Unit 4.3 (A): Classifications Flashcards
Placing organisms in groups of related species. Lists of characteristics of known organisms.
CLASSIFICATION
Matching characteristics of an “unknown” to lists of known organisms.
IDENTIFICATION
Provides** identification schemes** for identifying bacteria and archaea
Bergey’s Manual of Determinative Bacteriology
Provides phylogenetic information on bacteria and archaea
Bergey’s Manual of Systematic Bacteriology
standard reference for laboratory identification of bacteria.
Bergey’s Manual of Determinative Bacteriology
(the branch of microbiology dealing with human pathogens)
Medical microbiology
In the simplest form, a positive test would be assigned a value of 1, and a negative is assigned a value of 0. In most commercial testing kits, test results are assigned numbers ranging from 1 to 4 that are based on the relative reliability and importance of each test, and the resulting total is compared to a database of known organisms.
Numerical Rapid Identification
- Cells from a single colony are lysed, and their proteins are extracted in acetonitrile.
- Cellular proteins in the extract are read using a mass spectrophotometer that measures the molecular mass of proteins in the sample (Figure 10.10).
3.The data obtained are then compared to commercial databases.
Automated rapid identification
science that study blood serum and immune response that are evident in serum; involves reactions of microorganisms with specific antibodies
SEROLOGY
- samples of an unknown bacterium are placed in a drop of saline on each of several slides. Then a different known antiserum is added to each sample. The bacteria agglutinate (clump) when mixed with antibodies that were produced in response to that species or strain of bacterium; a positive test is indicated by the presence of agglutination.
slide agglutination test
known antibodies are placed in (and adhere to) the wells of a microplate, and an unknown type of bacterium is added to each well. A reaction between the known antibodies and the bacteria provides identification of the bacteria.
enzyme-linked immunosorbent assay (ELISA)
used to identify antibodies in a patient’s serum.
Western blottin
Identification of bacterial species and strains by determining their susceptibility to various phages. Also looks for similarities among bacteria like serological testing.
Phage Typing
bacterial viruses that usually cause lysis of the bacterial cells they infect.
Bacteriophages (phages)
designed to separate cellular fatty acids to compare them to fatty acid profiles of known organisms
Fatty Acid Profiles
can be used to identify bacteria in a sample without culturing the bacteria.
Flow cytometry
technique used in the lab to make millions of copies of a particular section of DNA; a common tool used in medical and biological research labs. It is used in the early stages of processing DNA forsequencing, for detecting the presence or absence of a gene to help identifypathogensduring infection, and when generating forensic DNA profiles from tiny samples of DNA.
POLYMERASE CHAIN REACTION (PCR)
an enzyme that copies DNA. It is isolated from a heat-loving bacterium that is naturally found in hot springs, so the enzyme doesn’t break down at the high temperatures necessary for copying DNA using apolymerasechain reaction.
Taq polymerase
a process of heating and cooling
THERMAL CYCLING
3 MAIN STAGES OF PCR
- when the double-stranded template **DNA is heated **to separate itinto two single strands.
- When the** temperature is lowered t**o enable the DNA primers to attach to the template DNA.
- when the temperature is raised and the new strand of DNA is made by the Taq polymerase enzyme.
- DENATURING
- ANNEALING
- EXTENDING
use an organism’s DNA base composition to draw conclusions about relatedness.
DNA Sequencing
The number and sizes of DNA fragments, or DNA fingerprints, produced by restriction enzymes are used to determine genetic similarities.
DNA Fingerprinting
DNA from two microorganisms is treated with the same restriction enzyme, and the restriction fragments (RFLPs) produced are separated by electrophoresis
DNA FIngerprint
The sequence of bases in ribosomal RNA can be used in the classification of organisms
Ribotyping: rRNA Sequencing
Single strands of DNA or RNA, from related organisms will hydrogen-bond to form a double-stranded molecule; this bonding is called nucleic acid hybridization.
Nucleic Acid Hybridization
A DNA probe used to identify bacteria.——- is used to detect specific DNA. This modification of southern blot is used to detect salmonella.
Southern Blotting
can quickly detect a pathogen in a host or the environment by identifying a gene that is unique to that pathogen
DNA Chip or Microarray
Fluorescent dye–labeled RNA or DNA probes are used to stain microorganisms in place, or in situ; A DNA or RNA probe attached to fluorescent dyes is used to identify chromosomes.
Fluorescent In Situ Hybridization (FISH)
- used to diagnosis Zika virus in pregnant women and identify the source of rabies viruses;
- use PCR, reverse-transcription PCR, and real-time PCR
Nucleic Acid Amplification Tests (NAATs)
a variation of thepolymerase chain reactionthat typically** measures RNA expression levels.**
RT-PCR, also known as**Reverse Transcriptase PCR, **
alledreal-time PCRor quantitativereal-time PCR, is aPCR-based technique that couples amplification of a target DNA sequence with quantification of the concentration of that DNA species in the reaction.
QuantitativePCR(qPCR)
ntification is based on successive questions, and each question has two possible answers.
Dichotomous Key
Is a depiction of patterns of shared characteristics among taxa
Cladogram
clade
Signifying that it consists of the ancestor species and all its descendant
monophyletic
clade
Is a grouping that consists of an ancestral species and some, but not all, of the descendants
paraphyletic
Includes numerous types of organisms that lack a common ancestor
polyphyletic
