Lecture 11: Genetic/Molecular Approaches to Study Bacterial Infections Flashcards
____: An approach to the study of genes and their functions
Genomics
___: To characterize biological experiments carried out entirely on a computer
In silico
True or False: One can learn about gene content, dynamic, and organization all in silico (basic genomic information)
True
- important key to study evolution of bacterial pathogen
____ uses in silico process of assigning hypothetical function by homology, using species filter (subtracting all homologues of one known genome from another to define share and unshared genes)
A. Gene Content
B. Gene Organization
A. Gene Content
True or False: Gene Content is an approach that may help find genes responsible for certain phenotypes
True
Genes are organized into ___ or groups
clusters
What type of genomics technology provides the ability to conduct genome-wide surveys of genetic variation and differences in expression profiles of different strains?
A. Gene Content
B. Microarray
Microarray
Once genes and combination of genes are identified, it is essential to understand how the genes were ACQUIRED due to genome dynamics in bacteria, creating ____ ____ In bacterial populations
genetic diversity
What are the three main forces that shape bacterial genomes?
- gene change
- gene loss
- gene gain
What are the two main ways that pathogenic phenotypes can be acquired?
- horizontal transfer of existing genes
- de novo mutation
True or False: Comparative genomics can be used to identify, genus, species, subspecies
True
The broader the pan-genome, the more ___ the organisms
diverse
_____: the entire gene pool for that pathogen, includes genes not shared by all strains
A. Core-genome
B. Pan-genome
C. Strain specific genes
D. Dispensible genes
B. Pan-genome
_____: set of genes found across all strains of a pathogen species
A. Core-genome
B. Pan-genome
C. Strain specific genes
D. Dispensible genes
A. Core-genome
_____: found in more than one strain, but not in all strains
A. Core-genome
B. Pan-genome
C. Strain specific genes
D. Dispensible genes
D. Dispensible genes
_____: found in only one strain of pathogen species
A. Core-genome
B. Pan-genome
C. Strain specific genes
D. Dispensible genes
C. Strain specific genes
_____: found in more than one strain, but not all strains
A. Core-genome
B. Pan-genome
C. Strain specific genes
D. Dispensible genes
D. Dispensible genes
___: small, genetic change that can occur within person’s DNA sequence
SNP’s
Insertion or deletion of a SNP may result in a shift in the ____ ____
translational frame
True or False: While SNPs are relatively common and found frequently throughout the genome, they serve as poor biological markers and are relatively unstable
False - they are great biological markers and are very stable
True or False: SNP’s can create a genetic predisposition
True
____ act as partial solutions, moving genomic information (in silico) to observable function (in vitro)
Microarrays
True or False: Microarrays are used to identify genes expressed (on or off) under different conditions
True
What are the three possible targets/immobilized DNA that can be used in microarrays?
DNA, cDNA, or oligonucleotides
True or False: Microarrays are based on hybridization probing, a technique of using fluorescently labeled nucleic acid molecules as “mobile probes” (single strand of sample)
True
What are the three types of microarrays?
- Microarray expression analysis
- CGH (comparative genomic hybridization)
- Mutation microarray analysis (detects mutations or SNP’s)
Which microarray is best suited for identifying changes in gene expression?
A. Microarray expression analysis
B. CGH (comparative genomic hybridization)
C. Mutation microarray analysis
A. Microarray expression analysis
Which microarray is best suited for detection of mutations or SNP’s?
A. Microarray expression analysis
B. CGH (comparative genomic hybridization)
C. Mutation microarray analysis
C. Mutation microarray analysis
Which microarray is best suited for detection of genomic gains and losses/change in number of copies of a certain gene?
A. Microarray expression analysis
B. CGH (comparative genomic hybridization)
C. Mutation microarray analysis
B. CGH (comparative genomic hybridization)
What is the immobilized/target for: Microarray expression analysis?
A. cDNA derived from mRNA
B. mRNA derived from DNA
C. large pieces of genomic DNA
A. cDNA derived from mRNA
What does the DNA in microarray expression analysis hybridize with?
A. mRNA
B. tRNA
C. cRNA
D. cDNA
A. mRNA
In microarray, what does green, red, yellow, and black represent?
green = control DNA (DNA/cDNA from non-virulent bacteria)
red = sample DNA (DNA/cDNA from virulent bacteria)
yellow = combo of sample and control DNA
black = neither control nor sample
What is the immobilized/target for: Comparative Genomic Hybridization?
A. cDNA derived from mRNA
B. mRNA derived from DNA
C. large pieces of genomic DNA
C. large pieces of genomic DNA
True or False: Comparative Genomic Hybridization allows for measuring genomic gains/losses
True
ok
____: A high-throughput, quantitative means of exploring the transcriptome of your organism of interest
RNA-Seq
True or False: RNA-Seq can be used to identify novel genes, as well as to determine expression, splicing, and mutation analysis
True
True or False: RNA-Seq has higher sensitivity and dynamic range compared to Microarray AND does not require reference gene
True
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