Gene Conservation Laboratory
Scoring & Photographing Gels

Scoring Gels

A lab worker scoring gels A lab worker scoring gels Detection of enzymes on electrophoretic gels is done by seeing the loci visually expressed in the staining process, which highlights the separation of the enzymes. The protein molecules move at different rates due to their size and shape as the gel essentially acts as a sieve. Each locus will have what we call a "common" allele. This simply means it is the most common expression of those loci for that particular species. The common will either be called a "1,1" (one one) or "AA". Our lab uses the numerical method as this works best with the computer-scoring program, which we have developed. Any variant, due to its different molecular weight, will migrate at a different rate than the common allele. This variant will either move further, or not as far, as the common. When we score, we are essentially looking at the differences, or lack of differences, in the expressed loci. The common allele is agreed upon by all of the different agencies and labs doing electrophoresis for a particular species, and often we will use a "control" sample that is of a known score for comparison. The variant may be scored as a 2, and the common as a 1. So if we see some of the enzyme in the 1 position, and some in the 2 position, it is known as a heterozygote. If the enzyme is expressed all in one position, it is called a homozygote. An example would be if in a row of ten samples, we saw a heterozygote at position 4 and a homozygote fast at position 7, we would score the gel thusly: 1,1-1,1-1,1-1,2-1,1-1,1-2,2-1,1-1,1-1,1. This is a basic scoring, but often more than one locus will show up at the same place, and scoring will become much more complicated.

 

Photographing Gels for Archives

A lab worker photographs gels e digitally photograph the stained gel to keep a copy for future reference. Frequently, the project leader will review the images to make sure the computer-recorded scores are correct. Sometimes discrepancies arise when analyzing the scores such as unusual frequencies between of heterozygotes and homozygotes and conflict between scorers. Also, it often happens that we score a variant, which had not previously been observed in a particular population or in a particular species. The photo images allow us to carefully go over the stained gel to recheck these scores, and to perhaps decide if we need to rerun any individuals or populations. We rerun any individual which was for some reason not clearly seen during the first run due to running or staining problems, or perhaps a mistake was made during the field collection. We also rerun gels when we wish to again observe a new or rare variant alongside a known variant.

 

Sockeye Salmon Allozyme Gel

A sockeye salmon allozyme gel This gel demonstrates a complicated stain showing more than one locus. The bottom locus has many possible bands, with at least 5 or more showing in the photo. Scoring is complex, and requires a scoring guide and a lot of experience for scoring. The top thick band is another locus, which often shows up with the lower locus. It is scored separately from the lower bands.

 

Chum Salmon Gel

Chum salmon gel This gel demonstrates a complicated stain showing more than one locus. The bottom locus has many possible bands, with at least 5 or more showing in the photo. Scoring is complex, and requires a scoring guide and a lot of experience for scoring. The top thick band is another locus, which often shows up with the lower locus. It is scored separately from the lower bands.

 

Questions and Answers

Q. What is an enzyme?
A. A protein that functions as a biological catalyst to accelerate chemical reactions in the cell that would proceed slowly or not at all in their absence.

Q. What is a locus?
A. Any genetically defined site on a chromosome, i.e. a gene, a part of a gene, or a DNA sequence.

Q. What is an allele?
A. One or more alternate forms of a locus.

Q. What is a genotype?
A. The genetic identity of the organism.

Q. What is a phenotype?
A. The appearance of the organism.

Q. What is a diploid?
A. Organisms with two chromosome sets (one paternal, the other maternal).

Q. What is a haploid?
A. Organisms with a single chromosome set.

Q. What is lineage?
A. A line of common descent.

Q. What is a homozygote?
A. Diploid organisms with two copies of one allele.

Q. What is a heterozygote?
A. Diploid organisms with one copy of two alleles.