Identification

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What is the classical approach to identifying DNA - 3

morphological characteristics differential staining biochemical tests

what do each group look like on EMB agar

-aerogenes-coli: black or dark centered colonies thyphoid - clear

Why is simple streaking on a complex culture not sufficient for getting a pure culture from nature - 2

1. many microgorganisms are present 2. the microorganism amy be present in a small porportionn to other organsims

two drawbacks to dichotomous keys

1. time consuming 2. genomic DNA or plasmid may change the characteristics of the cell and give false results

EMB agar - distinguish between what bacteria?

Aerogenes-coli group and thyphoid

Nomenclature system used

Binomial system - genus, speceis

How are bacterial species defined and how much of it percentage wise must be the same?

DNA- DNA hybridization 70% hybridization 16s rRNA seqeunces 97% similarity

3 Real world applications of identification

Diagnosis a disease cause of food contamination water treatment plant basic research

What are the two choices called in a dichotomous key?

Dichotomy

Steps of DNA fingerprinting- 4

Digest DNA into smaller fragments via restriction enzymes seperate the fragments based on size visualize the bands unique patter of bands identifies the Donor DNA

What is a good first choice to use in a dichotomous key?

Distinguish between broad categories - split the options into two, reliable test - gram stain, morphology, catalase

Order of classificaiton

Domain phylum class order family genus species

Common Biochemical tool used in the best fit method

Enterotube

What are 7 common things we exammine in identifcaiton procedures

Metabolic processes morphological characteristics serology phage typing amino acid sequencing fatty acid analysis by gas composition base composition of fatty acids

After using selective or differential media what do you do?

Move it to a complex agar (such as LB) to insure pure growth

What do you need for identifcaiton before you even begin?

PURE CULTURE

Why PCR is useful in idneifcation

Primers hybridize to complementary sequences to amplify the region of DNA these can then be sequenced

Nucleic Acid Hybridization

Southern blotting test if DNA from one organisms can bind with the organism of interest if so they may be similar

Steps to obtain a pure culture to be used for biochemical tests and morphological identification

Streak on a plate isolated is restreaked to test purity transferred to a slant of be used as a master culture

What cant we just use morphological characteristics?

There are a limited number of visible characteristics

Assumption made by dichotomous key

a set of characteristics unique to a species in at least one respsect

What is a dichotomous key

a tool used for the identification of an organisms based on a series of choices between alternative characteristics

What is serology

aggulination technqiues

What is an alternative to a dichotomous key?

best fit method

MacConkey Agar - what does it have and what do colones look like

bile salts, lactose, methyl red dye coliform bacteria are brick red with precipitated salts salmonella are clear gram positve cannot grow

What are common morphological characteristics? - 5

cell shape size arrangement presence of spores flagella

What 4 identifcaiton methods can we use when analyzing base composition of nucleic anlaysis

detmeine the entire seqeunce of bases in an organisms DNA DNA fingerprinting Hybridization PCR

What do we do to prevent the problems in using a complex culutre

differential and selective meida

What is differential media

differentiation between the bacteria

Mueller Tellurite agar distinguish between what bacteria? what does it contain

diphtheria bacteria tellurium

what do we look at in metabolic processes

enzymatic activities, utilization of carbon and nitrogen sources, waste prodcuts

Use of a personal computer - biolog, how does it work?

identify many bacteria use a microtiter plate, and detemines the oxidation of 95 different energy carbon sources that the bacteria is on. The test results are red by the computer and it determines which bacteria is present

What are we interested in finding in the biochemical tests

not the specific enzymes but some net end result

what is the best fit method and why is it better

use several tests at once and score the tests. The identifcaiton is made based on what organism the results show that it is closest to. Therefore even if one test gave a false result it can still be given the proper identifcaiton because it is still the most similar to a normal organism. it is also much more quick - use of primary tests to narrow it down from a large number of possibilites and secondary tests to identify it

What is phage typing

use to identify which phage (virus) a bacterium is susceptible to


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