The Thing They Did During COVID (PCR)
This is the process by which PCR is conducted, which uses application of heat to amplify large quantities of targeted genomic lcoi.
What is iterative theromcycling?
In contrast to PCR, Sanger sequencing requires only one primer and a 1:100 dye-labelled THIS to dNTPs - which acts as a chain terminator.
What are di-deoxynucleotide triphosphates (ddNTPs)?
Another name for mitochondria DNA is this - often visually represented as a circle in mitochondrial network diagrams.
What is a haplotype?
Microsatellites are comprised of tandem repeats of the same 2-6 bp, whereas a SNP is just a single bp change. One set of repeating bp is known as this.
What is a motif?
This "explosive" technique is used to code the entire genome of an individual, which is costly and time-consuming.
What is shotgun sequencing?
Usually 18-30 bp long, you need two primers - a forward and reverse - oriented in this direction for every PCR you run.
What is 3' to 5'? (Also accept 3' primer end closest to target region).
This process used to sequence genetic code is much more sensitive than gel electrophoresis because it can detect single bp differences in length. The dyed-labelled fragments are pulled up a tube and color is detected by fluorescence, which is used to make a chromatograph.
What is capillary electrophoresis?
In regards to genetics, this term is a surrogate for genetic diversity in a population - where a smaller of this experiences more genetic drift.
What is an effective population size?
Microsatellites are great to use in population- or individual-level ID. This is because microsatellites are unique to each individual - the term to describe the variety is this.
What is hypervariability?
As an alternative to Sanger seq, this technique uses dyes, a flow cell, and a camera to overlay DNA sequences and sequence the bp with the power of statistics.
What is sequencing by synthesis?
Originally found in a hot spring in Yellowstone, this characteristic makes Taq polymerase crucial to running PCR.
What is heat-resistant?
Sanger seq is useful in wildlife management - for instance, you could use it to detect these anomalies in homologous sequences across many individuals.
What are SNPs?
When looking at a visual mitochondrial network, you can tell a haplotype is more ancestral if it has the most amount of these.
What are colors (representing populations)?
When msats are being replicated, this happens where an extra motif is added into the sequence; this explains why the mutation rate is so high.
What is slippage?
During this phase of high throughput seq, DNA is fragmented into desirable lengths, denatured, and attached to "adapters" to prep for flow cell use.
What is library preparation?
After 30 cycles, PCR will slow down and stop doubling products due to low supply of this ingredient.
What are dNTPs?
This type of genomic material is great for species ID, because it has low variability within populations, but is highly variable between species.
What is mitochondrial DNA?
When considering how diverse a population is, these are the two distinctions you should make - the first is how many different haplotypes are present, and the second is how different the haplotypes are from each other.
What is richness and divergence?
What are primers?
Each dot on a flow cell represents a grouping of identical genomic fragments, called this.
What are clusters?
When using PCR to sequence, it's important to make sure that your individual samples stay separate - otherwise this might happen to your chromatogram.
What are overlapping peaks?
Mitochondrial rRNA and tRNA genes are useful as priming regions or identifying different species because they're very conserved, but this highly variable loci is great for individual ID or distinguishing closely-related species.
What is the D-loop?
When examining mitonetworks, seeing a genetically isolated population - with minimal/no connection to the ancestral haplotype - maybe an indication of this.
What is speciation?
Multiple loci can be combined in the same capillary (as long as the dyes are different) and the results can be overlayed on the chromatogram - this is the name of this technique.
What is multiplexing?
This excellent technique of high throughput sequencing uses restriction enzymes to cut fragments down to a desirable length, which are then targeted for SNP detection.
What is RADseq?