Identification of the Sex Pheromone of the Pink Grass Worm, Tmetolophota atristriga, Reveals Possible Population Differences in Male Response to Sex Pheromone.

The pink grass worm, Tmetolophota atristriga (Walker), is an endemic New Zealand noctuid moth species that is abundant throughout the North and South Islands. The larvae are minor defoliators of agricultural pasture. We investigated the sex pheromone of this species. Analysis of extract of the female sex pheromone gland identified six compounds: two monounsaturated compounds, (Z)-11-hexadecenal (Z11-16:Ald) and (Z)-11-hexadecenyl acetate (Z11-16:Ac), three saturated compounds, hexadecanal (16:Ald), hexadecyl acetate (16:Ac) and octadecan-1-ol (18:OH), and a triene hydrocarbon, (3Z,6Z,9Z)-tricosatriene (Z3Z6Z9-23:Hy). Several field-trapping experiments testing combinations of the six compounds were conducted. Results suggested that males of two different populations of T. atristriga responded differently to different blends of the compounds. Males of one population responded equally to a two-component blend as to other blends, including the one with all six compounds. By contrast, males of the second population responded only to the six-component blend or a ternary blend of Z11-16:Ald, Z11-16:Ac and Z3Z6Z9-23:Hy. In experiments testing different doses of Z11-16:Ald and Z11-16:Ac in a binary or a six-component blend, a 1 mg dose of the binary blend gave the greatest male catch for both populations. This is the second sex pheromone identification of a New Zealand species of Noctuidae and is the first reported occurrence of Z3Z6Z9-23:Hy as a sex pheromone component of any noctuid species.

Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae).

The Gila robusta species complex in the lower reaches of the Colorado River includes three nominal and contested species (G. robusta, G. intermedia, and G. nigra) originally defined by morphological and meristic characters. In subsequent investigations, none of these characters proved diagnostic, and species assignments were based on capture location. Two recent studies applied conservation genomics to assess species boundaries and reached contrasting conclusions: an ezRAD phylogenetic study resolved 5 lineages with poor alignment to species categories and proposed a single species with multiple population partitions. In contrast, a dd-RAD coalescent study concluded that the three nominal species are well-supported evolutionarily lineages. Here we developed a draft genome (~ 1.229 Gbp) to apply genome-wide coverage (10,246 SNPs) with nearly range-wide sampling of specimens (G. robusta N = 266, G. intermedia N = 241, and G. nigra N = 117) to resolve this debate. All three nominal species were polyphyletic, whereas 5 of 8 watersheds were monophyletic. AMOVA partitioned 23.1% of genetic variance among nominal species, 30.9% among watersheds, and the Little Colorado River was highly distinct (FST ranged from 0.79 to 0.88 across analyses). Likewise, DAPC identified watersheds as more distinct than species, with the Little Colorado River having 297 fixed nucleotide differences compared to zero fixed differences among the three nominal species. In every analysis, geography explains more of the observed variance than putative taxonomy, and there are no diagnostic molecular or morphological characters to justify species designation. Our analysis reconciles previous work by showing that species identities based on type location are supported by significant divergence, but natural geographic partitions show consistently greater divergence. Thus, our data confirm Gila robusta as a single polytypic species with roughly a dozen highly isolated geographic populations, providing a strong scientific basis for watershed-based future conservation.

Use of Diagnosis Codes to Find Blood Transfusion Adverse Events in Electronic Health Records.

OBJECTIVE: Electronic health records (EHRs) and big data tools offer the opportunity for surveillance of adverse events (patient harm associated with medical care). We used International Classification of Diseases, Ninth Revision, codes in electronic records to identify known, and potentially novel, adverse reactions to blood transfusion. METHODS: We used 49,331 adult admissions involving critical care at a major teaching hospital, 2001-2012, in the Medical Information Mart for Intensive Care III EHRs database. We formed a T (defined as packed red blood cells, platelets, or plasma) group of 21,443 admissions versus 25,468 comparison (C) admissions. The International Classification of Diseases, Ninth Revision, Clinical Modification , diagnosis codes were compared for T versus C, described, and tested with statistical tools. RESULTS: Transfusion adverse events (TAEs) such as transfusion-associated circulatory overload (TACO; 12 T cases; rate ratio [RR], 15.61; 95% confidence interval [CI], 2.49-98) were found. There were also potential TAEs similar to TAEs, such as fluid overload disorder (361 T admissions; RR, 2.24; 95% CI, 1.88-2.65), similar to TACO. Some diagnoses could have been sequelae of TAEs, including nontraumatic compartment syndrome of abdomen (52 T cases; RR, 6.76; 95% CI, 3.40-14.9) possibly being a consequence of TACO. CONCLUSIONS: Surveillance for diagnosis codes that could be TAE sequelae or unrecognized TAE might be useful supplements to existing medical product adverse event programs.

New sex pheromone blend for the lightbrown apple moth, Epiphyas postvittana.

The composition of the sex pheromone gland of the lightbrown apple moth, Epiphyas postvittana (Walker) was re-investigated. In addition to the two previously identified compounds, (E)-11-tetradecenyl acetate (E11-14Ac) and (E,E)-9,11-tetradecadienyl acetate (E9E11-14Ac), seven additional candidate pheromone compounds were identified: (E)-11-tetradecen-1-ol (E11-14OH), tetradecyl acetate, hexadecanal, (E)-11-hexadecenyl acetate (E11-16Ac), hexadecyl acetate, octadecanal, and octadecyl acetate. Gas chromatographic-electroantennographic detection analysis showed that only four (of the nine) compounds (E11-14OH, E11-14Ac, E9E11-14Ac, and E11-16Ac) elicited electrophysiological responses. When either E11-14OH or E11-16Ac were tested at various ratios in three-component blends with both E11-14Ac and E9E11-14Ac, no increase in trap catch was observed compared to that to the previously identified binary blend. However, when these two compounds (1% E11-14OH and 0.5% E11-16Ac) were both added to E11-14Ac and E9E11-14Ac, trap catch was roughly double that to the previously identified binary blend alone. The new four-component blend should be more sensitive for detecting this economically important insect, especially in low population areas (i.e., in newly invaded habitats). In addition, this new blend may enhance pheromone control of this pest, through approaches such as mating disruption, lure and kill, and mass trapping.

Finding Potential Adverse Events in the Unstructured Text of Electronic Health Care Records: Development of the Shakespeare Method.

BACKGROUND: Big data tools provide opportunities to monitor adverse events (patient harm associated with medical care) (AEs) in the unstructured text of electronic health care records (EHRs). Writers may explicitly state an apparent association between treatment and adverse outcome ("attributed") or state the simple treatment and outcome without an association ("unattributed"). Many methods for finding AEs in text rely on predefining possible AEs before searching for prespecified words and phrases or manual labeling (standardization) by investigators. We developed a method to identify possible AEs, even if unknown or unattributed, without any prespecifications or standardization of notes. Our method was inspired by word-frequency analysis methods used to uncover the true authorship of disputed works credited to William Shakespeare. We chose two use cases, "transfusion" and "time-based." Transfusion was chosen because new transfusion AE types were becoming recognized during the study data period; therefore, we anticipated an opportunity to find unattributed potential AEs (PAEs) in the notes. With the time-based case, we wanted to simulate near real-time surveillance. We chose time periods in the hope of detecting PAEs due to contaminated heparin from mid-2007 to mid-2008 that were announced in early 2008. We hypothesized that the prevalence of contaminated heparin may have been widespread enough to manifest in EHRs through symptoms related to heparin AEs, independent of clinicians' documentation of attributed AEs. OBJECTIVE: We aimed to develop a new method to identify attributed and unattributed PAEs using the unstructured text of EHRs. METHODS: We used EHRs for adult critical care admissions at a major teaching hospital (2001-2012). For each case, we formed a group of interest and a comparison group. We concatenated the text notes for each admission into one document sorted by date, and deleted replicate sentences and lists. We identified statistically significant words in the group of interest versus the comparison group. Documents in the group of interest were filtered to those words, followed by topic modeling on the filtered documents to produce topics. For each topic, the three documents with the maximum topic scores were manually reviewed to identify PAEs. RESULTS: Topics centered around medical conditions that were unique to or more common in the group of interest, including PAEs. In each use case, most PAEs were unattributed in the notes. Among the transfusion PAEs was unattributed evidence of transfusion-associated cardiac overload and transfusion-related acute lung injury. Some of the PAEs from mid-2007 to mid-2008 were increased unattributed events consistent with AEs related to heparin contamination. CONCLUSIONS: The Shakespeare method could be a useful supplement to AE reporting and surveillance of structured EHR data. Future improvements should include automation of the manual review process.

Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study.

To identify genetic variants contributing to end-stage renal disease (ESRD) in type 2 diabetes, we performed a genome-wide analysis of 115,352 single nucleotide polymorphisms (SNPs) in pools of 105 unrelated case subjects with ESRD and 102 unrelated control subjects who have had type 2 diabetes for > or =10 years without macroalbuminuria. Using a sliding window statistic of ranked SNPs, we identified a 200-kb region on 8q24 harboring three SNPs showing substantial differences in allelic frequency between case and control pools. These SNPs were genotyped in individuals comprising each pool, and strong evidence for association was found with rs2720709 (P = 0.000021; odds ratio 2.57 [95% CI 1.66-3.96]), which is located in the plasmacytoma variant translocation gene PVT1. We sequenced all exons, exon-intron boundaries, and the promoter of PVT1 and identified 47 variants, 11 of which represented nonredundant markers with minor allele frequency > or =0.05. We subsequently genotyped these 11 variants and an additional 87 SNPs identified through public databases in 319-kb flanking rs2720709 ( approximately 1 SNP/3.5 kb); 23 markers were associated with ESRD at P < 0.01. The strongest evidence for association was found for rs2648875 (P = 0.0000018; 2.97 [1.90-4.65]), which maps to intron 8 of PVT1. Together, these results suggest that PVT1 may contribute to ESRD susceptibility in diabetes.

Floral attractants for the female soybean looper, Thysanoplusia orichalcea (Lepidoptera: Noctuidae).

BACKGROUND: The soybean looper, Thysanoplusia orichalcea (F.), is a polyphagous insect pest of vegetable crops. Indonesian in origin, it has spread to Europe, India, Africa, Australia and New Zealand. The identification of an attractant for female T. orichalcea could enable the development of alternative pest management strategies to those provided by insecticides or sex pheromones, which are often only attractive to males. RESULTS: Traps baited with synthetic lures derived from Canada thistle, Cirsium arvense (L.) Scop., floral volatiles attracted female T. orichalcea. Phenylacetaldehyde, a floral compound attractive to many Lepidoptera and present in C. arvense, was tested alone as an attractant for the soybean looper and caught significantly more female than male T. orichalcea. Trap catch was greatest when phenylacetaldehyde was combined with five prevalent volatiles present in C. arvense headspace collections: 2-phenylethyl alcohol, methyl salicylate, dimethyl salicylate, benzaldehyde and benzyl alcohol. Twice as many female moths as males were collected. CONCLUSION: Successful trapping of female T. orichalcea in either a lure-and-kill or a mass trapping system may offer an effective way to manage its population size.

Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions.

The many reports of trans interactions between homologous as well as nonhomologous loci in a wide variety of organisms argue that such interactions play an important role in gene regulation. The yellow locus of Drosophila is especially useful for investigating the mechanisms of trans interactions due to its ability to support transvection and the relative ease with which it can be altered by targeted gene replacement. In this study, we exploit these aspects of yellow to further our understanding of cis as well as trans forms of enhancer-promoter communication. Through the analysis of yellow alleles whose promoters have been replaced with wild-type or altered promoters from other genes, we show that mutation of single core promoter elements of two of the three heterologous promoters tested can influence whether yellow enhancers act in cis or in trans. This finding parallels observations of the yellow promoter, suggesting that the manner in which trans interactions are controlled by core promoter elements describes a general mechanism. We further demonstrate that heterologous promoters themselves can be activated in trans as well as participate in pairing-mediated insulator bypass. These results highlight the potential of diverse promoters to partake in many forms of trans interactions.

Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange.

Position effects can complicate transgene analyses. This is especially true when comparing transgenes that have inserted randomly into different genomic positions and are therefore subject to varying position effects. Here, we introduce a method for the precise targeting of transgenic constructs to predetermined genomic sites in Drosophila using the C31 integrase system in conjunction with recombinase-mediated cassette exchange (RMCE). We demonstrate the feasibility of this system using two donor cassettes, one carrying the yellow gene and the other carrying GFP. At all four genomic sites tested, we observed exchange of donor cassettes with an integrated target cassette carrying the mini-white gene. Furthermore, because RMCE-mediated integration of the donor cassette is necessarily accompanied by loss of the target cassette, we were able to identify integrants simply by the loss of mini-white eye color. Importantly, this feature of the technology will permit integration of unmarked constructs into Drosophila, even those lacking functional genes. Thus, C31 integrase-mediated RMCE should greatly facilitate transgene analysis as well as permit new experimental designs.

Thigmotaxis Mediates Trail Odour Disruption.

Disruption of foraging using oversupply of ant trail pheromones is a novel pest management application under investigation. It presents an opportunity to investigate the interaction of sensory modalities by removal of one of the modes. Superficially similar to sex pheromone-based mating disruption in moths, ant trail pheromone disruption lacks an equivalent mechanistic understanding of how the ants respond to an oversupply of their trail pheromone. Since significant compromise of one sensory modality essential for trail following (chemotaxis) has been demonstrated, we hypothesised that other sensory modalities such as thigmotaxis could act to reduce the impact on olfactory disruption of foraging behaviour. To test this, we provided a physical stimulus of thread to aid trailing by Argentine ants otherwise under disruptive pheromone concentrations. Trail following success was higher using a physical cue. While trail integrity reduced under continuous over-supply of trail pheromone delivered directly on the thread, provision of a physical cue in the form of thread slightly improved trail following and mediated trail disruption from high concentrations upwind. Our results indicate that ants are able to use physical structures to reduce but not eliminate the effects of trail pheromone disruption.

Use of data mining at the Food and Drug Administration.

OBJECTIVES: This article summarizes past and current data mining activities at the United States Food and Drug Administration (FDA). TARGET AUDIENCE: We address data miners in all sectors, anyone interested in the safety of products regulated by the FDA (predominantly medical products, food, veterinary products and nutrition, and tobacco products), and those interested in FDA activities. SCOPE: Topics include routine and developmental data mining activities, short descriptions of mined FDA data, advantages and challenges of data mining at the FDA, and future directions of data mining at the FDA.

Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

BACKGROUND: Pooling genomic DNA samples within clinical classes of disease followed by genotyping on whole-genome SNP microarrays, allows for rapid and inexpensive genome-wide association studies. Key to the success of these studies is the accuracy of the allelic frequency calculations, the ability to identify false-positives arising from assay variability and the ability to better resolve association signals through analysis of neighbouring SNPs. RESULTS: We report the accuracy of allelic frequency measurements on pooled genomic DNA samples by comparing these measurements to the known allelic frequencies as determined by individual genotyping. We describe modifications to the calculation of k-correction factors from relative allele signal (RAS) values that remove biases and result in more accurate allelic frequency predictions. Our results show that the least accurate SNPs, those most likely to give false-positives in an association study, are identifiable by comparing their frequencies to both those from a known database of individual genotypes and those of the pooled replicates. In a disease with a previously identified genetic mutation, we demonstrate that one can identify the disease locus through the comparison of the predicted allelic frequencies in case and control pools. Furthermore, we demonstrate improved resolution of association signals using the mean of individual test-statistics for consecutive SNPs windowed across the genome. A database of k-correction factors for predicting allelic frequencies for each SNP, derived from several thousand individually genotyped samples, is provided. Lastly, a Perl script for calculating RAS values for the Affymetrix platform is provided. CONCLUSION: Our results illustrate that pooling of DNA samples is an effective initial strategy to identify a genetic locus. However, it is important to eliminate inaccurate SNPs prior to analysis by comparing them to a database of individually genotyped samples as well as by comparing them to replicates of the pool. Lastly, detection of association signals can be improved by incorporating data from neighbouring SNPs.

Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter.

Eukaryotic enhancers act over very long distances, yet still show remarkable specificity for their own promoter. To better understand mechanisms underlying this enhancer-promoter specificity, we used transvection to analyze enhancer choice between two promoters, one located in cis to the enhancer and the other in trans to the enhancer, at the yellow gene of Drosophila melanogaster. Previously, we demonstrated that enhancers at yellow prefer to act on the cis-linked promoter, but that mutation of core promoter elements in the cis-linked promoter releases enhancers to act in trans. Here, we address the mechanism by which these elements affect enhancer choice. We consider and explicitly test three models that are based on promoter competency, promoter pairing, and promoter identity. Through targeted gene replacement of the endogenous yellow gene, we show that competency of the cis-linked promoter is a key parameter in the cis-trans choice of an enhancer. In fact, complete replacement of the yellow promoter with both TATA-containing and TATA-less heterologous promoters maintains enhancer action in cis.

Development of single-dispenser pheromone suppression of Epiphyas postvittana, Planotortrix octo and Ctenopseustis obliquana in New Zealand stone fruit orchards.

BACKGROUND: Pheromones of two native leafrollers of economic importance to the New Zealand horticulture industry, Planotortrix octo [(Z)-8-tetradecenyl acetate and tetradecyl acetate] and Ctenopseustis obliquana [(Z)-5-tetradecenyl acetate and (Z)-8-tetradecenyl acetate], were reinvestigated and combined with pheromone of Epiphyas postvittana [light-brown apple moth, (E)-11-tetradecenyl actetate and (E, E)-9,11-tetradecen-1-yl acetate] to develop a single dispenser for mating disruption of three pest species for integrated pest management. RESULTS: Additional compounds identified from pheromone gland extracts were characterised as repellents for P. octo. However, for C. obliquana from Central Otago, a change in ratio of (Z)-5-tetradecenyl acetate and (Z)-8-tetradecenyl acetate and the addition of three compounds found in the gland (dodecyl acetate, tetradecyl acetate and hexadecanal) led to a significant improvement in catch over previous lures. Males from Central Otago showed antennal electrophysiological responses to hexadecanal, unlike C. obliquana from Auckland, which did not. Three multiple-species disruption blends were devised in a single dispenser to target E. postvittana, P. octo and C. obliquana. Disruption of traps was recorded in single-tree replicates with all three blends, but the five-component blend was overall most effective at disruption and was deployed area wide in commercial orchard plots. CONCLUSIONS: Deployment of single dispensers into commercial stone fruit orchards led to disruption of trapping for the three species and measurable reductions in insecticide use in cherries, peaches and nectarines without increased fruit damage (assessed in apricots).

Genome-wide SNP arrays as a diagnostic tool: clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite population.

An Old Order Mennonite child was evaluated for gross motor delay, truncal ataxia, and slow linear growth. The diagnostic evaluation, which included sub-specialty consultations, neuroimaging, and metabolic testing, was long, costly, and did not yield a diagnosis. Recognition of a similarly affected second cousin prompted a genome-wide homozygosity mapping study using high-density single nucleotide polymorphism (SNP) arrays. SNP genotypes from two affected individuals and their parents were used to localize the disease locus to a 14.9 Mb region on chromosome 6. This region contained 55 genes, including SLC17A5, the gene encoding the lysosomal N-acetylneuraminic acid transport protein. Direct sequencing of SLC17A5 in the proband revealed homozygosity for the 115C --> T (R39C) sequence variant, the common cause of Salla disease in Finland. Three additional affected Mennonite individuals, ages 8 months to 50 years, were subsequently identified by directed molecular genetic testing. This small-scale mapping study was rapid, inexpensive, and analytically simple. In families with shared genetic heritage, genome-wide SNP arrays with relatively high marker density allow disease gene mapping studies to be incorporated into routine diagnostic evaluations.