Toward cloning and mapping the genome of Drosophila

Detection of Bitter Taste Molecules Based on Odorant-Binding Protein-Modified Screen-Printed Electrodes

Bitter taste substances commonly represent a signal of toxicity. Fast and reliable detection of bitter molecules improves the safety of foods and beverages. Here, we report a biosensor using an easily accessible and cost-effective odorant-binding protein (OBP) of Drosophila melanogaster as a biosensitive material for the detection of bitter molecules. Based on the theoretical evaluation of the protein-ligand interaction, binding energies between the OBP and bitter molecules were calculated via molecular docking for the prediction and verification of binding affinities. Through one-step reduction, gold nanoparticles (AuNPs) and reduced graphene oxide (rGO) were deposited on the screen-printed electrodes for improving the electrochemical properties of electrodes. After the electrodes were immobilized with OBPs via layer-by-layer self-assembly, typical bitter molecules, such as denatonium, quinine, and berberine, were investigated through electrochemical impedance spectroscopy. The bitter molecules showed significant binding properties to the OBP with linear response concentrations ranging from 10^-9 to 10^-6 mg/mL. Therefore, the OBP-based biosensor offered powerful analytic techniques for the detection of bitter molecules and showed promising applications in the field of bitter taste evaluation.

Initial stage of genetic mapping inCiona intestinalis

The use of classic genetics is emerging in the ascidian Ciona intestinalis; recent advances in genomics and high-quality developmental and evolutionary studies have made this animal an attractive model for research purposes. Genetic mapping in Ciona will likely make a major contribution to ascidian genomics and developmental biology by providing support for genome assembly and annotation and for the isolation of genes with particular mutations, while construction of genetic maps advances classic genetics in this species. Two major issues must be overcome before fine genetic maps can be constructed: the choice of proper genetic backgrounds and the establishment of laboratory strains. A high degree of polymorphism is useful for genetic mapping if we consider particular combinations of genetic backgrounds and techniques, although it is necessary to pay attention to the confused classification of C. intestinalis. Thus, it is preferred to establish laboratory strains instead of using samples with various genetic backgrounds. As these issues are unresolved, only amplified fragment length polymorphism-based maps have been created, while bulk segregant analysis is expected to isolate markers flanking mutant loci. However, rich genomic resources should facilitate the next stage of genetic map construction based on type I markers using coding sequences. The meiotic events that occur in crossing experiments for mapping purposes should shed light on population genetics and speciation issues. The results of such investigations may provide feedback for comparative genomics and developmental genetics in the near future.

Primary genetic linkage maps of the ascidian, Ciona intestinalis

For whole-genome analysis in a basal chordate (protochordate), we used F1 pseudo-testcross mapping strategy and amplified fragment length polymorphism (AFLP) markers to construct primary linkage maps of the ascidian tunicate Ciona intestinalis. Two genetic maps consisted of 14 linkage groups, in agreement with the haploid chromosome number, and contained 276 and 125 AFLP loci derived from crosses between British and Neapolitan individuals. The two maps covered 4218.9 and 2086.9 cM, respectively, with an average marker interval of 16.1 and 18.9 cM. We observed a high recombinant ratio, ranging from 25 to 49 kb/cM, which can explain the high degree of polymorphism in this species. Some AFLP markers were converted to sequence tagged sites (STSs) by sequence determination, in order to create anchor markers for the fragmental physical map. Our recombination tools provide basic knowledge of genetic status and whole genome organization, and genetic markers to assist positional cloning in C. intestinalis.

First-generation linkage map of the warningly colored butterfly Heliconius erato

We report the first genetic linkage map of Heliconius erato, a species that shows remarkable variation in its warningly colored wing patterns. We use crosses between H. erato and its sister species, H. himera, to place two major color pattern genes, D and Cr, on a linkage map containing AFLP, allozyme, microsatellite and single-copy nuclear loci. We identified all 21 linkage groups in an initial genetic screen of 22 progeny from an F1 female x male H. himera family. Of the 229 markers, 87 used to identify linkage groups were also informative in 35 progeny from a sibling backcross (H. himera female x F1 male). With these, and an additional 33 markers informative in the second family, we constructed recombinational maps for 19 of the 21 linkage groups. These maps varied in length from 18.1 to 431.1 centimorgans (cM) and yielded an estimated total length of 2400 cM. The average distance between markers was 23 cM, and eight of the 19 linkage groups, including the sex chromosome (Z) and the chromosome containing the Cr locus, contained two or more codominant anchor loci. Of the three potential candidate genes mapped here, Cubitus interruptus (Ci), Decapentaplegic (Dpp) and Wingless (Wg), only Ci was linked, although loosely, to a known Heliconius color pattern locus. This work is an important first step for constructing a denser genetic map of the H. erato color pattern radiation and for a comparative genomic study of the architecture of mimicry in Heliconius butterflies.

Electron microscopic analysis of the banding pattern in the salivary gland chromosomes of Drosophila melanogaster. Divisions 11 through 20 of X

The banding pattern of the proximal half of the polytene salivary gland X chromosome of Drosophila melanogaster was studied using thin section electron microscopy. The bands were identified according to Bridges' revised light microscopic map. On Bridges' map, the divisions 11 to 20 contain 112 single bands and as many as 181 double bands. A majority of Bridges' single bands were identified in the thin sections. A total of 23 Bridges' single bands (and 4 bands of division 20) could not be found; in particular, bands were missing from the difficult regions 11DE, 15A, 15C and 16A. Electron microscopy showed the existence of 18 additional faint bands, 4 at the region 18D and 7 at 19EF. Bridges' faintest single bands and the new bands were best seen in formaldehyde fixed material. About 1/4 of Bridges' double bands were found to be made up of two separate bands each. The remaining Bridges' doublets include all kinds of bands: broad, narrow, dark, faint, puffed. Many of them look single in thin sections.

Electron micrograph map of the Drosophila melanogaster polytene chromosome 3R divisions 91 through 100

The banding pattern of the distal half of the polytene salivary gland 3R chromosome of Drosophila melanogaster was studied by means of the thin section electron microscopy. Bands were identified according to the revised light microscopic map of Bridges. Bridges' map contains 332 single bands and 137 double bands within the region 91 through 100. This makes a total of 606 bands when the doublets are counted as two bands each, but 469 bands when the doublets are counted as one band. In the electron micrographs we found a total of 443 bands within this region. 109 Bridges' singlets were easily detected in almost all thin sections, while 144 mainly faint bands could be seen only in some micrographs. 79 Bridges' single bands and one doublet (94D7-8) could not be found. 42 Bridges' doublets were made up of two separate bands each, 87 Bridges' doublets looked single, and three pairs of Bridges' doublets formed dark complexes in the thin sections. The telomere region with the most distal band 100F4-5 was gray. A total of 15 new bands, which are not drawn on Bridges' map, were detected. Most of the new bands were in the divisions 96 and 99.

Fine scale mapping in the sex locus region of the honey bee (Apis mellifera)

Isolating an unknown gene with fine-scale mapping is possible in a "non-model" organism. Sex determination in honey bees consists of a single locus (sex locus) with several complementary alleles. Diploid females are heterozygous at the sex locus, whereas haploid males arise from unfertilized eggs and are hemizygous. The construction of specific inbred crosses facilitates fine scale mapping in the sex locus region of the honey bee. The high recombination rate in the honey bee reduces the physical distance between markers compared with model organisms and facilitates a novel gene isolation strategy based on step-wise creation of new markers within small physical distances. We show that distances less than 25 kb can be efficiently mapped with a mapping population of only 1000 individuals. The procedure described here will accelerate the mapping, analysis and isolation of honey bee genes.

Unusually high recombination rate detected in the sex locus region of the honey bee (Apis mellifera)

Sex determination in Hymenoptera is controlled by haplo-diploidy in which unfertilized eggs develop into fertile haploid males. A single sex determination locus with several complementary alleles was proposed for Hymenoptera [so-called complementary sex determination (CSD)]. Heterozygotes at the sex determination locus are normal, fertile females, whereas diploid zygotes that are homozygous develop into sterile males. This results in a strong heterozygote advantage, and the sex locus exhibits extreme polymorphism maintained by overdominant selection. We characterized the sex-determining region by genetic linkage and physical mapping analyses. Detailed linkage and physical mapping studies showed that the recombination rate is <44 kb/cM in the sex-determining region. Comparing genetic map distance along the linkage group III in three crosses revealed a large marker gap in the sex-determining region, suggesting that the recombination rate is high. We suggest that a "hotspot" for recombination has resulted here because of selection for combining favorable genotypes, and perhaps as a result of selection against deleterious mutations. The mapping data, based on long-range restriction mapping, suggest that the Q DNA-marker is within 20,000 bp of the sex locus, which should accelerate molecular analyses.

Insect pheromones--an overview of biosynthesis and endocrine regulation

This overview describes, compares, and attempts to unify major themes related to the biosynthetic pathways and endocrine regulation of insect pheromone production. Rather than developing and dedicating an entirely unique set of enzymes for pheromone biosynthesis, insects appear to have evolved to add one or a few tissue-specific auxiliary or modified enzymes that transform the products of "normal" metabolism to pheromone compounds of high stereochemical and quantitative specificity. This general understanding is derived from research on model species from one exopterygote insect order (Blattodea) and three endopterygote insect orders (Coleoptera, Diptera, and Lepidoptera). For instance, the ketone hydrocarbon contact sex pheromone of the female German cockroach, Blattella germanica, derives its origins from fatty acid biosynthesis, arising from elongation of a methyl-branched fatty acyl-CoA moiety followed by decarboxylation, hydroxylation, and oxidation. Coleopteran sex and aggregation pheromones also arise from modifications of fatty acid biosynthesis or other biosynthetic pathways, such as the isoprenoid pathway (e.g. Cucujidae, Curculionidae, and Scolytidae), or from simple transformations of amino acids or other highly elaborated host precursors (e.g. Scarabaeidae and Scolytidae). Like the sex pheromone of B. germanica, female-produced dipteran (e.g. Drosophilidae and Muscidae) sex pheromone components originate from elongation of fatty acyl-CoA moieties followed by loss of the carbonyl carbon and the formation of the corresponding hydrocarbon. Female-produced lepidopteran sex pheromones are also derived from fatty acids, but many moths utilize a species-specific combination of desaturation and chain-shortening reactions followed by reductive modification of the carbonyl carbon. Carbon skeletons derived from amino acids can also be used as chain initiating units and elongated to lepidopteran pheromones by this pathway (e.g. Arctiidae and Noctuidae). Insects utilize at least three hormonal messengers to regulate pheromone biosynthesis. Blattodean and coleopteran pheromone production is induced by juvenile hormone III (JH III). In the female common house fly, Musca domestica, and possibly other species of Diptera, it appears that during hydrocarbon sex pheromone biosynthesis, ovarian-produced ecdysteroids regulate synthesis by affecting the activities of one or more fatty acyl-CoA elongation enzyme(s) (elongases). Lepidopteran sex pheromone biosynthesis is often mediated by a 33 or 34 amino acid pheromone biosynthesis activating neuropeptide (PBAN) through alteration of enzyme activities at one or more steps prior to or during fatty acid synthesis or during modification of the carbonyl group. Although a molecular level understanding of the regulation of insect pheromone biosynthesis is in its infancy, in the male California fivespined ips, Ips paraconfusus (Coleoptera: Scolytidae), JH III acts at the transcriptional level by increasing the abundance of mRNA for 3-hydroxy-3-methylglutaryl-CoA reductase, a key enzyme in de novo isoprenoid aggregation pheromone biosynthesis.

Loss of the tight junction MAGUK ZO-1 in breast cancer: relationship to glandular differentiation and loss of heterozygosity

Membrane-associated guanylate kinase homologs (MAGUKs) may play a role in cellular functions preventing tumorigenesis as indicated by the neoplastic phenotype caused by genetic loss of the MAGUK Dlg in Drosophila. To test this possibility, we examined the expression and subcellular localization of the tight junction MAGUK ZO-1, as well as the cell adhesion molecule E-cadherin, in paraffin-embedded breast cancer samples, using immunohistochemistry and confocal microscopy. As expected, normal tissue showed intense staining for ZO-1 at the position of the epithelial tight junctions, but this staining was reduced or lost in 69% of breast cancers analyzed (n = 48). In infiltrating ductal carcinomas (n = 38) there was a reduction in staining in 42% of well differentiated, in 83% of moderately differentiated and 93% of poorly differentiated tumors. ZO-1 staining was positively correlated with tumor differentiation (P = .011) and more specifically with the glandular differentiation of tumors (P = .0019). Reduction in ZO-1 staining was strongly correlated with reduced E-cadherin staining (P = 4.9 x 10(-5)). The results suggest that down-regulation of ZO-1 expression and its failure to accumulate at cell junctions may be causally related to cancer progression. To detect loss of heterozygosity, the ZO-1 gene tjp-1 was mapped relative to other markers in 15q13 and polymorphic markers flanking tjp-1 were identified. The marker D15S1019 showed loss of heterozygosity in 23% of informative tumors (n = 13). Loss of a tjp-1-linked marker suggests that genetic loss may, in some cases, be responsible for the reduction in ZO-1 expression in breast cancer.

A dense genetic map of the silkworm, Bombyx mori, covering all chromosomes based on 1018 molecular markers

A dense linkage map was constructed for the silkworm, Bombyx mori, containing 1018 genetic markers on all 27 autosomes and the Z chromosome. Most of the markers, covering approximately 2000 cM, were randomly amplified polymorphic DNAs amplified with primer-pairs in combinations of 140 commercially available decanucleotides. In addition, eight known genes and five visible mutations were mapped. Bombyx homologues of engrailed and invected genes were found to be closely linked, as in Drosophila melanogaster. The average interval between markers was approximately 2 cM, equal to approximately 500 kb. The correspondence of seven linkage groups to counterparts of the conventional linkage map was determined. This map is the first linkage map in insects having a large number of chromosomes (n = 28) that covers all chromosomes without any gaps.

Lufenuron, a chitin-synthesis inhibitor, interrupts development of Drosophila melanogaster

The chitin-synthesis inhibitor lufenuron was administered to Drosophila melanogaster to better understand the effects of chitin-synthesis interruption during the development and reproduction of this insect. When larvae were fed a diet containing a low concentration (< 1 ppm) of lufenuron, mortality was observed during either larval or pupal development, depending on the dose. Survivor adults were unable to fly, probably due to abnormal cuticular development in the wing hinge regions of the thorax. Larvae fed a higher concentration (10 ppm) completed development within that instar, but died during ecdysis to the next instar, presumably due to inadequate cuticle synthesis. Third instar larvae pupariated, but the puparium was abnormal, and pupation did not occur. Adults fed 10 ppm showed normal viability but slightly depressed oogenesis; additionally, although their eggs were fertilized, they failed to hatch. Examination of the embryos showed that they completed development but were unable to perforate the surrounding vitelline membrane, probably due to a weakened chitinous mouth hook assembly that was insufficiently rigid to effect hatching. These results identify stages during D. melanogaster development when chitin synthesis and deposition are critical. This information will be useful for identifying chitin-synthesis mutants of this insect.

Genetic dissection of sexual orientation: behavioral, cellular, and molecular approaches in Drosophila melanogaster

Insertional mutagenesis using P-element vectors yielded several independent mutations that cause male homosexuality in Drosophila melanogaster. Subsequent analyses revealed that all of these insertions were located at the same chromosomal division, 91B, where one of the inversion breakpoints responsible for the bisexual phenotype of the fruitless (fru) mutant has been mapped. In addition to the altered sexual orientation, the fru mutants displayed a range of defects in the formation of a male-specific muscle, the muscle of Lawrence. Since the male-specific formation of this muscle was dependent solely on the sex of the innervating nerve and not on the sex of the muscle itself, the primary site of action of the fru gene should be in the neural cells. satori, one of the P-insertion alleles of fru which we isolated, carried the lacZ gene of E. coli as a reporter, and beta-galactosidase expression was found in a subset of brain cells including those in the antennal lobe in the satori mutant. Targeted expression of a sex determination gene, transformer (tra), was used to produce chromosomally male flies with certain feminized glomeruli in the antennal lobe. Such sexually mosaic flies courted not only females but also males when the DM2, DA3 and DA4 glomeruli were feminized, indicating that these substructures in the antennal lobe may be involved in the determination of the sexual orientation of flies. Molecular cloning and analyses of the genomic and complementary DNAs indicated that transcription of the fru locus yields several different transcripts, one of which encodes a putative transcription regulator with a BTB domain and two zinc finger motifs. In the 5' non-coding region, three putative Transformer binding sites were identified. It appears plausible therefore that the fru gene is one of the elements in the sex determination cascade that controls sexual fates of certain neuronal cells. Improper sex determination in these neural cells may lead to altered sexual orientation and malformation of the male-specific muscle. Some implications of the results of our study on sexual orientation in other organisms will be discussed based on the Drosophila research.

Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching

Cross-species comparison is an effective tool used to identify genes and study their function in both normal and pathological conditions. We have applied the power of Drosophila genetics to the vast resource of human cDNAs represented in the expressed sequence tag (EST) database (dbEST) to identify novel human genes of high biological interest. Sixty-six human cDNAs showing significant homology to genes causing Drosophila mutant phenotypes were identified by screening dbEST using the "text string' option, and their map position was determined using both fluorescence in situ hybridization (FISH) and radiation hybrid mapping. Comparison between these genes and their putative partners in Drosophila may provide important insights into their function in mammals. Furthermore, integration of these genes into the transcription map of the human genome contributes to the positional candidate approach for disease gene identification.

The PIR-International Protein Sequence Database

From its origin the Protein Sequence Database has been designed to support research and has focused on comprehensive coverage, quality control and organization of the data in accordance with biological principles. Since 1988 the database has been maintained collaboratively within the framework of PIR-International, an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. The database is widely distributed and is available on the World Wide Web, via ftp, email server, on CD-ROM and magnetic media. It is widely redistributed and incorporated into many other protein sequence data compilations, including SWISS-PROT and the Entrez system of the NCBI.

The DRE sequence TATCGATA, a putative promoter-activating element for Drosophila melanogaster cell-proliferation-related genes

We have confirmed that the DNA replication-related element (DRE) consisting of an 8-bp palindrome, TATCGATA, and not neighboring sequences, are responsible for activating promoters of the Drosophila melanogaster (Dm) PCNA (proliferating cell nuclear antigen)- and DNA polymerase alpha-encoding genes in both cultured cell and transgenic fly systems. We have so far found 153 copies of DRE in the Dm gene database. 73 of them are concentrated within the 600-bp upstream regions from the transcription start points of 61 genes. Interestingly, many of these genes are involved in either DNA replication, transcription, translation, signal transduction, cell cycle or other putative regulatory functions, and are possibly related to cell proliferation. It seems likely that DRE is an element common to the regulation of cell-proliferation-related genes, although their expression patterns may be different depending on which of regulatory elements other than the DRE are combined.

Genome structure and evolution in Drosophila: applications of the framework P1 map

Physical maps showing the relative locations of cloned DNA fragments in the genome are important resources for research in molecular genetics, genome analysis, and evolutionary biology. In addition to affording a common frame of reference for organizing diverse types of genetic data, physical maps also provide ready access to clones containing DNA sequences from any defined region of the genome. In this paper, we present a physical map of the genome of Drosophila melanogaster based on in situ hybridization with 2461 DNA fragments, averaging approximately 80 kilobase pairs each, cloned in bacteriophage P1. The map is a framework map in the sense that most putative overlaps between clones have not yet been demonstrated at the molecular level. Nevertheless, the framework map includes approximately 85% of all genes in the euchromatic genome. A continuous physical map composed of sets of overlapping P1 clones (contigs), which together span most of the euchromatic genome, is currently being assembled by screening a library of 9216 P1 clones with single-copy genetic markers as well as with the ends of the P1 clones already assigned positions in the framework map. Because most P1 clones from D. melanogaster hybridize in situ with chromosomes from related species, the framework map also makes it possible to determine the genome maps of D. pseudoobscura and other species in the subgenus Sophophora. Likewise, a P1 framework map of D. virilis affords potential access to genome organization and evolution in the subgenus Drosophila.

Genome evolution: between the nucleosome and the chromosome

Intermediate between DNA sequences and broad patterns of karyotypic change there is a major gap in understanding genome structure and evolution. The gap is at the megabase level between genes and chromosomes. New methods for analyzing large DNA fragments cloned in yeast or bacterial vectors provide experimental access to genome evolution at the megabase level by enabling the assembly of megabase-size contiguous regions. Genome evolution at the megabase level can also be studied using high-resolution genetic maps. Rates and patterns of genome evolution in mammals (mouse versus humans) and Drosophila (D. virilis versus D. melanogaster) are compared and contrasted. Opportunities for research in genome evolution using the new technologies are enumerated and discussed.

Monoclonal antibodies directed against human tumor-associated antigens cross-react with Drosophila proteins in clusters

We reacted the Third International IASLC Workshop panel of monoclonal antibodies (MAbs) directed against human lung-tumor-associated epitopes with nitrocellulose blots of total proteins from adult fruit flies. Out of 63 MAbs tested, 9 showed a significant reaction with Drosophila proteins. Interestingly, in a double-blind analysis, most of the positive reactions fell into clusters that parallel the antibody reactivities against human tissues. In light of our findings, it becomes possible to screen expression vector libraries in order to isolate Drosophila cDNA that may have homology with human tumor-associated antigens.

The salivary gland chromosomes of Drosophila virilis: a cytological map, pattern of transcription and aspects of chromosome evolution

By combining information from microscopical observation and photography a graphical map of Drosophila virilis salivary gland chromosomes was constructed. About 1,560 individual bands are shown and patterns of transcription at about 360 sites are indicated. The application of the map is demonstrated by using genetic, morphological and in situ hybridization data to identify the white-Notch regions of D. virilis and Drosophila melanogaster as homologous chromosome segments with constant and variable features.

Use of reference libraries and hybridisation fingerprinting for relational genome analysis

The concept of relational genome analysis by hybridisation has been developed into a working system. Various genomic and cDNA libraries have been generated and are distributed via a reference system. Analysis procedures have been tested successfully in the mapping of the entire Schizosaccharomyces pombe genome. In another test-case for their refinement, analyses on the Drosophila genome are well under way. Human and mouse libraries are being studied on all levels, from generating YAC maps to partially sequencing representative cDNA libraries. The automation of the involved processes and the development of improved image detection and analysis are well advanced.

Molecules and cognition: the latterday lessons of levels, language, and lac. Evolutionary overview of brain structure and function in some vertebrates and invertebrates

The characteristics of the nervous systems of a number of organisms in different phyla are examined at the recombinant DNA, protein, neuroanatomic, neurophysiological, and cognitive levels. Among the invertebrates, special attention is paid to the advantages as well as the shortcomings of the fly Drosophila melanogaster, the worm Caenorhabditis elegans, the honey bee Apis mellifera, the sea hare Aplysia californica, the octopus Octopus vulgaris, and the squid Loligo pealei. Among vertebrates, the focus is on Homo sapiens, the mouse Mus musculus, the rat Rattus norvegicus, the cat Felis catus, the macaque monkey Macaca fascicularis, the barn owl Tyto alba, and the zebrafish Brachydanio rerio. Vertebrate nervous systems have also been compared in fossil vs. extant organisms. I conclude that complex nervous systems arose in the Early Cambrian via a big bang that was underpinned by a modular method of construction involving massive pleiotropy of gene circuits. This rapidity of construction had enormous implications for the degrees of freedom that were subsequently available to evolving nervous systems. I also conclude that at the level of neuronal populations and interactions of neuropiles there is no model system between phyla except at the basic macromolecular level. Further, I argue that to achieve a significant understanding of the functions of extant nervous systems we need to concentrate on fewer organisms in greater depth and manipulate genomes via transgenic technologies to understand the behavioral outputs that are possible from an organism. Finally, I analyze the concepts of "perceptual categorization" and "information processing" and the difficulties involved in the extrapolation of computer analogies to sophisticated nervous systems.

A combined molecular and cytogenetic approach to genome evolution in Drosophila using large-fragment DNA cloning

Methods of genome analysis, including the cloning and manipulation of large fragments of DNA, have opened new strategies for uniting molecular evolutionary genetics with chromosome evolution. We have begun the development of a physical map of the genome of Drosophila virilis based on large DNA fragments cloned in bacteriophage P1. A library of 10,080 P1 clones with average insert sizes of 65.8 kb, containing approximately 3.7 copies of the haploid genome of D. virilis, has been constructed and characterized. Approximately 75% of the clones have inserts exceeding 50 kb, and approximately 25% have inserts exceeding 80 kb. A sample of 186 randomly selected clones was mapped by in situ hybridization with the salivary gland chromosomes. A method for identifying D. virilis clones containing homologs of D. melanogaster genes has also been developed using hybridization with specific probes obtained from D. melanogaster by means of the polymerase chain reaction. This method proved successful for nine of ten genes and resulted in the recovery of 14 clones. The hybridization patterns of a sample of P1 clones containing repetitive DNA were also determined. A significant fraction of these clones hybridizes to multiple euchromatic sites but not to the chromocenter, which is a pattern of hybridization that is very rare among clones derived from D. melanogaster. The materials and methods described will make it possible to carry out a direct study of molecular evolution at the level of chromosome structure and organization as well as at the level of individual genes.

Use of recombinant inbred strains to map genes of aging

Recombinant inbred strains have been used in a number of organisms for segregation and linkage analysis of quantitative traits. One major advantage of the recombinant inbred (RI) methodology is that the genetic identity of individuals within a strain permits replicate measures of the same recombinant genotype. Such replicability is important for traits such as aging in Drosophila, where phenotypic expression is highly influenced by different environmental conditions. RI strain methodology has an added advantage for DNA marker-based linkage analysis of traits measured over the lifespan of the organism. The DNA can be extracted from individuals of the same genotype as those measured in a longevity study. In this paper an argument is presented for the use of a set of recombinant inbred strains to map the quantitative trait loci involved in the aging process in Drosophila. A unique use of a set of stable, transposable molecular markers to trace the quantitative trait loci involved is suggested.

The human genetic map

The introduction of new technology and increased effort from around the world is driving the completion of the human gene map. In parallel with the creation of the map, we are beginning to see the bio-medical benefits that are a direct consequence of learning more about our own genome.

The human genetic map

The introduction of new technology and increased effort from around the world is driving the completion of the human gene map. In parallel with the creation of the map, we are beginning to see the biomedical benefits that are a direct consequence of learning more about our own genome.

Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

Two genomic regions with unusually low recombination rates in Drosophila melanogaster have normal levels of divergence but greatly reduced nucleotide diversity, apparently resulting from the fixation of advantageous mutations and the associated hitch-hiking effect. Here we show that for 20 gene regions from across the genome, the amount of nucleotide diversity in natural populations of D. melanogaster is positively correlated with the regional rate of recombination. This cannot be explained by variation in mutation rates and/or functional constraint, because we observe no correlation between recombination rates and DNA sequence divergence between D. melanogaster and its sibling species, D. simulans. We suggest that the correlation may result from genetic hitch-hiking associated with the fixation of advantageous mutants. Hitch-hiking thus seems to occur over a large fraction of the Drosophila genome and may constitute a major constraint on levels of genetic variation in nature.

Towards a Drosophila genome map

A physical map of the genome of Drosophila melanogaster has been created using 965 yeast artificial chromosome (YAC) clones assigned to locations in the cytogenetic map by in situ hybridization with the polytene salivary gland chromosomes. Clones with insert sizes averaging about 200 kb, totaling 1.7 genome equivalents, have been mapped. More than 80% of the euchromatic genome is included in the mapped clones, and 75% of the euchromatic genome is included in 161 cytological contigs ranging in size up to 2.5 Mb (average size 510 kb). On the other hand, YAC coverage of the one-third of the genome constituting the heterochromatin is incomplete, and clones containing long tracts of highly repetitive simple satellite DNA sequences have not been recovered.