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W C Black

Publications and source records attributed to W C Black.

At least 19 recordsLinked to original sources
PubMed2006

Heated oligonucleotide ligation assay (HOLA): an affordable single nucleotide polymorphism assay.

Most single nucleotide polymorphism (SNP) detection requires expensive equipment and reagents. The oligonucleotide ligation assay (OLA) is an inexpensive SNP assay that detects ligation between a biotinylated "allele-specific detector" and a 3' fluorescein-labeled "reporter" oligonucleotide. No ligation occurs unless the 3' detector nucleotide is complementary to the SNP nucleotide. The original OLA used chemical denaturation and neutralization. Heated OLA (HOLA) instead uses a thermal stable ligase and cycles of denaturing and hybridization for ligation and SNP detection. The cost per genotype is approximately US$1.25 with two-allele SNPs or approximately US$1.75 with three-allele SNPs. We illustrate the development of HOLA for SNP detection in the Early Trypsin and Abundant Trypsin loci in the mosquito Aedes aegypti (L.) and at the a-glycerophosphate dehydrogenase locus in the mosquito Anopheles gambiae s.s.

Aedes↗
PubMed2005

Dengue 2 genotypes in the state of Oaxaca, Mexico.

To genetically characterize dengue 2 (DEN-2) viruses in Oaxaca, Mexico, the C protein, and a portion of the prM protein genes of 8 isolates from the 2001 DEN epidemic were sequenced. The sequences were compared to those of prototype DEN-2 viruses from various parts of the world. Phylogenetic analysis suggested that the 2001 isolates of DEN-2 were of the American/Asian genotype and were most similar to the Jamaica and Venezuelan isolates MARA3, LARD1996 and LARD1910. Molecular analyses confirmed the origin of the isolates. This study indicates that DEN-2 strains of American/Asian genotype probably from Southeast Asian are circulating in Oaxaca.

Animals↗
PubMed2005

Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus.

Genome sizes and the organization of repetitive DNA were determined in the hard ticks Ixodes scapularis and Boophilus microplus using reassociation kinetics. The I. scapularis genome contains approximately 2.15 pg (2.1x10(3) Mbp) of DNA and consists of no foldback (FB), 27% highly repetitive (HR), 39% moderately repetitive (MR), and 34% unique DNA. The B. microplus genome contains 7.5 pg (7.1x10(3) Mbp) DNA, and consists of 0.82% FB, 31% HR, 38% MR, and 30% unique DNA. In both species, repetitive sequences occur in a mixture of long and short period interspersion but most (65-80%) of the DNA follows a pattern of short period interspersion. Genome size and organization in the three tick species so far examined are distinct from other arthropods in having a greater proportion of MR, a lower proportion of unique and HR DNA of very low sequence complexity.

Animals↗
PubMed2004

Quantitative trait loci affecting dengue midgut infection barriers in an advanced intercross line of Aedes aegypti.

Quantitative trait loci (QTL) affecting the ability of the Aedes aegypti midgut to become infected with Dengue 2 virus (DEN2) were mapped in the F5 generation of an advanced intercross line (AIL). A strain of Ae. aegypti previously selected for DEN2 susceptibility was crossed to a new strain selected for refractoriness to midgut infection. In P1 and F1 parents and 147 F5 offspring, genotypes at forty-four cDNA loci were analysed. A new sex linked QTL and a second QTL on chromosome II with genotypes subject to balancing selection were detected that condition midgut susceptibility. Alleles at these QTL contributed additively in determining susceptibility and accounted for approximately 24% of the phenotypic variance. Markers associated with a midgut escape barrier were inconsistently supported.

Aedes↗
PubMed2003

Amplifying whole insect genomes with multiple displacement amplification.

Many applications in insect genetics require repeated analyses on individual organisms. These include population genetic and genomics, linkage mapping, molecular systematics and map-based positional cloning. However, using the polymerase chain reaction, a limited number of analyses are possible with DNA isolated from whole bodies or parts of small or preserved specimens. We describe the optimization of a new technique, Multiple Displacement Amplification, for 100-400-fold amplification of whole mosquito genomes. We demonstrate that MDA amplifies genomic DNA directly from an adult leg or from organisms as small as a first instar mosquito larva. Genetic polymorphisms revealed at individual loci are the same whether using the original genomic DNA or MDA DNA as a template.

Aedes↗
PubMed2002

Developmental- and tissue-specific expression of an inhibitor of apoptosis protein 1 homologue from Aedes triseriatus mosquitoes.

We have identified a homologue of the Drosophila inhibitor of apoptosis protein 1 in Aedes triseriatus mosquitoes (designated AtIAP1). The AtIAP1 gene maps to a single locus on chromosome 2. The translation product is a 403 amino acid protein that contains two baculovirus IAP repeat (BIR) domains and a RING finger motif. AtIAP1 mRNA was detectable by RT-PCR amplification in all the mosquito developmental stages (embryos, first-fourth instar larvae, early and late pupae, adults) and adult tissues (midguts, ovaries) examined. In contrast, immunoblots with AtIAP1-specific antibodies revealed that the protein was detectable only in certain developmental stages (first instar larvae, early pupae, adults) and tissues (ovaries). AtIAP1-specific serum also recognized proteins in Ae. aegypti, Ae. albopictus and Culex tritaeniorhynchus. Immunoblot analysis revealed that similar amounts of IAP1 were expressed in LaCrosse virus infected and uninfected Ae. albopictus cell cultures.

Aedes↗
PubMed2002

Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution.

Rearrangements of mitochondrial DNA gene order have been suggested as a tool for defining the pattern of evolutionary divergence in arthropod taxa. We have employed a combination of highly conserved insect-based polymerase chain reaction (PCR) primers with long-PCR to survey 14 noninsect arthropods for mitochondrial gene rearrangements. The size of the amplified fragments was used to order the primer containing genes. Five chelicerates exhibit amplicons that are consistent with the presumptive ancestral arthropod mtDNA gene order. These five species comprise two soft ticks, two prostriate hard ticks, and an opilionid. Six other chelicerates, all metastriate hard ticks, have a different arrangement that was originally discovered by this procedure and has been previously detailed in a complete mtDNA sequence. Three new arthropod mtDNA gene arrangements are described here. They were discovered in a terrestrial crustacean (Isopoda) and two myriapods (Chilopoda, centipede; Diplopoda, millipede). These rearrangements include major realignments of some of the large coding regions and two possible new positions for the tRNA(Met) (M) gene in arthropods. The long-PCR approach affords an opportunity to quickly screen divergent taxa for major rearrangements. Taxa exhibiting rearrangements can be targeted for DNA sequencing of gene boundaries to establish the details of the mtDNA organization.

Animals↗
PubMed2002

Molecular characterization of California serogroup viruses isolated in Russia.

Nucleotide sequencing was used to characterize unidentified California (CAL) serogroup virus isolates from Russia. These viruses were isolated from mosquitoes and humans during epidemiologic investigations on the role of CAL serogroup viruses in the increased incidence of arboviral encephalitis in Russia. Most of the isolates were identified serologically as snowshoe hare (SSH), Inkoo (INK), and Tahyna (TAH) viruses, but some of the isolates were difficult to classify serologically, suggesting that they could be reassortant viruses. There is evidence that at least 2 of these viruses are not reassortant viruses. Sequence analysis revealed that the Russian viruses differ from other Eurasian and North American CAL serogroup viruses in all of the segments analyzed. They are most closely related to SSH virus. Whether they differ sufficiently to be considered a new group of SSH-like viruses remains to be determined.

Animals↗
PubMed2001

Phylogeny of the major lineages of Membracoidea (Insecta: Hemiptera: Cicadomorpha) based on 28S rDNA sequences.

Analysis of sequences from a 3.5-kb region of the nuclear ribosomal 28S DNA gene spanning divergent domains D2-D10 supports the hypothesis, based on fossil, biogeographic, and behavioral evidence, that treehoppers (Aetalionidae and Membracidae) are derived from leafhoppers (Cicadellidae). Maximum-parsimony analysis indicated that treehoppers are the sister group of a lineage comprising the currently recognized cicadellid subfamilies Agalliinae, Megophthalminae, Adelungiinae, and Ulopinae. Based on this phylogenetic estimate, the derivation of treehoppers approximately coincided with shifts in physiology and behavior, including loss of brochosome production and a reversal from active, jumping nymphs to sessile, nonjumping nymphs. Myerslopiidae, traditionally placed as a tribe of the cicadellid subfamily Ulopinae, represented a basal lineage distinct from other extant membracoids. The analysis recovered a large leafhopper lineage comprising a polyphyletic Deltocephalinae (sensu stricto) and its apparent derivatives Koebeliinae, Eupelicinae (polyphyletic), Selenocephalinae, and Penthimiinae. Clades comprising Macropsinae, Neocoelidiinae, Scarinae, Iassinae, Coelidiinae, Eurymelinae + Idiocerinae, Evacanthini + Pagaroniini, Aphrodinae + Ledrinae (in part), Stenocotini + Tartessinae, and Cicadellini + Proconiini were also recovered with moderate to high branch support. Cicadellinae (sensu lato), Ledrinae, Typhlocybinae, and Xestocephalinae were consistently polyphyletic on the most-parsimonious topologies, but constraining these groups to be monophyletic did not significantly increase the length of the cladograms. Relationships among the major lineages received low branch support, suggesting that more data are needed to provide a robust phylogenetic estimate.

Animals↗
PubMed2001

Distribution of genetic variation among chromosomal forms of Anopheles gambiae s.s: introgressive hybridization, adaptive inversions, or recent reproductive isolation?

A series of four papers in this issue explores the reproductive status of the five chromosomal forms of An. gambiae s.s. using molecular techniques to examine the variation among twelve different genes located throughout the An. gambiae s.s. genome. Results of these and previous studies are consistent with a hypothesis of at least partial barriers to gene flow between some chromosomal forms in the Ivory Coast and other West African countries to the north and west, but introgression between S and M types in Benin and countries to the east. Collectively, these studies indicate the need for a broader geographical sampling of An. gambiae s.s., increased research on mechanisms of prezygotic reproductive isolation and field-based studies of survival and fecundity in hybrids to test for postzygotic reproductive isolation.

Adaptation, Physiological↗
PubMed2001

Microsatellite loci are not abundant in all arthropod genomes: analyses in the hard tick, Ixodes scapularis and the yellow fever mosquito, Aedes aegypti.

Plasmid libraries enriched for microsatellites were generated in the tick, Ixodes scapularis and in the mosquito Aedes aegypti. Libraries were enriched for genomic DNA containing (AC)n, (AG)n, (ATG)n, (CAG)n, (TAG)n, (AAT)n, (CTGY)n or (GATA)n motifs. Clones containing each motif were sequenced in both species for PCR primer design. In I. scapularis, most primers amplified a single locus and alleles varied in the number of microsatellite repeats and segregated as codominant markers. In contrast (AC)n, (TAG)n and (GATA)n microsatellite loci extracted from Ae. aegypti appeared to be members of multigene families. A primer pair designed to amplify a particular TAG locus instead amplified many independently segregating loci, some of which did not contain TAG microsatellites. Alleles at the TAG loci segregated as dominant markers and there was limited evidence for length variation among alleles. These results suggest that microsatellite loci are not universally abundant in arthropod genomes nor do alleles always segregate as codominant markers.

Aedes↗
PubMed2001

SSCP analysis of cDNA markers provides a dense linkage map of the Aedes aegypti genome.

An intensive linkage map of the yellow fever mosquito, Aedes aegypti, was constructed using single-strand conformation polymorphism (SSCP) analysis of cDNA markers to identify single nucleotide polymorphisms (SNPs). A total of 94 A. aegypti cDNAs were downloaded from GenBank and primers were designed to amplify fragments <500 bp in size. These primer pairs amplified 94 loci, 57 (61%) of which segregated in a single F(1) intercross family among 83 F(2) progeny. This allowed us to produce a dense linkage map of one marker every 2 cM distributed over a total length of 134 cM. Many A. aegypti cDNAs were highly similar to genes in the Drosophila melanogaster genome project. Comparative linkage analysis revealed areas of synteny between the two species. SNP polymorphisms are abundant in A. aegypti genes and should prove useful in both population genetics and mapping studies.

Aedes↗
PubMed2001

Population genomics: genome-wide sampling of insect populations.

Modern population genetics underwent a major paradigm shift during the last decade of the 20th century with the discovery that thousands of genes of known function and position in a genome can be analyzed simultaneously in a single individual. The impact of this technology on insect population genetics is potentially profound. Sampling distributions of genetic statistics can now be derived from many individual loci or among many segregating sites within a gene. Inferences regarding random mating, gene flow, effective population sizes, disequilibrium, and relatedness among populations can now be based on patterns of variation at many loci. More importantly, genome-wide sampling enables population geneticists to distinguish effects that act on the whole genome from those that act on individual loci or nucleotides. We introduce the term "population genomics" to describe the process of simultaneous sampling of numerous variable loci within a genome and the inference of locus-specific effects from the sample distributions. The four critical assumptions implicit in the population genomics approach are explained in detail. Studies adopting this paradigm are reviewed, and the steps necessary to complete a population genomics study are outlined.

Animals↗
PubMed2001

CT screening for lung cancer: not ready for routine practice.

Lung cancer continues to be a major worldwide health problem. Multiple strategies are being explored in an attempt to reduce lung cancer mortality, including a renewed interest in screening. Multiple low-dose spiral computed tomography (CT) trials have been proposed, as proponents predict that small nodules will represent early-stage disease and detecting them will ultimately translate into improvements in outcomes. At this time, however, only prevalence-screening data are available, and it remains to be seen if CT will truly reduce mortality. The appropriate hypothesis-driven studies still must be performed and the results carefully analyzed before CT screening for lung cancer can be accepted as the standard of care.

Humans↗
PubMed2001

[Studies of cost-effectiveness and cost-usefulness in radiology].

In the current context of significant increase of health care costs over the last decades, and in a system of global budget for health care, the concept of cost-effectiveness is one of the leading elements in the political decision making process for a given strategy. Therefore, it is important for the physician to be able to understand and critically interpret cost-effectiveness and cost-utility analyses. This article tries to illustrate comprehensively some of their key concepts. The perspective and the time horizon of the study should be clearly specified. The cost-effectiveness ratio is a synthetic summary based on a micro-costing approach in order to determine the true costs (numerator), and on an effectiveness (utility) assessment which should take into account the preferences of the community (denominator) in order to allow comparisons between interventions of different natures. Advances in the development of decision analysis softwares and in the standardization of the methodology of these studies have yielded considerable improvement in the reliability of their results. Several persisting methodological problems are the scope of current research, such as the discounting rate and the calculation of the minimal sample size required to reach a statistically significant threshold.

Cost-Benefit Analysis↗
PubMed2001

[Decision analysis in radiology].

Decision analysis is a technique which allows to clarify in an explicit, probabilistic and quantitative way the possible answers to a problem and to help the decision making process. The creation of algorithms, graphically displayed as decision trees in most cases, requires the introduction of quantitative information of two types: probabilities of the events that result from answering to the initial question, and utilities of the possible outcomes of these events. The choice of the optimal solution is based on the calculation of combinations of these data. Although the construction of models can be complex and time-consuming, their practical use has been simplified by the ease and user-friendliness of available softwares. To date, the applications of decision analysis in medicine have focused on cost-effectiveness studies and on the simulation of randomized trials. At the individual level, clinical applications of decision analysis could provide in a near future an interesting tool for the clinician involved in patient management. Even when doubts remain regarding the reliability of the data entered into the model, further sensitivity analysis provide a convenient way to test the validity of the drawn conclusions. This article hopefully offers a simplified and practical approach to basic decision analysis.

Decision Support Techniques↗
PubMed2000

Chemical and gamma-ray mutagenesis of the white gene in Aedes aegypti.

A molecular understanding of an insect gene can be facilitated by analysing the phenotypes of mutants for that gene. Protocols were developed for both chemical and gamma-ray mutagenesis in Aedes aegypti using the white (w) gene as an assay. Wild-type adult males were subjected to varying doses of either ethyl methanesulphonate (0. 1%, 0.5% or 1%) or gamma rays (1500 R or 3000 R), mated to females homozygous for the recessive w mutation, and progeny screened for the w phenotype, indicating non-complementation. The expression of newly induced w alleles was either complete or mosaic. Gamma-ray mutagenesis resulted in high (1.65 or 6.39%, depending on dose) induction of mutant alleles for the w gene, but not for a different gene, red-eye (0.15%). Gamma-ray-induced w alleles did not revert at a reasonable frequency following additional irradiation, suggesting that the high rate of gamma-ray-induced w mutagenesis is not due to a transposon insertion event.

Aedes↗