Classification of Organisms

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Classification of Organisms by Mind Map: Classification of Organisms

1. Is the science that studies serum and immune responses that are evident in serum

2. Based on association coeficient 0.0 (no matches) 1.0 (100% match) 80% similarity – same species 65% similarity – same genus

3. Nomenclature

3.1. Called the binomial nomenclature

3.2. Genus name + specific epithet (species)

3.3. General rules

3.3.1. Genus name always capitalized

3.3.2. Species name is never capitalised

3.3.3. Species name is never used without the genus name

3.3.4. Species name is never used without the genus name

3.3.5. Genus name may be used without species name

3.3.6. Genus and species are always italicized (or underlined)

3.3.7. Species name: never abbreviated

3.3.8. . Less simple genus abbreviation if different genus start with same alphabet. e.g. Enterococcus faecalis (En. faecalis)

3.4. Rules can be found in:

3.4.1. For protozoa and parasitic worms : International Code of Zoological Nomenclature

3.4.2. For fungi and algae : International Code of Botanical Nomenclature

3.4.3. For bacteria : International Code for Nomenclature of Bacteria

3.5. Inspiration of names

3.5.1. Shape

3.5.2. Where it was found

3.5.3. nutrients that it uses

3.5.4. What diseases it caused ?

3.6. Who discovered it ?

3.7. The meaning of the names of some microorganisms

3.7.1. Escherichia coli Named after Theodor Escherich (1988); found in colon

3.7.2. Saccharomyces cerevisiae Saccharo, sugar; myco, mold; cerevisiae, beer

3.7.3. Lactococcus lactis Lacto, milk; kokkus, berry

4. Identification and classification

4.1. Methods for identifying and classifying microorganisms

4.1.1. Morphology characteristics Characteristics studied: - cell type (prokaryote or eukaryote) - shape and size - cellular grouping (chain, clump) - external structures (flagella, motility) - internal structures (inclusion granules)

4.1.2. Differential staining Gram stain Gram positive : Purple Gram negative : Pink Acid-fast stain Stain bacteria with waxy material Negative staining for capsules Use india ink to provide a contrasting background then stain with safranin Endospore staining Schaeffer-Fulton endospore stain Endospore appear green within pink cells Flagella staining Use a mordant and stain carbolfuchsin to coat the flagella

4.1.3. Biochemical tests To verify its metabolic activity - Phenol Red broth - Casease Test - Gelatin Test - Lipase Test - Starch hydrolysis - Motility test - Catalase test

4.1.4. Numerical taxonomy Computer assisted taxonomy

5. Serology

5.1. Meaning

5.1.1. Proteins are then transferred to a nitrocellulose filter by blotting

5.1.2. The filter is exposed to known antibodies, and washed (if there is matching antigen and antibody, the antibody will be retained)

5.2. Tests

5.2.1. Unknown bacteria placed on several slides

5.2.2. A different known antiserum is placed on each sample

5.2.3. Agglutination – positive reaction

5.3. Serological techniques

5.3.1. a. Enzyme-linked immunosorbent assay (ELISA) Fast and utilised a computer scanner to read result ELISA performed in microtiter plate

5.3.2. Western blotting steps Proteins from an unknown bacterium or virus are separated by electrophoresis (proteins separated according to molecular weights) A second antibody which will bind to all antibodies, with enzyme linked, is exposed to the filter, and washed Enzyme reaction occurred and signal can be observed

6. Phage typing

6.1. Function

6.1.1. Determine which phage a bacterium is susceptible to

6.1.2. Bacteriophages cause lysis of bacteria that they infect Bacteriophages infect only particular species or even strains

6.2. Steps

6.2.1. Prepare a lawn of bacteria

6.2.2. Drop different spots of known phage

6.2.3. Lysis indicate matching phage and bacteria

7. Fatty acids profile

7.1. Bacteria synthesize a wide variety of fatty acids

7.2. These fatty acids are constant for a particular species

7.3. Compare with fatty acid profiles of know organisms for classification and identification of unknown

8. DNA base composition

8.1. Function

8.1.1. were used to know the degree of relatedness between the related organisms.

8.1.2. closely related organisms can have many identical or similarities in bases pair of DNA.

9. DNA fingerprinting

9.1. function

9.1.1. Use of restriction enzyme to produce banding pattern

9.1.2. RE cuts specific base sequence

9.1.3. The more similar the DNA fingerprints, the more closely related the organisms are.

10. Nucleic acid hybridization

10.1. principle

10.1.1. When dsDNA is heated, complementary strands will separate as the H bonds between bases break

10.2. function

10.2.1. This technique can be used to determine extent of similarity based on degree of reunion

11. Techniques that apply the principle of nucleic acid hybridization:

11.1. Southern blotting

11.1.1. Function for detection of a specific DNA sequence in DNA samples

11.2. DNA chips

11.2.1. DNA from unknown organism is labelled with a fluorescent dye, added to the chip. Hybridization of the probe and unknown DNA is detected by fluorescence

11.3. Ribotyping and Ribosomal RNA Sequencing

11.3.1. function molecular technique for bacterial identification and characterization that uses information from rRNA-based phylogenetic analyses

11.4. Fluorescent In Situ Hybridization (FISH)

11.4.1. function Fluorescence in situ hybridization (FISH) is a kind of cytogenetic technique which uses fluorescent probes binding parts of the chromosome to show a high degree of sequence complementarity.

12. Methods use to classify and identify microorganisms after various analyses

12.1. Dichotomous keys

12.1.1. Widely used for identification

12.1.2. Identification is based on successive questions, and each question has two possible answers

12.1.3. Very little to do with phylogenetic relationships

12.2. Cladograms

12.2.1. Show evolutionary relationships among organisms If ssDNA are cooled, complementary strands will reunite

12.2.2. Constructed based on rRNA sequences with the aid of softwares