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We calculate the forces required to package (or, equivalently, acting to eject) DNA into (from) a bacteriophage capsid, as a function of the loaded (ejected) length, under conditions for which the DNA is either self-repelling or self-attracting. Through computer simulation and analytical theory, we find the loading force to increase more than 10-fold (to tens of piconewtons) during the final third of the loading process; correspondingly, the internal pressure drops 10-fold to a few atmospheres (matching the osmotic pressure in the cell) upon ejection of just a small fraction of the phage genome. We also determine an evolution of the arrangement of packaged DNA from toroidal to spool-like structures.

We report a strategy for encapsulating and condensing DNA. When T5 phage binds to its membrane protein receptor, FhuA, its double stranded DNA (120,000 bp) is progressively released base pair after base pair in the surrounding medium. Using cryoelectron microscopy, we have visualized the structures formed after T5 phage DNA is released into neutral unilamellar proteoliposomes reconstituted with the receptor FhuA. In the presence of spermine, toroidal condensates of circumferentially wrapped DNA were formed. Most significantly, the sizes of these toroids were shown to vary, from 90 to 200 nm in their outer diameters, depending on the number of DNA stands transferred. We have also analyzed T5 DNA release in bulk solution containing the detergent-solubilized FhuA receptor. After DNA release in a spermine containing solution, huge DNA condensates with a diameter of about 300 nm were formed containing the DNAs from as many as 10-20 capsids. At alkaline pH, the condensates appeared as large hollow cylinders with a diameter of 200 nm and a height of 100-200 nm. Overall, the striking feature of our experiments is that, because of the progressive release of DNA from the phage capsid, the mechanism of toroid formation is fundamentally different from that in the classical studies in which highly dilute, "naked" DNA is condensed by direct addition of polyvalent cations; as a consequence, our method leads to toroids of arbitrary size.

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

Nanoparticles deposited at the air-water interface are observed to form circular domains at low density and stripes at higher density. We interpret these patterns as equilibrium phenomena produced by a competition between an attraction and a longer-ranged repulsion. Computer simulations of a generic pair potential with attractive and repulsive parts of this kind, reproduce both the circular and stripe patterns. Such patterns have a potential use in nanoelectronic applications.

Genome-related databases have already become an invaluable part of the scientific landscape. The role played by these databases will only increase as the volume and complexity of relevant biology data rapidly expand. We are far enough into the genome project and into the development of these databases to assess their attributes and to reexamine some of the conceptual organizations and approaches they are taking. It is clear that there are needs for both highly detailed and simplified database views, the latter being especially needed to make expert domain data more accessible to nonspecialists.

Under a wide variety of conditions, the addition of condensing agents to dilute solutions of random-coil DNA gives rise to highly compact particles that are toroidal in shape. The size of these condensates is remarkably constant and is largely independent of DNA molecular weight and basepair sequence, and of the nature of condensing agent (e.g., multivalent cation, polymers, or added cosolvent). We show how this optimum size is determined by the interactions between topological defects, which unavoidably strain the circumferentially wound DNA strands in the torus.

We develop a statistical thermodynamic model for the phase evolution of DNA-cationic lipid complexes in aqueous solution, as a function of the ratios of charged to neutral lipid and charged lipid to DNA. The complexes consist of parallel strands of DNA intercalated in the water layers of lamellar stacks of mixed lipid bilayers, as determined by recent synchrotron x-ray measurements. Elastic deformations of the DNA and the lipid bilayers are neglected, but DNA-induced spatial inhomogeneities in the bilayer charge densities are included. The relevant nonlinear Poisson-Boltzmann equation is solved numerically, including self-consistent treatment of the boundary conditions at the polarized membrane surfaces. For a wide range of lipid compositions, the phase evolution is characterized by three regions of lipid to DNA charge ratio, rho: 1) for low rho, the complexes coexist with excess DNA, and the DNA-DNA spacing in the complex, d, is constant; 2) for intermediate rho, including the isoelectric point rho = 1, all of the lipid and DNA in solution is incorporated into the complex, whose inter-DNA distance d increases linearly with rho; and 3) for high rho, the complexes coexist with excess liposomes (whose lipid composition is different from that in the complex), and their spacing d is nearly, but not completely, independent of rho. These results can be understood in terms of a simple charging model that reflects the competition between counterion entropy and inter-DNA (rho < 1) and interbilayer (rho > 1) repulsions. Finally, our approach and conclusions are compared with theoretical work by others, and with relevant experiments.

Signaling molecules of the transforming growth factor beta (TGF-beta) family contribute to numerous developmental processes in a variety of organisms. However, our understanding of the mechanisms which regulate the activity of and mediate the response to TGF-beta family members remains incomplete. The product of the Drosophila decapentaplegic (dpp) locus is a well-characterized member of this family. We have taken a genetic approach to identify factors required for TGF-beta function in Drosophila by testing for genetic interactions between mutant alleles of dpp and a collection of chromosomal deficiencies. Our survey identified two deficiencies that act as maternal enhancers of recessive embryonic lethal alleles of dpp. The enhanced individuals die with weakly ventralized phenotypes. These phenotypes are consistent with a mechanism whereby the deficiencies deplete two maternally provided factors required for dpp's role in embryonic dorsal-ventral pattern formation. One of these deficiencies also appears to delete a factor required for dpp function in wing vein formation. These deficiencies remove material from the 54F-55A and 66B-66C polytene chromosomal regions, respectively. As neither of these regions has been previously implicated in dpp function, we propose that each of the deficiencies removes a novel factor or factors required for dpp function.

A Drosophila melanogaster sequence homologous to the mammalian growth factor-stimulated TSC-22 gene was isolated in an enhancer trap screen for genes expressed in anterodorsal follicle cells during oogenesis. This sequence includes a 225 aa residue open reading frame that encompasses a leucine zipper motif immediately preceded by a highly conserved region (TSC box), similarly located but distinct from the basic domain of bZIP proteins. The gene encoding this sequence, bunched (bun), has been independently isolated and characterized with respect to its role in peripheral nervous system development and eye development (Treisman, J.E., Lai, Z.-C. and Rubin, G.M. (1995) Shortsighted acts in the decapentaplegic pathway in the Drosophila eye development and has homology to a mouse TGF-beta-responsive gene. Development 121, 2835-2845). In agreement with the expression of the enhancer detector insertion, in situ hybridization reveals that bun transcripts localize to the anterior dorsal follicle cells at stages 10-12 of oogenesis. Changes in bun enhancer trap expression in genetic backgrounds that disrupt the grk/Egfr signaling pathway suggest that bun is regulated by growth factor patterning of dorsal anterior follicle cell fates. Clonal analysis shows that bun is required for the proper elaboration of dorsal cell fates leading to the formation of the dorsal appendages.

Using an elaborate set of cis-regulatory sequences, the decapentaplegic (dpp) gene displays a dynamic pattern of gene expression during development. The C-terminal portion of the DPP protein is processed to generate a secreted signaling molecule belonging to the transforming growth factor-beta (TGF-beta) family. This signal, the DPP ligand, is able to influence the developmental fates of responsive cells in a concentration-dependent fashion. Here we examine the sequence level organization of a significant portion of the dpp locus in Drosophila melanogaster and use interspecific comparisons with D. simulans, D. pseudoobscura and D.virilis to explore the molecular evolution of the gene. Our interspecific analysis identified significant selective constraint on both the nucleotide and amino acid sequences. As expected, interspecific comparison of protein coding sequences shows that the C-terminal ligand region is highly conserved. However, the central portion of the protein is also conserved, while the N-terminal third is quite variable. Comparison of noncoding regions reveals significant stretches of nucleotide identity in the 3' untranslated portion of exon 3 and in the intron between exons 2 and 3. An examination of cDNA sequences representing five classes of dpp transcripts indicates that these transcripts encode the same polypeptide.

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (and phenotypes), aberrations, transposons, pointers to sequence data, clones, stock lists, Drosophila workers and bibliographic references. The Encyclopedia of Drosophila is a joint effort between FlyBase and the Berkeley Drosophila Genome Project which integrates FlyBase data with those from the BDGP.

cDNAs encoding the Drosophila 70-kDa S6 kinase (S6K) were isolated by low-stringency hybridization with mammalian p70S6k probes. Conceptual translation of S6k cDNA sequences yields a product containing all of the canonical features typical of serine/threonine kinases and has 78% amino acid identity in the catalytic domain with the human p70S6k homologue. The S6k gene, located at polytene chromosome site 65D, gives rise to two predominant transcripts of 3.0 and 5.0 kb and at least two smaller transcripts (< 3.0 kb) that are found in whole-animal RNAs at all stages of development. Blood cells derived from the hematopoietic organs of ribosomal protein S6 (RpS6air8) mutant animals express higher levels of the smaller S6k transcripts, suggesting tissue- or genotype-specific differences in the regulation of the S6k gene. Drosophila S6K expressed in COS or NIH 3T3 cells phosphorylates mammalian RPS6 in a mitogen-dependent wortmannin- and rapamycin-sensitive manner, suggesting that its regulation is similiar to mammalian p70S6k.

DLAR is a receptor-like, transmembrane protein-tyrosine phosphatase in Drosophila that is expressed almost exclusively by developing neurons. Analysis of Dlar loss-of-function mutations shows that DLAR plays a key role during motoneuron growth cone guidance. Segmental nerve b (SNb) motor axons normally exit the common motor pathway, enter the ventral target region, and then synapse on specific ventral muscles. In Dlar mutant embryos, SNb axons bypass their normal target region and instead continue to extend along the common pathway. SNd motor axons also make pathfinding errors, while SNa and SNc axons appear normal. Thus, DLAR controls the ability of certain motor axons to navigate specific choices points in the developing Drosophila nervous system.

We have identified the molecular lesions associated with six point mutations in the Drosophila TGF-beta homologue decapentaplegic (dpp). The sites of these mutations define residues within both the pro and ligand regions that are essential for dpp function in vivo. While all of these mutations affect residues that are highly conserved among TGF-beta superfamily members, the phenotypic consequences of the different alleles are quite distinct. Through an analysis of these mutant phenotypes, both in cuticle preparations and with molecular probes, we have assessed the functional significance of specific residues that are conserved among the different members of the superfamily. In addition, we have tested for conditional genetic interactions between the different alleles. We show that two of the alleles are temperature sensitive for the embryonic functions of dpp, such that these alleles are not only embryonic viable as homozygotes but also partially complement other dpp hypomorphs at low temperatures. Our results are discussed with regard to in vitro mutagenesis data on other TGF-beta-like molecules, as well as with regard to the regulation of dpp cell signaling in Drosophila.

Intercellular signaling molecules of the transforming growth factor-beta (TGF-beta) superfamily are required for pattern formation in many multicellular organisms. The decapentaplegic (dpp) gene of Drosophila melanogaster has several developmental roles. To improve our understanding of the evolutionary diversification of this large family we identified dpp in the grasshopper Schistocerca americana. S. americana diverged from D. melanogaster approximately 350 million years ago, utilizes a distinct developmental program, and has a 60-fold-larger genome than D. melanogaster. Our analyses indicate a single dpp locus in D. melanogaster and S. americana, suggesting that dpp copy number does not correlate with increasing genome size. Another TGF-beta superfamily member, the D. melanogaster gene 60A, is also present in only one copy in each species. Comparison of homologous sequences from D. melanogaster, S. americana, and H. sapiens, representing roughly 900 million years of evolutionary distance, reveals significant constraint on sequence divergence for both dpp and 60A. In the signaling portion of the dpp protein, the amino acid identity between these species exceeds 74%. Our results for the TGF-beta superfamily are consistent with current hypotheses describing gene duplication and diversification as a frequent response to high levels of selective pressure on individual family members.

Signaling by TGF beta-related factors requires ligand-induced association between type I and type II transmembrane serine/threonine kinases. In Drosophila, the saxophone (sax) and thick veins (tkv) genes encode type I receptors that mediate signaling by decapentaplegic (dpp), a member of the bone morphogenetic protein (BMP) subgroup of TGF beta-type factors. In this report, we demonstrate that the Drosophila punt gene encodes atr-II, a previously described type II receptor that on its own is able to bind activin but not BMP2, a vertebrate ortholog of dpp. Mutations in punt produce phenotypes similar to those exhibited by tkv, sax, and dpp mutants. Furthermore, punt will bind BMP2 in concert with tkv or sax, forming complexes with these receptors. We suggest that punt functions as a type II receptors for dpp and propose that BMP signaling in vertebrates may also involve sharing of type II receptors by diverse ligands.

The dpp/BMP family of TGF beta-related factors controls numerous events in pattern formation and morphogenesis. How these polypeptide signals are received and transduced by target cells is largely unknown. We combine molecular and genetic approaches to establish that the Drosophila saxophone (sax) gene encodes a dpp receptor. We compare the structural properties and expression patterns of sax with a second dpp receptor encoded by the thick veins (tkv) gene. While the sax gene is expressed ubiquitously, tkv is expressed in a highly localized and dynamic pattern during development. Some, but not all, of the tkv expression pattern parallels that of dpp. Ubiquitous expression of a tkv transgene rescues both tkv and sax loss-of-function mutations. Thus, there is at least partial functional overlap of the sax and tkv receptors in vivo. We consider these observations in terms of possible ligand-receptor interactions during Drosophila development.

Previous results suggested that the hobo transposable element is active predominantly in the germline of Drosophila. We investigate germline restriction of hobo transposition by testing in vitro modified elements for their ability to mobilize marked elements in vivo. Although intact hobo elements are germline specific, an hsp70 promoter-hobo transposase fusion is active in the soma. Analysis of the hsp70-promoted transcript does not provide evidence for splicing. Moreover, the hobo promoter confers germline bias to a highly sensitive reporter, delta 2-3 P transposase. These results indicate that hobo transposition is germline specific due to regulation of transposase production at the level of transcription. Thus, although hobo is similar to the P transposable element in organization and tissue specificity, it differs in the underlying mechanism governing germline specific activity.

We show that when a heat-shock-driven gene that encodes the yeast FLP recombinase is injected into preblastoderm Drosophila embryos, it promotes intermolecular recombination between two coinjected plasmids that bear the specific recombination target sequence, FRT. Minimal, 34-bp FRT sites in the two plasmids are sufficient for their cointegration. The reaction is efficient enough to produce detectable recombinants when one of the plasmids is present in as little as 1000 molecules per embryo. This is comparable to the concentration of unique chromosomal sites, raising the possibility that integration of injected plasmid DNA into FRT-bearing fly chromosomes may also be achievable. Since integrants might be stabilized against the reverse excision reaction if the recombinase could be provided in a sharp pulse, it is encouraging that efficient plasmid cointegration is also achieved when in vitro synthesized FLP RNA rather than DNA is injected into the embryos.

We have analyzed the contributions made by maternal and zygotic genes to the establishment of the expression patterns of four zygotic patterning genes: decapentaplegic (dpp), zerknüllt (zen), twist (twi), and snail (sna). All of these genes are initially expressed either dorsally or ventrally in the segmented region of the embryo, and at the poles. In the segmented region of the embryo, correct expression of these genes depends on cues from the maternal morphogen dorsal (dl). The dl gradient appears to be interpreted on three levels: dorsal cells express dpp and zen, but not twi and sna; lateral cells lack expression of all four genes; ventral cells express twi and sna, but not dpp and zen. dl appears to activate the expression of twi and sna and repress the expression of dpp and zen. Polar expression of dpp and zen requires the terminal system to override the repression by dl, while that of twi and sna requires the terminal system to augment activation by dl. The zygotic expression patterns established by the maternal genes appear to specify autonomous domains that carry out independent developmental programs, insofar as mutations in the genes that are expressed ventrally do not affect the initiation or ontogeny of the expression patterns of the genes that are expressed dorsally, and vice versa. However, interactions between the zygotic genes specific to a particular morphological domain appear to be important for further elaboration of the three levels specified by dl. Two of the genes, dpp and twi, are unaffected by mutations in any of the tested zygotic dorsal-ventral genes, suggesting that dpp and twi are the primary patterning genes for dorsal ectoderm and mesoderm, respectively.

Imaginal disks, the primordia of the adult appendages in Drosophila, are divided into anterior and posterior compartments. However, the developmental role of such compartments remains unclear. The expression of decapentaplegic (dpp), a pattern formation gene required for imaginal disk development, has the intriguing property of being expressed in a line at or near the boundary between these compartments. Here, we compare the distribution of dpp-driven reporter gene expression to the pattern of expression of the engrailed (en) gene, known to be required for the maintenance of the compartment boundary. Using confocal microscopy to obtain single cell resolution, we have determined that the majority of the en+ imaginal disk cells expressing the dpp-driven reporter genes about those cells expressing en, while a small percentage of dpp reporter gene expressing cells also express en. In posterior regions of en mutant disks, where compartmentalization is abnormal, we observe ectopic expression of the dpp-driven reporter genes. We conclude that the pattern of dpp expression in imaginal disks is delimited in part through the direct or indirect repression by engrailed. Our results lead us to question the widely held assumption that the anterior edge of en expression demarcates the A/P compartment boundary.

We have sequenced HFL1 from D. melanogaster, the only cloned hobo element shown to have transposase activity. The 2959 bp HFL1 sequence predicts a 2.0 kb open reading frame (ORF1) with substantial amino acid similarity to the transposases of Activator (Ac) from maize (Zea mays) and Tam3 from snapdragon (Antirrhinum majus). Mutational analysis of a C-terminal region of ORF1 conserved with Ac and Tam3 indicates that it is essential for hobo transposase activity. This is an example of extensive amino acid sequence identity between short inverted repeat elements in different kingdoms. We discuss the possibility that the conservation of hobo, Ac, and Tam3 transposases represents an example of horizontal transmission of genetic information between plants and animals.