Toxicogenomics Flashcards
1
Q
Genomics
A
-the study of processes at genome-wide scales
example
-genomics-DNA
-transcriptomics-RNA
2
Q
Transcriptomics
A
- mRNA transcript levels for many genes (medical research and animal biology)
- Individual genes to transcriptome-wide screens-react to a stressor (microarrays, RNA-sequencing)
- Snapshot as to what was going on at the time of sampling
3
Q
Microarray Process
A
- extract total RNA
- label RNA using fluorescent dyes
- hybridize labelled targets
- laser excitation
- scan emitted fluorescent signal
- image analysis
- intensity=how much of gene was expressed
4
Q
Microarrays
A
- cDNA microarrays-cDNA fragments on a microscope slide
- Oligonucleotide microarrays-fixed lengths olives on a microscope slide
- each new iteration generated more data for less $$
- needed molecular information for the study species in order to create slide
5
Q
Dose-response relationship-larval fish
A
- exposed to pyrethroid pesticide permethrin
- used a heatmap-colourful way to show a lot of gene expression data
- relative to the control groups the gene expression changes were greater in higher concentration
- high concentration-many genes involved in the extreme response were involved in cell death and DNA repair
6
Q
next generation sequencing
A
-techniques used are not species-specific
ie DNA is DNA is DNA
-applicable to any organism we are interested in studying
7
Q
Transcriptomics process
A
- sequence the transcriptome (All mRNA in tissue) and create a reference trascriptome
- align RNA sequences from your samples to your reference transcriptome and count the number of transcripts in your sample
- number of mRNA transcripts=gene expression
8
Q
Dog Tick and DEET
A
- measure gene expression in individuals from different treatments
- exposure to DEET causes dog ticks to rapidly change expression of Phase I detoxification genes
- ticks avoid DEET when they detect it
9
Q
TMF
A
- lampricide to control invasive sea lamprey in the great lakes
- detoxified in many fishes through conversion to TFM-glucuronide via UDPGT enzyme
- TFM-glucuronide is more hydrophilic and can be cleared quickly from the body
- TMF accumulates in their tissues to exert its toxic effects
10
Q
Transcriptomics/genomics
A
- can count the number of mRNA transcripts to look for difference between your treatments
- align the mRNA transcripts and look for sequence difference between them (works for DNA too)-single nucleotide polymorphisms
11
Q
Pollution tolerance in killfish
A
- tolerant-evolved in environments built up tolerance to PCB
- sensitive populations die off at lower PCB concentrations than tolerant ones
- gene deletions result in tolerance
- single mutation can lead to pesticide resistance
12
Q
Aryl hydrocarbon receptors
A
- PCB binds to
- transcription factor protein
- activated, moves into the nucleus, switches on the transcription of 60 genes
- proteins that regulate whether a gene will expressed to make its encoded protein
13
Q
tracking sources of invasive mosquitoes
A
- mosquitoes that carry yellow fever in Australia and New Zealand
- used SNP
- mosquiotes found in airports had mutations in sodium channels
- mutations related to resistance to pyrethroid pesticides
- variation in sequence use to determine source of population (location)