BIOC17H3 Lecture Notes - Lecture 3: Phagocytosis, Veterinary Virology, Ribosomal Rna
5 Jul 2018
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- Protocol to go from different features to identify/classify microbes
oIsolation look at
physiology look at
detailed physiology
(eg. Biochemical
tests)
obiochemical tests:
determine the
presence of
metabolic enzymes
and pathways
phage tests:
recognize
different
bacteria (b/c
different
surface
proteins)
oalso use serological
tests (use antibodies to
test for specific
antigens)
- use MS to determine
molecular composition of the
species eg. FAME) then do
molecular genotypic analysis
- - one of the first ways to compare bacteria in pure culture would be to see DNA
hybridization (get DNA, denature, get the ssDNA of org you know and attach to filter
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do the same for org. that you don’t know look to see how much hybridized to the
ssDNA of the known one)
can quantify using radioactivity eg. Use radioactive phosphorus (eg.
Grow B in media w/ radio phosphorus all DNA in b will be radioactive
will then be able to see much how radioactivity is in the filter once
they’re hybrized)
control: leave A w/ A
test: look at B vs As hybridization
oif see complete: same organisms
opartial: related
ono: unrelated
-Nucleic acid composition: G-C content
othe content is characteristic of
different taxonomic groups
oChemical: hydrolysis followed by HPLC
oPhysical: based on the melting temperature of the DNA (higher G-C = higher
melting temperature b/c 3 H-bonds vs 2)
-Genomic profiling (typing) methods
oGenerate fragments of genomic DNA utilizing restriction enzymes and/or PCR
fragments are separated by electrophoresis and the band patterns from
different microbes are compared w/ known samples
oProcess: purify genome obtain genetic material of known microbe treat w/
restriction enzyme (will cut DNA
at the same part), so cut w/
multiple diff. ones sep.
pattern using gel
electrophoresis then PCR
Sites for cutting and
how many these sites
are in a genome vary
among species
Allows you to see if
they’re from the same
species/genome/family
etc.
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find more resources at oneclass.com
-Sequencing of genomes
oProcess: isolate pure culture of microbe send
bacteria for full genome sequencing can be
done rapidly using pyrosequencing and illumine
methods
oProblems: too much information
oMost powerful and direct method for comparing
genes and genomes
oComplete genomes can now be sequences and
compared in a short time period
oAllows for a: physical map of the genome,
genome structure, Gc content, gene content, gene sequence, gene position in
the genome, taxonomic and phylogeny value
Microbes and Taxonomy
- Linnaean taxonomy is based on the category species, but the definition of species for
large organisms is not applicable to microbes
-Species: group of organisms consisting of morphologically similar individuals capable of
interbreeding and producing fertile offspring
oMicrobial species:
collection of strains that
share many stable
properties and differ
significantly from other
groups of strains
Strain = pure
culture (need to
isolate the
microbe first,
then identify/classify the species and strains
The first pure culture you obtain is the first strain type for that bacteria
oStrains: strains that belong to a given species can differ in
Biochemists and physiology biovars/biotype
Morphol
ogy
morphovars/morphotypes
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Protocol to go from different features to identify/classify microbes: isolation look at physiology look at detailed physiology (eg. biochemical tests, biochemical tests: determine the presence of metabolic enzymes and pathways. Sites for cutting and how many these sites are in a genome vary among species. Allows you to see if they"re from the same species/genome/family etc. Linnaean taxonomy is based on the category species, but the definition of species for large organisms is not applicable to microbes. Species: group of organisms consisting of morphologically similar individuals capable of interbreeding and producing fertile offspring: microbial species: collection of strains that share many stable properties and differ significantly from other groups of strains. Strain = pure culture (need to isolate the microbe first, then identify/classify the species and strains. The first pure culture you obtain is the first strain type for that bacteria: strains: strains that belong to a given species can differ in. Antigenic properties serovars/serotypes (recognize antibodies, phage.
