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At least 253 records · Page 14Linked to original sources
PubMed2004

Strategies of the home-team: symbioses exploited for vector-borne disease control.

Symbioses between eukaryotes and unicellular organisms are quite common, with examples copiously disseminated throughout the earth's biota. Arthropods, in particular, owe much of their ecological success to their microbial flora, which often provide supplements either lacking in the limited host diet or which the hosts are unable to synthesize. In addition to harboring beneficial microbes, many arthropods (vectors) also transmit pathogens to the animals and plants upon which they prey. Vector-borne diseases exact a high public health burden and additionally have a devastating impact on livestock and agriculture. Recent scientific discoveries have resulted in the development of powerful technologies for studying the vector's biology, to discover the weak links in disease transmission. One of the more challenging applications of these developments is transgenesis, which allows for insertion of foreign DNA into the insect's genome to modify its phenotype. In this review, we discuss an approach in which the naturally occurring commensal flora of insects are manipulated to express products that render their host environment inhospitable for pathogen transmission. Replacing susceptible insect genotypes with modified counterparts with reduced pathogen transmission ability, might provide a new set of armaments in the battle for vector-borne disease reduction.

Animals↗
PubMed2006

FlyBase: genomes by the dozen.

FlyBase (http://flybase.org/) is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied species in this family, but recent determination of the genomic sequences of an additional 11 Drosophila species opens up new avenues of research for other Drosophila species. This extensive sequence resource, encompassing species with well-defined phylogenetic relationships, provides a model system for comparative genomic analyses. FlyBase has developed tools to facilitate access to and navigation through this invaluable new data collection.

Animals↗
PubMed1993

The lepidopteran mitochondrial control region: structure and evolution.

For several species of lepidoptera, most of the approximately 350-bp mitochondrial control-region sequences were determined. Six of these species are in one genus, Jalmenus; are closely related; and are believed to have undergone recent rapid speciation. Recent speciation was supported by the observation of low interspecific sequence divergence. Thus, no useful phylogeny could be constructed for the genus. Despite a surprising conservation of control-region length, there was little conservation of primary sequences either among the three lepidopteran genera or between lepidoptera and Drosophila. Analysis of secondary structure indicated only one possible feature in common--inferred stem loops with higher-than-random folding energies--although the positions of the structures in different species were unrelated to regions of primary sequence similarity. We suggest that the conserved, short length of control regions is related to the observed lack of heteroplasmy in lepidopteran mitochondrial genomes. In addition, determination of flanking sequences for one Jalmenus species indicated (i) only weak support for the available model of insect 12S rRNA structure and (ii) that tRNA translocation is a frequent event in the evolution of insect mitochondrial genomes.

Animals↗
PubMed1993

Synthesis of functional GABAA receptors in stable insect cell lines.

We have synthesised the beta 1-subunit of the bovine GABAA receptor in stable, continuous insect (Spodoptera frugiperda) cell lines. A cDNA was integrated randomly into the insect cell genome under control of a baculovirus immediate early (IE-1) gene promoter. Transformed cells were obtained by co-transfection of the insect cells with pIEK1.GR beta 1, encoding the beta 1 subunit cDNA, and pIEK1.neo, encoding the neomycin resistance gene. G-418-resistant clones were selected and expanded into continuous cell lines synthesising functional, GABA-gated, homo-oligomeric chloride channels. These cell lines had significant advantages over the transient baculovirus expression system for the characterisation of receptors using electrophysiological recording techniques.

Animals↗
PubMed2003

Cassette vectors for conversion of Fab fragments into full-length human IgG1 monoclonal antibodies by expression in stably transformed insect cells.

Phage display technology allows for the production and rapid selection of antigen-specific, Fab antibody fragments. For purposes of immune therapy, though, complete antibodies that retain the Fc domain are often required. In this regard, we designed cassette vectors for converting human Fab fragments selected from combinatorial phage display libraries into full-length IgG(1) monoclonal antibodies (MAbs). Two expression vectors, pIEI-Light and pIEI-Heavy, were engineered to contain respective light- and heavy-chain human signal sequences downstream of the baculovirus immediate early gene promoter, IEI. Vector pIEI-Heavy also contains the coding region for each of the human IgG(1) constant domains. To generate complete antibody genes, the cassette vectors possess convenient restriction enzyme sites for rapid in-frame cloning of coding regions for full-length light chains in pIEI-Light and for the heavy-chain variable domains in pIEI-Heavy of Fab fragments. Using these constructs and a method that allows for stable transformation of insect cells, complete light- and heavy-chain genes can be inserted into the insect cell genome and subsequently expressed under the control of the baculovirus IEI promoter. This cassette vector system was used to generate stably transformed insect cells that continuously secreted functional full-length, IgG(1) MAbs. The expressed antibodies exhibited light and heavy chains of the appropriate molecular sizes and retained the ability to bind antigen. We conclude that our cassette vectors could serve as valuable tools for generating human IgG(1) antibodies.

Amino Acid Sequence↗
PubMed1994

Genetic manipulation of insect vectors as a strategy for the control of vector-borne disease.

A variety of very effective methods have been employed for suppressing insect vector populations, including the application of biological control agents and the elimination of breeding sites, with a continuing and heavy reliance on the use of chemical insecticides. However, the development of insecticide resistance by vector insects, the cost of developing and registering new insecticidal compounds, and the increase in legislation to combat the detrimental effects of insecticidal residues on the environment, have emphasized the need to assess alternative strategies for vector control. What is required is a completely novel approach to either suppress vector populations, or to alter their ability to transmit disease-causing organisms in such a way as to have a profound and long-lasting effect on disease transmission. Genetic manipulation of insect vectors may provide just such an approach. The major requirements for genome manipulation in insects and the progress which has been made to create transgenic vector insects are reviewed. The potential applications of this methodology are then explored in the context of its future use for the control of vector-borne diseases.

Animals↗
PubMed2003

The Drosophila melanogaster genome sequencing and annotation projects: a status report.

The sequence and genome annotations of Drosophila melanogaster were initially published in late 1999 and early 2000. Since then, the Berkeley Drosophila Genome Project (BDGP) and FlyBase have improved the quality of the sequence and reviewed the annotations by hand, respectively, to produce an account of the fruit fly genome that is of the highest quality. This review discusses the main features of this process, both from the point of view of the biology revealed in the end result and in the development of software that has been central to this genome sequencing and annotation project.

Animals↗
PubMed2004

A draft sequence for the genome of the domesticated silkworm (Bombyx mori).

We report a draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes. Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content.

Algorithms↗
PubMed1998

Characterization of the P25 silk gene and associated insertion elements in Galleria mellonella.

Insect silk genes attract attention by their precise territorial and developmental regulations and extremely high expression rates. Our present investigations demonstrated that the P25 silk gene of Galleria mellonella is down-regulated by ecdysteroid hormones. The gene was identified within 5217 nucleotides (nt) of two genomic clones. In contrast to other silk genes, Galleria P25 lacks the canonical TATA box. Transcription is initiated within a region of three nucleotides that lie at the end of a capsite initiator sequence ACAGT and about 90 nt downstream from a CAAT box. A stretch of 32 nt with a core sequence CTTTT was detected in the 5' region of Galleria P25 as well as in the presumptive regulatory regions of all other silk genes that are expressed in the posterior silk gland. However, consensus sequences reported for the regulatory regions of Bombyx silk genes are not obvious in Galleria P25. The coding sequence of this gene included 654 nt, is interrupted by 4 introns, and ends in position +3369; a potential polyadenylation signal starts at +4382. The gene contains 3 copies of a short interspersed nuclear element (SINE), which are located in the upstream region (-833 to -579) and in the first (+542 to +840) and second (+2259 to +2556) introns. The repeat, which was named Gm1, occurs in some other Galleria genes and exhibits homology to Bm1 SINE of the silkworm and to a similar element of a spider. Another insertion of at least 150 nt and with loosely defined borders is present in the 3' untranslated region (UTR) of Galleria P25. It includes a box (+3453 to +3552) of 99 nt that is tentatively called Lep1 because it was disclosed also in some other Lepidoptera. Lep1 seems to represent the core region of insertion elements that occur in the genomes of lepidopteran insects in various species specific and region specific modifications.

Amino Acid Sequence↗
PubMed2007

Biosynthesis of the 2-pyridone tenellin in the insect pathogenic fungus Beauveria bassiana.

Genomic DNA from the insect pathogenic fungus Beauveria bassiana was used as a template in a PCR with degenerate primers designed to amplify a fragment of a C-methyl transferase (CMeT) domain from a highly reduced fungal polyketide synthase (PKS). The resulting 270-bp PCR product was homologous to other fungal PKS CMeT domains and was used as a probe to isolate a 7.3-kb fragment of genomic DNA from a BamH1 library. Further library probing and TAIL-PCR then gave a 21.9-kb contig that encoded a 12.9-kb fused type I PKS-NRPS ORF together with ORFs encoding other oxidative and reductive enzymes. A directed knockout experiment with a BaR cassette, reported for the first time in B. bassiana, identified the PKS-NRPS as being involved in the biosynthesis of the 2-pyridone tenellin. Other fungal PKS-NRPS genes are known to be involved in the formation of tetramic acids in fungi, and it thus appears likely that related compounds are precursors of 2-pyridones in fungi. B. bassiana tenellin KO and WT strains proved to be equally pathogenic towards insect larvae; this indicated that tenellin is not involved in insect pathogenesis.

Amino Acid Sequence↗
PubMed2006

Sequence analysis and quantification of transposase cDNAs of transposon TCp3.2 in Cydia pomonella larvae.

The Tc1-like transposable element TCp3.2 was previously found to be horizontally transferred from the genome of Cydia pomonella to the C. pomonella granulovirus (CpGV). In this study, the transcription of transposase genes of endogenous TCp3.2 copies in the insect host genome was investigated. Cloning and sequencing of cDNAs prepared from TCp3.2 transposase transcripts resulted in the identification of a 199-bp-long intron. Sequence heterogeneities among different cDNA clones suggested that multiple copies of the transposase are transcribed, but that a part of these copies encode a defective transposase. The actin gene of C. pomonella was cloned and sequenced, and used to standardise quantitative real time PCR on prepared cDNA of the TCp3.2 transposase. Comparison of cDNA levels of TCp3.2 transposase prepared from mock and CpGV-infected C. pomonella larvae did not provide evidence that CpGV infection influenced the transcription level of TCp3.2 transposase.

Amino Acid Sequence↗
PubMed2026

Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.

The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb (A. andreniformis) and 4.3 Mb (A. florea), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% using the Hymenoptera database and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content (∼6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,189 genes for A. andreniformis and 12,207 genes for A. florea, with ∼98% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, with the potential to offer new insights into the genetic basis of dwarf honey bee adaptations.

Male↗
PubMed2002

Programmed cell death takes flight: genetic and genomic approaches to gene discovery in Drosophila.

Programmed cell death (PCD) is an essential and wide-spread physiological process that results in the elimination of cells. Genes required to carry out this process have been identified, and many of these remain the subjects of intense investigation. Here, we describe PCD, its functions, and some of the consequences when it goes awry. We review PCD in the model system, the fruit fly, Drosophila melanogaster, with a particular emphasis on cell death gene discovery resulting from both genetics and genomics-based approaches.

Animals↗
PubMed2003

How many genes in a genome?

Despite the current good level of annotation, the Drosophila genome still holds surprises. A recent study has added perhaps 2,000 genes to the predicted total, and raises a number of questions about how genome annotation data should be stored and presented.

Animals↗
PubMed2004

Assessing the relative rate of (mitochondrial) genomic change.

I report a framework for assessing whether one mitochondrial genome is significantly more rearranged than another. This relative rate of gene rearrangement test (RGR) behaves according to expectation, distinguishing between highly rearranged and mildly rearranged insect mitochondrial genomes. It may be more broadly applied to assess the relative rate of nuclear gene rearrangement.

Animals↗
PubMed2000

The distribution of genes in the Drosophila genome.

In the present work we show that in the Drosophila genome (which covers a 37-51% GC range at a DNA size of approx.50kb) a linear correlation holds between GC (or GC(3)50kb) genomic sequences embedding them. This correlation allows us to position the two compositional distributions of (a) coding sequences, and (b) of long DNA segments relative to each other and to calculate gene concentration across the compositional range of the Drosophila genome. Using this approach, we show that gene concentration increases with increasing GC of the regions embedding the genes, reaching a 7-fold higher level in the GC-richest regions compared with the GC-poorest regions. The gene distribution of the Drosophila genome is, therefore, similar to (although less striking than) that of the human genome, whereas it is very different from those of the Arabidopsis genome, which has about the same size as the Drosophila genome.

Animals↗
PubMed2004

The Ensembl automatic gene annotation system.

As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, and EST sequences. The gene-building system rests on top of the core Ensembl (MySQL) database schema and Perl Application Programming Interface (API), and the data generated are accessible through the Ensembl genome browser (http://www.ensembl.org). To date, the Ensembl predicted gene sets are available for the A. gambiae, C. briggsae, zebrafish, mouse, rat, and human genomes and have been heavily relied upon in the publication of the human, mouse, rat, and A. gambiae genome sequence analysis. Here we describe in detail the gene-building system and the algorithms involved. All code and data are freely available from http://www.ensembl.org.

Animals↗