Toxicogenomics Flashcards

1
Q

Genomics

A

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

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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
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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
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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
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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
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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

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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
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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
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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
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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
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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
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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
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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)
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