Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web

MOTIVATION

The increasing availability of biological databases on the World-Wide Web and hypertext links between them has made a wealth of information easily accessible to biologists. Additional retrieval capabilities can be achieved by storing explicitly specified biological relationships between different entities as discrete database entries.

RESULTS

We have built CySPID, a prototype database about the cytoskeleton that explores the approach of explicitly representing biological relationships. The stored relationships are displayed along with other retrieved information, can be used to make hyperlinks to related entities, and can be used to search for entities with specified properties. CySPID is extensible in that new types of relationships may be created without altering the database schema.

AVAILABILITY

CySPID is available for public use (http://ycmi.med.yale.edu/cyspid/). The CGI scripts used by CySPID are available upon request.

Examination of the function of two kelch proteins generated by stop codon suppression

The Drosophila kelch gene produces a single transcript with a UGA stop codon separating two open reading frames (ORF1 and ORF2). From the transcript, 76 kDa ORF1 and 160 kDa full-length (ORF1 + ORF2) proteins are made. The expression of these two proteins is regulated in a tissue-specific manner causing the ratio of full-length to ORF1 protein to vary in different tissues. The only detected defect for kelch mutants is female sterility, and kelch protein is localized to the ovarian ring canals. kelch mutant ring canals are disorganized and have partly occluded lumens, causing a failure to transport cytoplasm. ORF1 and full-length kelch proteins co-sediment with ring canals suggesting that both proteins are found in the ring canals. Transgenetic analysis reveals that ORF1 kelch protein is sufficient to rescue ring canal morphology and fertility. In addition, we have mutated the UGA stop codon to a UAA stop codon and to three sense codons that allow constitutive readthrough. Analysis of these mutants reveals that a full-length kelch protein can partially compensate for the loss of endogenous kelch, but the residue included at the stop codon is critical for function. Finally, these studies suggest that the mechanism of stop codon suppression of kelch is by tRNA suppression.

Formation of the Drosophila ovarian ring canal inner rim depends on cheerio

In Drosophila oogenesis, the development of a mature oocyte depends on having properly developed ring canals that allow cytoplasm transport from the nurse cells to the oocyte. Ring canal assembly is a step-wise process that transforms an arrested cleavage furrow into a stable intercellular bridge by the addition of several proteins. Here we describe a new gene wc named cheerio that provides a critical function for ring canal assembly. Mutants in cheerio fail to localize ring canal inner rim proteins including filamentous actin, the ring canal-associated products from the hu-li tai shao (hts) gene, and kelch. Since hts and kelch are present but unlocalized in cheerio mutant cells, cheerio is likely to function upstream from each of them. Examination of mutants in cheerio places it in the pathway of ring canal assembly between cleavage furrow arrest and localization of hts and actin filaments. Furthermore, this mutant reveals that the inner rim cytoskeleton is required for expansion of the ring canal opening and for plasma membrane stabilization.

Single amino acid mutations in Drosophila fascin disrupt actin bundling function in vivo

Fascins bundle actin filaments into large, tightly packed hexagonal arrays that support diverse cellular processes including microvillar projections and filopodial extensions. In Drosophila, fascin is encoded by the singed locus. Severe singed mutants have gnarled bristles and are female sterile due to a defect in rapid cytoplasm transport during oogenesis. In this paper, we report the results of a large EMS mutagenesis screen to generate new singed alleles. A mutation that changes glycine 409 to glutamic acid results in partial inactivation of fascin in vivo; singedG409E mutants have kinked bristles and are fertile with a mild nurse cell cytoplasm transport defect. This mutation is in a small conserved domain near the C-terminus of fascin. A mutation that changes serine 289 to asparagine almost completely inactivates fascin in vivo; singedS289N mutants have gnarled bristles and are sterile due to a severe defect in nurse cell cytoplasm transport caused by the absence of nurse cell cytoplasmic actin bundles. A subsequent EMS mutagenesis screen for dominant suppressors of singedS289N sterility revealed an intragenic suppressor mutation that changes serine 251 to phenylalanine and restores much of fascin's function. These two mutations, S289N and S251F, draw attention to a central domain in fascin.

Cytoskeletal functions during Drosophila oogenesis

Organismal morphogenesis is driven by a complex series of developmentally coordinated changes in cell shape, size, and number. These changes in cell morphology are in turn dependent on alterations in basic cytoarchitecture. Elucidating the mechanisms of development thus requires an understanding of the cytoskeletal elements that organize the cytoplasm of differentiating cells. Drosophila oogenesis has emerged as a versatile system for the study of cytoskeletal function during development. A series of highly coordinated changes in cytoskeletal organization are required to produce a mature Drosophila oocyte, and these cytoskeletal transformations are amenable to a variety of experimental approaches. Genetic, molecular, and cytological studies have shed light on the specific functions of the cytoskeleton during oogenesis. The results of these studies are reviewed here, and their mechanistic implications are considered.

The villin-like protein encoded by the Drosophila quail gene is required for actin bundle assembly during oogenesis

Mutations in the Drosophila quail gene result in female sterility due to the disruption of cytoplasmic transport from the nurse cells into the oocyte late in oogenesis. Nurse cells from quail mutant egg chambers fail to assemble cytoplasmic actin filament bundles correctly. We have cloned the quail gene and found that it encodes a protein with homology to the vertebrate actin-regulating protein villin. Unlike vertebrate villin, which is restricted to specialized absorptive epithelial cells, the villin-like protein encoded by quail is germline specific in adult flies. Antibodies directed against the quail protein show a striking colocalization with filamentous actin in the nurse cells and the oocyte. Our results demonstrate that the villin-like product of quail is required for the formation of cytoplasmic actin filament bundles in nurse cells, possibly by regulating both the polymerization and organization of actin filaments as demonstrated for vertebrate villin in vitro.

The specialized cytoskeleton of the Drosophila egg chamber

The Drosophila egg chamber is emerging as a uniquely versatile system for studying cytoskeletal rearrangements during development. Initial determination of the oocyte fate and subsequent growth of the oocyte depend on a series of highly coordinated changes in cell architecture. Homologs or relatives of many known cytoskeletal proteins play key roles in these events.

Morphogenesis of Drosophila ovarian ring canals

We analyzed the structure of cytoplasmic bridges called ring canals in Drosophila egg chambers. Two mutations, hu-li tai shao (hts) and kelch, disrupt normal ring canal development. We raised antibodies against the carboxy-terminal tail of hts and found that they recognize a protein that localizes specifically to ring canals very early in ring canal assembly. Accumulation of filamentous actin on ring canals coincides with the appearance of the hts protein. kelch, which is localized to the ring canals hours after hts and actin, is necessary for maintaining a highly ordered ring canal rim since kelch mutant egg chambers have ring canals that are obstructed by disordered actin and hts. Anti-phosphotyrosine antibodies immunostain ring canals beginning early in the germarium before hts and actin and throughout egg chamber development. The use of antibody reagents to analyze the structure of wild-type and mutant ring canals has shown that ring canal development is a dynamic process of cytoskeletal protein assembly, possibly regulated by tyrosine phosphorylation of some ring canal components.

Drosophila singed, a fascin homolog, is required for actin bundle formation during oogenesis and bristle extension

Drosophila singed mutants were named for their gnarled bristle phenotype but severe alleles are also female sterile. Recently, singed protein was shown to have 35% peptide identity with echinoderm fascin. Fascin is found in actin filament bundles in microvilli of sea urchin eggs and in filopodial extensions in coelomocytes. We show that Drosophila singed is required for actin filament bundle formation in the cytoplasm of nurse cells during oogenesis; in severe mutants, the absence of cytoplasmic actin filament bundles allows nurse cell nuclei to lodge in ring canals and block nurse cell cytoplasm transport. Singed is also required for organized actin filament bundle formation in the cellular extension that forms a bristle; in severe mutants, the small disorganized actin filament bundles lack structural integrity and allow bristles to bend and branch during extension. Singed protein is also expressed in migratory cells of the developing egg chamber and in the socket cell of the developing bristle, but no defect is observed in these cells in singed mutants. Purified, bacterially expressed singed protein bundles actin filaments in vitro with the same stoichiometry reported for purified sea urchin fascin. Singed-saturated actin bundles have a molar ratio of singed/actin of approximately 1:4.3 and a transverse cross-banding pattern of 12 nm seen using electron microscopy. Our results suggest that singed protein is required for actin filament bundle formation and is a Drosophila homolog of echinoderm fascin.

Profilin mutations disrupt multiple actin-dependent processes during Drosophila development

The chickadee gene of Drosophila encodes profilin, a small actin binding protein. We present the first analysis of the effects of profilin deletion in a multicellular organism. Genomic deletions of the chickadee locus result in a late embryonic lethal phenotype indicating that profilin is essential in flies. In addition, viable alleles of chickadee with defects in oogenesis, spermatogenesis and bristle formation provide insight into profilin function in a variety of cell types. Defects in oogenesis include the previously described failure to assemble nurse cell actin filament bundles in addition to abnormal regulation of mitosis, binucleate cells and stalled cell migration. Malformed bristles are a result of aberrant actin assembly. Monoclonal antibodies against Drosophila profilin were generated to study profilin's cellular and subcellular localization.

kelch encodes a component of intercellular bridges in Drosophila egg chambers

Oocyte maturation in Drosophila is supported by a cluster of 15 germline-derived nurse cells whose cytoplasm is transported into the oocyte through intercellular bridges called ring canals. kelch was isolated as a female sterile mutation affecting cytoplasm transport. We have cloned the kelch gene and found that it encodes an unusual transcript containing two open reading frames (ORF1 and ORF2) separated by a single UGA stop codon. At least two protein products are made from the kelch mRNA: a short protein from ORF1 and a longer protein from both ORF1 and ORF2 as a result of partial suppression of the UGA codon. The kelch ORF1 product is conserved, and antibodies directed against it are localized specifically to ring canals. Our results suggest that kelch produces a component of ring canals that regulates the flow of cytoplasm between cells.

chickadee encodes a profilin required for intercellular cytoplasm transport during Drosophila oogenesis

The entire cytoplasmic contents of 15 highly polyploid nurse cells are transported rapidly to the oocyte near the end of Drosophila oogenesis. chickadee is one of a small group of genes whose mutant phenotype includes a disruption of this nurse cell cytoplasm transport. We have cloned the chickadee gene and found that cDNA clones encode a protein 40% identical to yeast and Acanthamoeba profilin. The nurse cells from chickadee egg chambers that lack ovary-specific profilin fail to synthesize cytoplasmic actin networks correctly. In addition, the nurse cell nuclei in chickadee egg chambers become displaced and often partially stretched through the channels leading into the oocyte, blocking the flow of cytoplasm. We suggest that the newly synthesized cytoplasmic actin networks are responsible for maintaining nuclear position in the nurse cells.

Constructing deletions with defined endpoints in Drosophila

Chromosomes bearing small deletions are valuable tools in Drosophila genetics. We have investigated a method for efficiently constructing precise chromosomal deficiencies. Two P transposable elements were positioned within a progenitor strain at the sites of the desired deletion endpoints. Deletions spanning the two transposons were recovered at high frequency when P element transposase was expressed in these flies, but only if the flanking P elements were in a cis rather than a trans configuration. Appropriate progenitor strains can now be constructed to delete virtually any chromosomal region by utilizing an extensive collection of lines containing single P element insertions throughout the Drosophila genome.

Insertional mutagenesis of the Drosophila genome with single P elements

A versatile genetic method for identifying and cloning Drosophila melanogaster genes affecting any recognizable phenotype is described. Strains are constructed in which the insertion of a single P transposable element has caused a new mutation, greatly simplifying the genetic and molecular analysis of the affected gene. Mutagenesis is initiated by crossing two strains, each of which contains a specially designed P element. One element (jumpstarter), encoding P element transposase, efficiently mobilizes the second nonautonomous transposon (mutator), whose structure facilitates selection and cloning of new insertion mutations. Random mutator transpositions are captured in individual stocks that no longer contain jumpstarter, where they remain stable. This method was used to construct 1300 single P element insertion stocks which were then screened for recessive mutations. A library of single-element insertion strains will allow the structure and function of Drosophila genes to be readily correlated, and should have many other applications in Drosophila molecular genetics.

Postprandial blush in multiphase bone scanning

The presence of transient soft-tissue activity in the left side and the lower midportion of the abdomen on the early phases of the multiphase bone scan represents postprandial physiologic hyperemia of the small intestine. The bowel uptake was present in all 33 patients ingesting food between 15 min and 3.5 hr before scanning. In those patients who had not eaten within 4 hr of the study, only 25% demonstrated bowel activity. The observation of bowel uptake is important in differentiating a physiologic phenomenon from pathologic accumulations of activity. Pathology should be ruled out when bowel activity is not located in the usual left flank and lower mid-abdomen, or is present in a fasting individual.

Amplification of the X-linked Drosophila chorion gene cluster requires a region upstream from the s38 chorion gene

Genomic sequences controlling follicle cell-specific amplification of the X-linked Drosophila chorion gene cluster were mapped by P element-mediated transformation. Several DNA fragments containing the s38 gene and flanking sequences induced tissue-specific amplification, although replication levels were subject to position effects. Deletion analysis identified a 467-bp region upstream from the s38 transcription start site that contained sequences essential in cis for amplification. The essential region shared 32 bp of imperfect sequence homology with a previously identified region necessary for third chromosome chorion gene cluster amplification. This homologous segment contained a repetitive motif consisting of perfect and imperfect AATAC repeats; it was localized near the boundary of the essential domain since most, but not all, the repeats could be deleted without eliminating transposon-induced amplification. The repetitive region was not required for developmentally regulated s38 transcription, therefore our results identified at least one element required for amplification but not for chorion gene transcription. The homologous repetitive sequences within the amplification-essential regions may constitute part of the replication origins used to differentially replicate the two chorion domains during oogenesis.

The additional guanylate at the 5' terminus of Escherichia coli tRNAHis is the result of unusual processing by RNase P

In eucaryotes the 5'-terminal guanylate moiety of mature tRNAHis is added posttranscriptionally. To determine whether the same mechanism occurs in procaryotes, we processed in vitro-derived Escherichia coli tRNAHis precursors to mature tRNA, either in E. coli extracts or by using pure M1-RNA, the catalytic component of RNase P. The results show that the extra guanylate at the 5' end of mature E. coli tRNAHis is encoded in the gene and is found in tRNA as the result of an unusual cleavage by RNase P.

Processing of precursor tRNAs in Drosophila. Processing of the 3' end involves an endonucleolytic cleavage and occurs after 5' end maturation

Transfer RNA biosynthesis is a complex process which includes size trimming and nucleotide modification of an initial tRNA precursor. We have examined the temporal order and the nature of tRNA processing events in a Drosophila in vitro transcription/processing system using Drosophila tRNA genes as templates. RNA sequence analysis of processing products indicates that processing at both 5' and 3' ends occurs by endonucleolytic cleavage. The time course of processing of an initial tRNA precursor to mature tRNA reveals that trimming at the 5' end precedes 3' end maturation.

Structure and transcription of eukaryotic tRNA genes

The availability of cloned tRNA genes and a variety of eukaryotic in vitro transcription systems allowed rapid progress during the past few years in the characterization of signals in the DNA-controlling gene transcription and in the processing of the precurser RNAs formed. This will be the subject matter discussed in this review.