A protein interaction map of Drosophila melanogaster.

Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.

Gene expression analysis by transcript profiling coupled to a gene database query.

We describe an mRNA profiling technique for determining differential gene expression that utilizes, but does not require, prior knowledge of gene sequences. This method permits high-throughput reproducible detection of most expressed sequences with a sensitivity of greater than 1 part in 100,000. Gene identification by database query of a restriction endonuclease fingerprint, confirmed by competitive PCR using gene-specific oligonucleotides, facilitates gene discovery by minimizing isolation procedures. This process, called GeneCalling, was validated by analysis of the gene expression profiles of normal and hypertrophic rat hearts following in vivo pressure overload.

Putative Drosophila pheromone-binding proteins expressed in a subregion of the olfactory system.

Four genes expressed in the olfactory system of Drosophila melanogaster have been identified by subtractive hybridization. Two of these genes, OS-E and OS-F, are related to genes encoding moth pheromone-binding proteins. The OS-E and OS-F genes are tightly linked and are expressed in a subregion of the antenna (the primary olfactory organ). A protein sequence analysis suggests the possibility that pheromone-binding proteins are members of a larger class of proteins, extending beyond the olfactory system. The predicted product of a third gene, OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins. The fourth gene, OS-C, encodes a novel 13-kDa protein that contains a putative nuclear import sequence and an acid-rich region. The expression patterns of these genes differ within the antenna; their transcript distributions support the notion of specialized roles for different olfactory sensilla. The functions of the OS gene products have not been demonstrated; however, the potential identification of pheromone-binding proteins in Drosophila, a species with well characterized genetics, may offer a means of analyzing the function of these molecules that is not available in other systems.

Growth cone behavior on gradients of substratum bound laminin.

We have tested the ability of a gentle gradient of neurite-promoting activity to orient the extension of embryonic growth cones. Gradients of neurite-promoting activity were made with biologically active, tritium-labeled laminin. The distributions of laminin bound to glass substrata were visualized by autoradiography and quantified with an image processing system. Embryonic chick sympathetic ganglia were explanted onto laminin gradients and cultured. No tendency for neurites to be oriented up-gradient was detected by examining the morphology of explants. Time-lapse studies of individual growth cones detected no up- or down-gradient bias in growth cone motility. These results suggest that growth cone orientation is relatively insensitive to a graded distribution of a naturally occurring neurite-promoting molecule.

A transient rise in cytosolic calcium follows stimulation of quiescent cells with growth factors and is inhibitable with phorbol myristate acetate.

We have used aequorin as an indicator for the intracellular free calcium ion concentration [( Ca++]i) of Swiss 3T3 fibroblasts. Estimated [Ca++]i of serum-deprived, subconfluent fibroblasts was 89 (+/-20) nM, almost twofold higher than that of subconfluent cells growing in serum, whose [Ca++]i was 50 (+/-19) nM. Serum, partially purified platelet-derived growth factor (PDGF), and fibroblast growth factor (FGF) stimulated DNA synthesis by the serum-deprived cells, whereas epidermal growth factor (EGF) did not. Serum immediately and transiently elevated the [Ca++]i of serum-deprived cells, which reached a maximal value of 5.3 microM at 18 s poststimulation but returned to near prestimulatory levels within 3 min. Moreover, no further changes in [Ca++]i were observed during 12 subsequent h of continuous recording. PDGF produced a peak rise in [Ca++]i to approximately 1.4 microM at 115 s after stimulation, and FGF to approximately 1.2 microM at 135 s after stimulation. EGF caused no change in [Ca++]i. The primary source of calcium for these transients was intracellular, since the magnitude of the serum-induced rise in [Ca++]i was reduced by only 30% in the absence of exogenous calcium. Phorbol 12-myristate 13-acetate (PMA) had no effect on resting [Ca++]i. When, however, quiescent cells were treated for 30 min with 100 nM PMA, serum-induced rises in [Ca++]i were reduced by sevenfold. PMA did not inhibit growth factor-induced DNA synthesis and was by itself partially mitogenic. We suggest that if calcium is involved as a cytoplasmic signal for mitogenic activation of quiescent fibroblasts, its action is early, transient, and can be partially substituted for by PMA. Activated protein kinase C may regulate growth factor-induced increases in [Ca++]i.