FlyBase: genes and gene models

Abstract

FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosphila species.

Illuminating the role of caspases during Drosophila oogenesis

“…Using a strategy similar to the DEVD-containing constructs used by Luo et al, 24 we made a construct consisting of cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) linked by the amino-acid sequence Val-Ile-Glu-Thr-Asp-Gly-Ala (VIETDGA) (Figure 1a). A mitochondrial outer membrane targeting sequence 17 was fused to the C-terminus of YFP. Upon cleavage by caspases, the CFP would no longer be tethered to the mitochondrion- localized YFP and could diffuse throughout the cell.…”

“…In C. elegans, the ced-1/-6/-7 and ced-2/-5/-10/-12 pathways have been found to be partially redundant for phagocytosis during cell death in nematodes. 9 Several Drosophila homologues for these genes are known, 17 but most of the published research examines professional phagocytes. Follicle cells functioning as phagocytes would be expected to express one or more recognition receptors.…”

“…36 We found that the CD36-related protein Crq was not expressed on follicle cells during the engulfment of apoptotic blebs (S Mazzalupo and L Cooley, unpublished). Draper (drpr, FBgn0027594), a Drosophila ortholog of CED-1 that is expressed on hemocytes/macrophages, 17 is another molecule to test for expression on the follicle cells. Future research should be aimed at determining what signals the follicle cell use in order to induce these receptors and what molecules are expressed on the surface of the apoptotic blebs.…”

“…17 The sense primer 5 0 -CGGAGCGCAAGCTTCTAGACTCCGAGCTG-3 0 and the antisense primer 5 0 -CCCTCGAGGATCCGAATTCCGTCTAAGAGCGTGTCG-3 0 were used with cDNA made from wild-type RNA. This also created HindIII and XhoI restriction sites and a stop codon to ligate it in-frame to the Cterminus of YFP.…”

“…16 Finally, the mutations reported in dcp-1 were later found to affect two genes. 17 When dcp-1 alone is mutated, there is no effect on late-stage nurse cell death. 12,18 Therefore, genetic analysis of individual caspase-encoding genes has not provided evidence for caspase function during normal oogenesis.…”