Notes:
1) Phenetic classification is the way to classify organisms based on their obvious similar features.
2) Numerical taxonomy is a computer assisted taxonomy where the organisms sorted into groups of mutual similarity based on the large number of observable properties. The final result expressed in simple matching coefficient or Jaccard coeffifcient. If the the coefficient showed 0.0 ( no matches) , 1.0 ( 100% match). Therefore, look for the higer percentage of matches to classify the bacteria.
3) Phylogenetic classification is the way to classify organisms based on evolutionary relationships by direct comparison of genetic material and gene products.
4) Highly conserved genetic sequence and advancement in sequencing technique make the phylogenetic classification possible.
5) Phylogenetic tree shows the evolutionary relationship among grouop of species.
6) To classify and identify microorganisms, we can study the morphological characteristics (shape, size, cell type, external structure and internal strcuture ) by using differential staining and biochemical tests.
- Differential staning - gram, acid-fast, negative, endospore and flagella staining
- Biochemical tests - Phenol Red broth (to test the capability of microbes in utilizing sugar), Gelatin test (to test the capability of the microbes to produce gelatinase), Lipase test (to test the capability of microbes to produce lipase), Strach hydrolysis ( to test the capability of microbes to produce exoenzyme that hydrolyse starch), Mortility test (to test whether the microbes able to move or not), Catalase test (to test the capability of the microbes to produce catalase which decompose hydrogen peroxide into oxygen and water.
8) Serology is the science that studies serum and immune response that are evident in serum.
9) Slide agglutination test is where unknown bacteria placed on several slides and a different known antiserum is placed on each sample. If agglutination occurred, it indicated positive rection because antibody produced will combine with antigens and precipitates the antigen.
10) There are two serology methods:
- Enzyme-linked immunosorbent assay (ELISA)
- fast and utilised a computer scanner to read result
- Western blotting
- Proteins are then transferred to a nitrocellulose filter by blotting
- The filter is exposed to known bacteria. If there is matching antigen and antibody, the antibody will retained.
9) Phage typing is to determine which phage a bacterium is susceptible to by dropping different spots of known phage on lawn of bacteria. Lysis indicate matching phage and bacteria.
10) Fatty acid profiles is to compare the fatty acid of unknown organisms with the fatty acid of unknown organisms.
11) The amount of DNA base composition can also use to find the two organisms that are closely related. The difference of more than 10% in their amount of GC is mostly not related.
12) DNA fingerprinting is to determine the similarity of DNA fingerprinting of two organisms to test how closely related they are by using restriction enzyme to cuts the specific base sequence.
13) Nucleic acid hybridization is used to measure the ability of DNA strands from one organisms to hybridize with another based one the drgree of reunion. When double strand of SNA is heated, the complementary strands will seperate and when single strand DNA are cooled, the complementary strands will reunite.
14) There are few technique that apply the technique of nucleic acid hybridization:
- Southern Blotting
- DNA chips
- The hybridization of the probe and unknown DNA is detected by fluorescence because fluorescent dye is added to the chips.
- Ribotyping and RIbosomal RNA sequencing
- rRNA sequence can be obtained by PCR of the DNA coding for rRNA
- Fluorescent In Situ Hybridization (FISH)
- Probe enter treated cell to react with target
-sensitive and do not require high number of cells
15) There are two methods to classify and identify microorganisms after various analyses:
- Dichotomous Keys
- Cladograms
Activities: No activity carried out except for teaching...^^
My own explorace:
1) Serum is the blood plasma not including the fibrinogens. Serum includes all proteins not used in blood clotting (coagulation) and all the electrolytes, antibodies, antigens, hormones, and any exogenous substances.
2) Bacteria can identified using 16S rRNA sequence comparisons phylogenetic while fungus can identified using 18S rRNA sequence comparisons phylogenetic.
3) Biochemical tests are mostly for bacteria only and the result of biochemical test will refer to the Bergey's manual to do classification.
4) Enteric bacteria are bacteria of the intestines.
Reflection:
For a proper classification and identification, at least 50 attributes should be tested. I don't know whether I got the patient to finish all 50 tests if I am that scientists. Every details and observation have to do very precisely are really not an easy work. All these tests maybe very interesting, but it can also easily get bored if these tests have to do again and again.
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