CMMB 563 Final Questions with Accurate
Answers
2 parts of genome annotation correct answer 1. Gene calling
2. Functional assignment of called genes
Alternative gelling agent to agar correct answer Gellan gum
An example of when syntrophy is required correct answer The fermentation of
butyrate/propionate cannot be accomplished without a methanogen to keep the
hydrogen concentration low to make the fermentation exothermic.
Anamox correct answer anaerobic ammonia oxidation. Conversion of ammonium
and nitrite to N2 under anoxic conditions.
anexic correct answer free of other living things except for the one being studied
Annotation telephone correct answer The loss of integrity of a
gene/protein/domain family by the sequential addition of
genes/proteins/domains that resemble additions to the family but eventually do
not have the same function as the original biochemically characterized protein.
autochthonous correct answer Grows on recalcitrant substrates like cellulose or
humic acids
Binning correct answer Putting similar contigs together to yield MAGs. Based on
tetranucleotide frequencies and differential coverage
,Candidate division/phyla correct answer Candidate phylum is an uncultured
phylum.
Candidatus correct answer any taxonomic clade that can be described
biochemically in its environment but cannot be isolated in pure culture.
Challenges in assembling a complex metagenome correct answer 1. Lots of
repeats
2. Lots of gaps in low-abundance genomes
3. Closely related strains cause problems
COG correct answer Cluters of Orthologous Groups of proteins. Any group of at
least 3 proteins that are more similar to each other than they are to any other
proteins from the same genomes most likely to belong to an orthologous family.
COG are functionally grouped. COGs are based on genes.
COG Functional groupings correct answer 26 functional categories of COGs
denoted with a letter
Contig correct answer set of overlapping DNA fragments that have been
assembled in the correct order to form a continuous stretch of DNA sequence
Copiotrophic correct answer nutrient rich
Culturing strategies for favouring K-selected bacteria correct answer 1. Low
nutrient media
, 2. Long incubations
3. Bioreactors instead of batch incubations
4. Sequencing batch reactors for biomass retention
5. Inhibit fast growing bacteria (with egg lecithin)
6. Add recalcitrant substrates
Description of COG database construction correct answer Reciprocal BLASTs
between members of the COG
Does r or K-selected bacteria have better stress tolerance? correct answer K-
selected bacteria has better stress tolerance than r-selected bacteria
EC# correct answer Enzyme commission number: Not an annotation system, but a
hierarchical nomenclature system used to assign enzyme functionality. 4 digit
number. Often assigned to KEGGs as part of the annotation
Enzyme kinetics of r and K strategists correct answer r-strategists: high Vmax, low
affinity, high minimum substrate concentration required for growth
K-strategists: low Vmax, high affinity, low minimum substrate concentration
required for growth
Example of a microbe that has undergone genome reduction correct answer
Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus
Udaeobacter copiosus'
Example of a successful high-throughput culturing experiment correct answer
Culturing of Candidatus Peligibacter ubique (SAR11) (the most abundant bacteria
Answers
2 parts of genome annotation correct answer 1. Gene calling
2. Functional assignment of called genes
Alternative gelling agent to agar correct answer Gellan gum
An example of when syntrophy is required correct answer The fermentation of
butyrate/propionate cannot be accomplished without a methanogen to keep the
hydrogen concentration low to make the fermentation exothermic.
Anamox correct answer anaerobic ammonia oxidation. Conversion of ammonium
and nitrite to N2 under anoxic conditions.
anexic correct answer free of other living things except for the one being studied
Annotation telephone correct answer The loss of integrity of a
gene/protein/domain family by the sequential addition of
genes/proteins/domains that resemble additions to the family but eventually do
not have the same function as the original biochemically characterized protein.
autochthonous correct answer Grows on recalcitrant substrates like cellulose or
humic acids
Binning correct answer Putting similar contigs together to yield MAGs. Based on
tetranucleotide frequencies and differential coverage
,Candidate division/phyla correct answer Candidate phylum is an uncultured
phylum.
Candidatus correct answer any taxonomic clade that can be described
biochemically in its environment but cannot be isolated in pure culture.
Challenges in assembling a complex metagenome correct answer 1. Lots of
repeats
2. Lots of gaps in low-abundance genomes
3. Closely related strains cause problems
COG correct answer Cluters of Orthologous Groups of proteins. Any group of at
least 3 proteins that are more similar to each other than they are to any other
proteins from the same genomes most likely to belong to an orthologous family.
COG are functionally grouped. COGs are based on genes.
COG Functional groupings correct answer 26 functional categories of COGs
denoted with a letter
Contig correct answer set of overlapping DNA fragments that have been
assembled in the correct order to form a continuous stretch of DNA sequence
Copiotrophic correct answer nutrient rich
Culturing strategies for favouring K-selected bacteria correct answer 1. Low
nutrient media
, 2. Long incubations
3. Bioreactors instead of batch incubations
4. Sequencing batch reactors for biomass retention
5. Inhibit fast growing bacteria (with egg lecithin)
6. Add recalcitrant substrates
Description of COG database construction correct answer Reciprocal BLASTs
between members of the COG
Does r or K-selected bacteria have better stress tolerance? correct answer K-
selected bacteria has better stress tolerance than r-selected bacteria
EC# correct answer Enzyme commission number: Not an annotation system, but a
hierarchical nomenclature system used to assign enzyme functionality. 4 digit
number. Often assigned to KEGGs as part of the annotation
Enzyme kinetics of r and K strategists correct answer r-strategists: high Vmax, low
affinity, high minimum substrate concentration required for growth
K-strategists: low Vmax, high affinity, low minimum substrate concentration
required for growth
Example of a microbe that has undergone genome reduction correct answer
Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus
Udaeobacter copiosus'
Example of a successful high-throughput culturing experiment correct answer
Culturing of Candidatus Peligibacter ubique (SAR11) (the most abundant bacteria
