostconsist of 4 polypeptide chains, two heavy chains and two light chains joinedby disulfide bonds. They make two identical halves with specific variable portions of H & L whereantigen attaches. The constantportion shows what type it is (IgG, IgM, IgA, IgD, and IgE). The variable portionmust fit the determining site
IgG

80-85% of the antibodies, most abundantin the body.



Thesmallest in molecular weight.



Capableof passing through placenta, provides for protection of newborns.



Havea long half-life.



Capableof complement fixation.



Complement-chemical substance used to coat antigen (opsonization) makes it easilydestroyable.



Enhancesphagocytosis.



Capableof neutralizing toxins.


1. IgM:


5-10% of antibodies.



Heaviestantibody, because it is made of 5 different parts in a circle.



Isa complement fixation.



Firstto appear after an infection. Since theyare larger and less mobile they are the first sent in and the first toget “killed” in combat.



Enhancesphagocytosis.



Hasagglutinate cells.



Effectiveagainst microorganisms.


IgA:

15% of the antibodies in serum.



Foundin two forms:



SerumIgA found in blood.



SecratoryIgA found in mucosal secretions (saliva and tears).


IgD:

.2%of antibodies in serum



Slightlylarger than IgG antibodies.



Leastabundant


Havethe shortest life span
IgE;

Participate inallergic rxn.



This is the “bad guy” that gives youallergies.



Bound to mast cells.


Vaccines


A beneficial application ofimmunology.



Asuspension of microorganisms that will induce a state of immunity in a host



couldbe:



suspensionof attenuated (weaken state) microorganism



killedby heat or chemical treatment



inactivatedtoxins (products of organisms)



producedby cellular components




Killed Vaccines-

Used for typhus, typhoid,whooping cough of B. pertussis


Killedtwo ways-


Chemical means- organism isgrown then exposed to phenol, acetone, or formalin



Heat means- organism is grownthen killed by heat using minimum time and temp.




Inactivated Vaccines-


Microorganisms aregrown then passed through hundreds of serial transfers in an unfavorablemedia (they are weak because they don’t get their nutrients).



Usedfor BCG for tuberculosis


Inactivated toxins or toxic vaccines

These are rendered non-toxic byheat or formalin and adjuvants(something you add to something) are also used to slowthe release and to enhance immunity.



Used for toxins from. C.diphtheria and Clostridium tetani


Vaccines using Microbial Components
ex. purified pili (plasmid transfer) to preventcolonization, purified capsular polysaccharides.
Viral Vaccination

Both inactivated and attenuatedforms used



Heat to inactivate virus isdiscouraged, ultra-violet light could be used.



Someproblems are hypersensitivity and that a live virus is present.