Toxicogenomics

Question 1

Genomics

Answer 1

-the study of processes at genome-wide scales
example
-genomics-DNA
-transcriptomics-RNA

Question 2

Transcriptomics

Answer 2

• 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

Question 3

Microarray Process

Answer 3

• 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

Question 4

Microarrays

Answer 4

• 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

Question 5

Dose-response relationship-larval fish

Answer 5

• 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

Question 6

next generation sequencing

Answer 6

-techniques used are not species-specific
ie DNA is DNA is DNA
-applicable to any organism we are interested in studying

Question 7

Transcriptomics process

Answer 7

• 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

Question 8

Dog Tick and DEET

Answer 8

• 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

Question 9

TMF

Answer 9

• 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

Question 10

Transcriptomics/genomics

Answer 10

• 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

Question 11

Pollution tolerance in killfish

Answer 11

• 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

Question 12

Aryl hydrocarbon receptors

Answer 12

• 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

Question 13

tracking sources of invasive mosquitoes

Answer 13

• 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)