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At least 127 records · Page 7Linked to original sources
PubMed2006

Estimating the genomewide rate of adaptive protein evolution in Drosophila.

When polymorphism and divergence data are available for multiple loci, extended forms of the McDonald-Kreitman test can be used to estimate the average proportion of the amino acid divergence due to adaptive evolution--a statistic denoted alpha. But such tests are subject to many biases. Most serious is the possibility that high estimates of alpha reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in alpha is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of alpha from the same model organisms have also varied widely. This study clarifies the reasons for these discrepancies, identifying several method-specific biases in widely used estimators and assessing the power of the methods. As part of this process, a new maximum-likelihood estimator is introduced. This estimator is applied to a newly compiled data set of 115 genes from Drosophila simulans, each with each orthologs from D. melanogaster and D. yakuba. In this way, it is estimated that alpha approximately 0.4+/-0.1, a value that does not vary substantially between different loci or over different periods of divergence. The implications of these results are discussed.

Adaptation, Physiological↗
PubMed2005

Quality of transgenic laboratory strains of Cochliomyia hominivorax (Diptera: Calliphoridae).

Genetically modified, mass reared insects present novel possibilities for the future of insect control. One concern about manipulation of insects is a possible loss of strain quality due to the introduction of a foreign gene of any sort into the insect genome. Eight transgenic strains of screwworm, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), were compared with the wild-type parental laboratory strain in laboratory culture. Measurements of average fertility, fecundity, larval productivity, and longevity were analyzed. Two transgenic strains had significantly lower larval productivity than controls, one of which was explained by a homozygous lethal insertion of the transgene. Another strain produced significantly fewer eggs than controls. Overall strain characteristics, including measurements from egg, larva, pupa, and adult stages, were compared. Transgenic colonies did not consistently show significantly lower individual or aggregate strain quality characteristics than the control parental colony; hence, the presence of the transgene used to produce the strains tested did not incur a discrete cost to the colonies of laboratory-reared C. hominivorax.

Animals↗
PubMed2006

Sequencing a new target genome: the Boophilus microplus (Acari: Ixodidae) genome project.

The southern cattle tick, Boophilus microplus (Canestrini), causes annual economic losses in the hundreds of millions of dollars to cattle producers throughout the world, and ranks as the most economically important tick from a global perspective. Control failures attributable to the development of pesticide resistance have become commonplace, and novel control technologies are needed. The availability of the genome sequence will facilitate the development of these new technologies, and we are proposing sequencing to a 4-6X draft coverage. Many existing biological resources are available to facilitate a genome sequencing project, including several inbred laboratory tick strains, a database of approximately 45,000 expressed sequence tags compiled into a B. microplus Gene Index, a bacterial artificial chromosome (BAC) library, an established B. microplus cell line, and genomic DNA suitable for library synthesis. Collaborative projects are underway to map BACs and cDNAs to specific chromosomes and to sequence selected BAC clones. When completed, the genome sequences from the cow, B. microplus, and the B. microplus-borne pathogens Babesia bovis and Anaplasma marginale will enhance studies of host-vector-pathogen systems. Genes involved in the regeneration of amputated tick limbs and transitions through developmental stages are largely unknown. Studies of these and other interesting biological questions will be advanced by tick genome sequence data. Comparative genomics offers the prospect of new insight into many, perhaps all, aspects of the biology of ticks and the pathogens they transmit to farm animals and people. The B. microplus genome sequence will fill a major gap in comparative genomics: a sequence from the Metastriata lineage of ticks. The purpose of the article is to synergize interest in and provide rationales for sequencing the genome of B. microplus and for publicizing currently available genomic resources for this tick.

Animals↗
PubMed2005

A new domain family in the superfamily of alkaline phosphatases.

During the course of our large-scale genome analysis a conserved domain, currently detectable only in the genomes of Drosophila melanogaster, Caenorhabditis elegans and Anopheles gambiae, has been identified. The function of this domain is currently unknown and no function annotation is provided for this domain in the publicly available genomic, protein family and sequence databases. The search for the homologues of this domain in the non-redundant sequence database using PSI-BLAST, resulted in identification of distant relationship between this family and the alkaline phosphatase-like superfamily, which includes families of aryl sulfatase, N-acetylgalactosomine-4-sulfatase, alkaline phosphatase and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM). The fold recognition procedures showed that this new domain could adopt a similar 3-D fold as for this superfamily. Most of the phosphatases and sulfatases of this superfamily are characterized by functional residues Ser and Cys respectively in the topologically equivalent positions. This functionally important site aligns with Ser/Thr in the members of the new family. Additionally, set of residues responsible for a metal binding site in phosphatases and sulphtases are conserved in the new family. The in-depth analysis suggests that the new family could possess phosphatase activity.

Alkaline Phosphatase↗
PubMedDate not supplied

[The malaria mosquitoes (Diptera, Culicidae, Anopheles) of the Amudarya river valley].

Five malaria mosquitoes were identified in the Amudarya river valley. An. pulcherrimus, An. martinius, An. superpictus, and An. hyrcanus inhabit in the plain of the valley. An. superpictus, An. pulcherrimus, An. hyrcanus, and An. claviger occur in the head of the Amudarya river. The nucleotide composition of the second inner transcribed spacer (ITS2) of ribosomal DNA and the locus of cytochromoxidase I (COI) of mitochondrial DNA was determined in the closely related species An. martinius and An. artemievi. It is shown that the loci in question may be used to diagnose twin species of the maculipennis complex.

Amino Acid Sequence↗
PubMed2005

Design of a system for combined analysis of microarray-based gene expression and FlyBase-derived annotation in Drosophila.

In recent years, researchers began to utilize both the experimental microarray data and the annotation data from FlyBase to identify Drosophila genes that might encode certain functions. So far, they have to manually combine data from both the microarray experiment and the FlyBase, which is a slow and tedious process. The goal of this research is to construct a flexible relational database system that integrates the microarray data with annotation information from FlyBase.

Animals↗
PubMed1984

Expression of disease symptoms in cauliflower mosaic virus genomic hybrids.

In an effort to determine if particular regions of the cauliflower mosaic virus (CaMV) genome could be associated with particular phenotypic characters, strains of CaMV differing markedly in biological properties were recombined to produce hybrids. DNA from pairs of (infectious) genomic clones was cleaved with restriction endonucleases, then mixed and ligated. Recombinants were found by screening transformants in E. coli, or by selection in vivo for infectious hybrids. Recombinants in infected turnip plants were characterized by restriction endonuclease mapping of their DNA to confirm the hybrid genotype. New hybrid strains that induced less severe disease, or conversely, more severe disease than either parent were observed. The experiments revealed that typical disease expression, consisting of leaf chlorosis and mottling, mapped to a genome segment containing open reading frame VI (ORF VI) and the full-length promoter. This basic disease symptom was found to be influenced by other regions of the genome. Insect transmissibility mapped to ORF II. The ability to develop generalized infections in solanaceous plants was tested in hybrids between CaMV CM1841 and a variant that infects Datura stramonium systemically. In this case the systemic mobilization of virus appeared to be controlled by ORF VI, suggesting that this gene may function in cell-to-cell movement of virus.

DNA, Recombinant↗
PubMed1997

Non random DNA evolution.

A model for testing random molecular evolution is proposed. Randomness of recurrent mutation is defined based on isotropy and zero covariance among nucleotide sites. Assuming an equal rate of mutation for the bases A, T, G, and C, in both DNA strands, a mutational matrix of transformation A, T, G, and C with 6 parameters is developed. Under this model the equilibrium proportions (F) of the bases are FA = FT = (D + E)/[2(D + E + H + J)] and FG = FC = (H + J)/[2(D + E + H + J)], D, E, H, J being 4 of the 6 matrix parameters. Thus the expected (FA + FT)/(FG + FC) ratio can also be tested. If the average rate of mutation is 10(-8) per nucleotide site and cell replication, the equilibrium for every site, in most species, is reached in 10(8) years. Eight DNA segments from human, bacteria, fungus and insect genomes were chosen to test these proportions and their heterogeneity among coding and non coding subsegments. While FG was similar to FC as expected, FA was highly different from FT Huge heterogeneities were found between coding and non coding segments and among non coding segments. These results are a strong evidence for non randomness of molecular evolution.

Animals↗
PubMed2003

P elements are found in the genomes of nematoceran insects of the genus Anopheles.

We report the identification of genomic sequences in various anopheline mosquitoes (family Culicidae: suborder Nematocera: order Diptera) showing homology to the class II, short inverted-terminal-repeat (ITR) transposable element P from Drosophila melanogaster (family Drosophilidae; suborder Brachycera: order Diptera). Anopheles gambiae appears to have at least six distinct P elements. Other anopheline species, including four additional members of the An. gambiae species complex (An. arabiensis, An. merus, An. melas and An. quadriannulatus), Anopheles stephensi (all subgenus Cellia), An. quadrimaculatus (subgenus Anopheles) and Anopheles albimanus (subgenus Nyssorhynchus) also possess P elements similar to those found in An. gambiae. Ten distinct P element types were identified in the genus Anopheles. At least two of the An. gambiae elements appears to be intact and potentially functional. Phylogenetic analysis of the anopheline P elements reveals them to belong to a distinctly different clade from the brachyceran P elements.

Amino Acid Sequence↗
PubMed2001

Genome interdependence in insect-bacterium symbioses.

Symbioses between unicellular and multicellular organisms have contributed significantly to the evolution of life on Earth. As exemplified by several studies of bacterium-insect symbioses, modern genomic techniques are providing exciting new information about the molecular basis and the biological roles of these complex relationships, revealing for instance that symbionts have lost many genes for functions that are provided by the host, but that they can provide amino acids that the host cannot synthesize.

Animals↗
PubMed1990

Heterochromatization and euchromatization of whole genomes in scale insects (Coccoidea: Homoptera).

In several families of scale insects (coccids), the sex of an embryo is determined by the number of genetically active genomes present (one = males, two = females). In mealybugs (Pseudococcidae), both males and females develop from fertilized eggs but, in the embryos that develop into males, the set of chromosomes (genome) of paternal origin (PG) becomes heterochromatic (H) and genetically inactive and is not transmitted to the offspring. The mechanism that reduces the number of active genomes in male embryos may vary between families and even between congeneric species. Thus, in male embryos of most armored scale species (Diaspididae), the PG is eliminated, while in a few species it becomes H. In two genera of soft scales (Coccidae), males develop from unfertilized eggs when one of two identical genomes of maternal origin becomes H. In most male tissues, one genome remains H. However, in several tissues that become polyploid by endoreduplication, the PG becomes E and genetically active. The tissues in which the PG becomes E often vary between species and the analysis of hybrid males demonstrated that whether the PG becomes H or remains E is determined by the genome of maternal origin. The euchromatization of the PG in the haploid sector of mosaic male embryos and the presence of spermatocytes with two E genomes (instead of one E and one H), following the irradiation of young mealybug males, strongly suggest that the maintenance of the H state requires the presence of a genetically active genome.

Animals↗
PubMed1995

Heterogeneity of rice ragged stunt oryzavirus genome segment 9 and its segregation by insect vector transmission.

Genomic heterogeneity of genome segment 9 (S9) of rice ragged stunt virus (RRSV) was investigated and a point mutation was found to be responsible for an electrophoretic mobility shift of S9 on polyacrylamide gel electrophoresis (PAGE). A new form of S9 (S9L) which migrated slightly faster than natural S9 (S9U) had the same length with A-->C transversion at nt 843. Synthetic S9 with a C:G pair at nt 843 migrated slightly faster than that with an A:U pair. Therefore, we conclude that the single point mutation shifts the electrophoretic mobility. Using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP), we could detect S9U and S9L alone or mixture in insect vectors after acquisition as well as in infected rice plants.

Animals↗