Zebrafish offer special advantages both for characterizing embryonic development and for designing a database system. The zebrafish embryo, nearly unique among commonly studied vertebrates, contains large numbers of identifiable cells, some of which have already been characterized in terms of their detailed anatomical, physiological and developmental properties (Table 2). In embryos, the zebrafish nervous system, for example, is relatively simple [Kimmel90], all neurons are visible in living specimens [Westerfield93], individual identified cells can be transplanted and followed over time with fluorescent labels [Eisen91a,b], and gene expression can be be monitored and altered in individual cells [Westerfield92]. Zebrafish also provide a unique opportunity to apply genetic analysis to the study of development because efficient methods are available for generating, isolating, and characterizing mutations [Kimmel89, Mullins93]. With the recent advent of a genetic map [Postlethwait94], methods for generating transgenic zebrafish [Stuart88], and large scale screens that have generated many thousands of mutant zebrafish [Mullins93], it is now possible to study the functions of particular genes. A final important advantage of zebrafish is that their use as an experimental animal is still new; relatively few labs are actively studying zebrafish, and communication among these labs (provided by a newsletter and an Internet news server) is excellent. At the first open meeting of the entire zebrafish research community last spring, the pressing need for a unified database was recognized and there was unanimous agreement to work together to establish an on-line database system. Implementation of a database system will significantly enhance our ability to study the functional relationships among various neuronal properties.
Name Type # Location Refs
CaD inter 2 1/hemi- rhombomere 7 9
Cap motor 60 1//hemi-spinal seg 2,12,13
CaV inter 4 2/hemi-rhombomere 7 9
CoPA inter 21 spinal cord 4,8
CoSA inter 21 spinal cord 8
DoB inter 21 spinal cord 8
DoLA inter 21 spinal cord 8
M inter 2 1/hemi-rhombomere 4 9
MeL inter 12 6 in each nucleus 11
mlf
MeM inter 8 4 in each nucleus 11
mlf
MiD2cl inter 2 1/hemi-rhombomere 5 9
MiD2cm inter 2 1/hemi-rhombomere 5 9
MiD2i inter 2 1/hemi-rhombomere 5 9
MiD3cl inter 2 2/hemi-rhombomere 6 9
MiD3cm inter 2 2/hemi-rhombomere 6 9
MiD3i inter 2 2/hemi-rhombomere 6 9
MiM1 inter 2 1/hemi-rhombomere 4 9
Mip motor 60 1//spinal hemi-seg 2,12,13
MiR1 inter 2 1/hemi-rhombomere 4 9
MiR2 inter 2 1/hemi-rhombomere 5 9
MiV1 inter 12 6/hemi-rhombomere 4 9
MiV2 inter 10 5/hemi-rhombomere 5 9
MP muscle 240 3-5 in each myotome 5
RB sensory 150 dorsal spinal cord 4,6,10
RoI2C inter 4 2/hemi-rhombomere 2 9
RoI2R inter 2 1/hemi-rhombomere 2 9
RoL1 inter 4 2/hemi-rhombomere 1 9
RoL2 inter 4 2/hemi-rhombomere 2 9
RoL3 inter 2 1/hemi-rhombomere 3 9
RoM1C inter 2 1/hemi-rhombomere 1 9
RoM1R inter 2 1/hemi-rhombomere 1 9
RoM2L inter 2 1/hemi-rhombomere 2 9
RoM2M inter 2 1/hemi-rhombomere 2 9
RoM3L inter 2 1/hemi-rhombomere 3 9
RoM3M inter 4 2/hemi-rhombomere 3 9
Rop motor 60 1//hemi-spinal seg 2,12,13
RoR1 inter 2 1/hemi-rhombomere 1 9
RoV3 inter 6 3/hemi-rhombomere 3 9
T inter 16 caudal hindbrain 7
Vap moto 60 ~.3/spinal hemi-seg 1,3
VeLD inter 90 spinal cord 8
VG inter 2 2/hemi-rhombomere 6 7,9
Table 2. Some of the uniquely identified and unique classes of neurons and muscle cells in the zebrafish. Abbreviations: inter, interneuron; motor, motoneuron; seg, segment; mlf, medial longitudinal fasciculus. Refs: 1, Eisen, Neuron 8:231, 1992; 2, Eisen et al., Nature 320:269, 1986; 3, Eisen et al., J. Neurosci. 10:34, 1990; 4, Eisen & Pike, Neuron 6:767, 1991; 5, Felsenfeld et al., Devel. 108:443, 1991; 6 Grunwald et al., Dev. Biol. 126:115, 1988; 7, Kimmel et al., J. Comp. Neurol. 233:365, 1985; 8, Kuwada et al., J. Neurosci. 10:1299, 1990; 9, Metcalfe et al., J. Comp. Neurol. 251:147, 1986; 10, Metcalfe et al., Devel. 110:491, 1990; 11, Mendelson, J. Comp. Neurol. 251:160, 1986; 12, Myers et al., J. Neurosci. 6:2278, 1986; 13, Westerfield et al., J. Neurosci. 6:2267, 1986.
Our goals also have significance for computer science database research:
We plan to use the Internet to create a system of database servers located initially at two sites linked by the Internet to each other and to public databases such as GenBank and MEDLINE. We will meet on a biannual basis, and more frequently by video conferencing, to design the system. The implementation of the database will be coordinated with the mouse and human brain database projects. This will aid in understanding relationships among different vertebrate nervous systems. Linking data describing synteny relationships, mutant phenotypes and gene expression patterns among species will provide tools for identifying new developmental genes and the molecular mechanisms of disease. We intend the database system to serve as a prototype for other scientific communities.
Continue on to Specific Aim 1