SECTION II: Experimental Data

Abstract Class: DATA_ITEM

OVERVIEW: Mutants and Chromosomes

Introduction:

Before giving a detailed description of the FISH, CHROMOSOME, and ALTERATION classes, it is useful to characterize how these three classes interact to represent mutant and wild-type strains of fish.

Schematic of relationships (ER diagram):

Discussion:

As indicated in the schematic above, FISH data records correspond directly to mutant and wild-type strains of zebrafish; whenever a new mutant or wild-type line is developed, a new FISH record is be submitted to the database. As detailed in the following pages, FISH records focus primarily on the physical animal (vs. detailed genetic information) — information on a strain’s lineage, availability, who discovered it, etc..

The genetic information about a strain is captured in CHROMOSOME records, which correspond directly to mutated chromosomes present in a mutant strain. Note that only mutant chromosomes are represented; FISH records for wild-type strains have no CHROMOSOME records associated with them. Because zebrafish have 25 chromosomes, a given mutant FISH record may have between zero and 25 CHROMOSOME records associated with it. Because most mutants have only one or two mutated chromosomes, it will be rare that a FISH record has more than one or two CHROMOSOME records associated with it. By cross-breeding, a given mutation can be transferred to a new mutant line. In this way, a given CHROMOSOME record may ultimately be associated with many different FISH records.

Within a mutant chromosome, any number of specific genetic alterations may have occurred which, taken together, result in the mutant phenotype. It may not be known (at least not initially) which of these specific alterations is responsible for various phenotypic characteristics of the mutant. Each of these specific genetic alterations is represented by an ALTERATION record. It is at the ALTERATION level that the specific location and nature of chromosomal changes are recorded. In sum, FISH records represent mutant and wild-type strains and serve as conceptual “containers” for CHROMOSOME records, which represent mutant chromosomes. In turn, CHROMOSOME records serve as conceptual containers for ALTERATION records, which describe specific changes to chromosomes.