Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq

BACKGROUND

Parent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between the parental haplotypes. ASE is detectable by differential expression analysis (DEA) applied to the counts of RNA-seq read pairs aligned to parental references, but aligners do not always choose the correct parental reference.

RESULTS

We used public data for species that are known to hybridize. We measured our ability to assign RNA-seq read pairs to their proper transcriptome or genome references. We tested software packages that assign each read pair to a reference position and found that they often favored the incorrect species reference. To address this problem, we introduce a post process that extracts alignment features and trains a random forest classifier to choose the better alignment. On each simulated hybrid dataset tested, our machine-learning post-processor achieved higher accuracy than the aligner by itself at choosing the correct parent-of-origin per RNA-seq read pair.

CONCLUSIONS

For the parent-of-origin classification of RNA-seq, machine learning can improve the accuracy of alignment-based methods. This approach could be useful for enhancing ASE detection in interspecies hybrids, though RNA-seq from real hybrids may present challenges not captured by our simulations. We believe this is the first application of machine learning to this problem domain.

Multi-symptom Relief with Propylene Glycol-Hydroxypropyl-Guar Nanoemulsion Lubricant Eye Drops in Subjects with Dry Eye Disease: A Post-Marketing Prospective Study

INTRODUCTION

The study aimed to evaluate multi-symptom relief of dry eye manifestations with the use of propylene glycol-hydroxypropyl-guar (PG-HPG) nanoemulsion lubricant eye drops, among subjects with dry eye disease (DED).

METHODS

This was a post-marketing, prospective, single-arm study conducted in the USA. Subjects aged ≥ 18 years, with tear breakup time (TBUT) ≤ 10 s for both eyes, dry eye questionnaire-5 (DEQ-5) "watery eyes" symptom score 1-4, symptoms of burning/stinging, sore and tired eyes as determined by impact of dry eye on everyday living-symptom bother (IDEEL-SB) questionnaire, and IDEEL-SB score 16-65 were included. Subjects were required to complete IDEEL-SB and DEQ-5 at days 0, 14 ± 2, and 28 ± 2, and self-administer one drop of PG-HPG four times daily for 28 ± 2 days. Primary endpoints were change from baseline at day 28 in symptoms of sore, stinging/burning, and tired eyes on IDEEL-SB; and symptom of watery eyes on DEQ-5. Other endpoints evaluated were corneal staining and TBUT at baseline and day 28 ± 2; symptom relief (5-point Likert scale) at day 28 ± 2, and safety.

RESULTS

Of 119 subjects enrolled, 95 completed the study (mean ± SD age 61.2 ± 13.0 years; female 69.5%). Mean IDEEL-SB scores reduced significantly from baseline at day 28 for symptoms of aching/sore eyes (change from baseline - 1.0 ± 1.1), burning/stinging eyes (change from baseline - 1.1 ± 0.9), and tired eyes (change from baseline - 1.1 ± 1.0) (all p < 0.0001). Mean DEQ-5 score for watery eye symptoms significantly reduced from baseline at day 28 (change from baseline - 0.9 ± 1.0, p < 0.0001). Corneal staining at day 28 was comparable to baseline. TBUT improved from baseline to day 28. On a Likert scale, more than 50% of subjects reported relief from symptoms of sore, stinging, and burning eyes. Three (3.1%) subjects reported treatment-emergent adverse events (non-ocular).

CONCLUSIONS

PG-HPG nanoemulsion lubricant eye drops significantly improved multiple dry eye symptoms in subjects with DED over 28 days, with no new safety concerns.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier, NCT05056155.

Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata

Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome-wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm-based hybridization barrier between A. arenosa and A. lyrata ssp. petraea.

Spatial and temporal regulation of parent-of-origin allelic expression in the endosperm

Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.

Regulation of Parent-of-Origin Allelic Expression in the Endosperm

Genomic imprinting is an epigenetic phenomenon established in the gametes prior to fertilization that causes differential expression of parental alleles, mainly in the endosperm of flowering plants. The overlap between previously identified panels of imprinted genes is limited. To investigate imprinting, we used high-resolution sequencing data acquired with sequence-capture technology. We present a bioinformatics pipeline to assay parent-of-origin allele-specific expression and report more than 300 loci with parental expression bias in Arabidopsis (Arabidopsis thaliana). In most cases, the level of expression from maternal and paternal alleles was not binary, instead supporting a differential dosage hypothesis for the evolution of imprinting in plants. To address imprinting regulation, we systematically employed mutations in regulative epigenetic pathways suggested to be major players in the process. We established the mechanistic mode of imprinting for more than 50 loci regulated by DNA methylation and Polycomb-dependent histone methylation. However, the imprinting patterns of most genes were not affected by these mechanisms. To this end, we also demonstrated that the RNA-directed DNA methylation pathway alone does not substantially influence imprinting patterns, suggesting that more complex epigenetic pathways regulate most of the identified imprinted genes.

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation

Background

The 50-year-old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.

Results

The C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K⁺ channels. As a test of utility, RNA sequence data from Zika-infected cells were mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of nonhost reads.

Conclusions

The C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.

Development of a Novel Dry, Sticky Trap Design Incorporating Visual Cues for Drosophila suzukii (Diptera: Drosophilidae)

Drosophila suzukii Matsumura (Diptera: Drosophilidae) is currently one of the most serious invasive pests for berry crops and cherries worldwide. The development of an effective monitoring trap that is reliable at detecting small populations to guide management decisions is greatly needed. To develop a novel dry trapping system, D. suzukii were trapped under field conditions in cherry orchards and raspberry high tunnels using various baited dry trap designs that were compared with the currently available deli-cup style traps that utilize a liquid bait or drowning solution. In a test in cherry orchards, red panel and combination yellow panel plus red sphere traps captured significantly more flies than yellow panel traps when all were baited with a Scentry lure. In a separate test in cherry, red sphere traps with the Scentry lure captured significantly more flies than the deli-cup traps with the Scentry lure or with the yeast sugar bait, and red panel traps with the Scentry lure captured significantly more flies than deli-cup traps with the Scentry lure. In raspberry high tunnels, red sphere traps with the Scentry lure captured significantly more flies than deli-cup traps with the Scentry lure. Red traps baited with the same lure as clear deli-cup traps consistently captured more D. suzukii, demonstrating that traps integrating a visual cue in combination with an olfactory cue are superior tools for monitoring D. suzukii. A dry trap requires less labor and maintenance than cup traps containing a liquid, improving the ease of use of D. suzukii monitoring traps.

Diagnostic Value of Early Magnetic Resonance Imaging After Acute Lateral Ankle Injury

We report a retrospective study of 171 consecutive patients with a lateral ankle sprain. All the patients with direct or blunt force trauma were excluded. Within 21 days of injury, 115 (67.25%) patients had undergone magnetic resonance imaging to evaluate for more serious or significant injuries. The average patient age was 44.09 years. Of the 115 patients, 75 (65.23%) had findings noted to be "significant." MRI can serve as a valuable and underused tool in the evaluation of acute lateral ankle injuries. The underuse of MRI might explain the high degree of variability in patients recovering from a lateral ankle sprain.

A draft genome sequence for the Ixodes scapularis cell line, ISE6

Background: The tick cell line ISE6, derived from Ixodes scapularis, is commonly used for amplification and detection of arboviruses in environmental or clinical samples.

Methods: To assist with sequence-based assays, we sequenced the ISE6 genome with single-molecule, long-read technology.

Results: The draft assembly appears near complete based on gene content analysis, though it appears to lack some instances of repeats in this highly repetitive genome. The assembly appears to have separated the haplotypes at many loci. DNA short read pairs, used for validation only, mapped to the cell line assembly at a higher rate than they mapped to the Ixodes scapularis reference genome sequence.

Conclusions: The assembly could be useful for filtering host genome sequence from sequence data obtained from cells infected with pathogens.

The Ring Verruca Plantaris in Cantharidin Use A Case Report

Verrucae (warts) are the most common viral infections of the skin, affecting 7% to 10% of the general population. Typically caused by human papillomavirus type 1, plantar warts manifest as benign proliferation of the epithelial cells on the feet. It has been cited that up to one-third of nongenital warts become recalcitrant, and biopsy is often required to confirm diagnosis and direct appropriate treatment. These treatments can vary from various types of oral medications, acids, ablative modalities, and injections. In this article, we present a case of a recalcitrant plantar wart that appeared to circumferentially spread from the initial site after first-line treatment and presumed resolution with the product cantharidin. The development of ring warts is a known complication associated with cantharidin use, with little described rationale to the presentation.

A host subtraction database for virus discovery in human cell line sequencing data

The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses.

The Rare Lesser Metatarsal Bipartite Sesamoid A Case Report

Sesamoid bones and accessory ossicles are common incidental findings on radiographs. These can occasionally become symptomatic, usually after a precipitating event such as an injury or overuse, or they can be incidental findings unrelated to the presenting pathology. The aim of this study was to highlight a rare case of a bipartite fifth metatarsal sesamoid bone and to review previous literature regarding sesamoid bones and accessory ossicles.

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula

Background

Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner.

Results

Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly.

Conclusions

Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3971-4) contains supplementary material, which is available to authorized users.

Line-Trapping of Codling Moth (Lepidoptera: Tortricidae): A Novel Approach to Improving the Precision of Capture Numbers in Traps Monitoring Pest Density

This field study of codling moth, Cydia pomonella (L.), response to single versus multiple monitoring traps baited with codlemone demonstrates that precision of a given capture number is alarmingly poor when the population is held constant by releasing moths. Captures as low as zero and as high as 12 males per single trap are to be expected where the catch mode is three. Here, we demonstrate that the frequency of false negatives and overestimated positives for codling moth trapping can be substantially reduced by employing the tactic of line-trapping, where five traps were deployed 4 m apart along a row of apple trees. Codling moth traps spaced closely competed only slightly. Therefore, deploying five traps closely in a line is a sampling technique nearly as good as deploying five traps spaced widely. But line trapping offers a substantial savings in time and therefore cost when servicing aggregated versus distributed traps. As the science of pest management matures by mastering the ability to translate capture numbers into estimates of absolute pest density, it will be important to employ a tactic like line-trapping so as to shrink the troublesome variability associated with capture numbers in single traps that thwarts accurate decisions about if and when to spray. Line-trapping might similarly increase the reliability and utility of density estimates derived from capture numbers in monitoring traps for various pest and beneficial insects.

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species

BACKGROUND

Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests.

RESULTS

We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes.

CONCLUSIONS

The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.

Hybrid assembly with long and short reads improves discovery of gene family expansions

Background

Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation.

Methods

We developed a hybrid assembly pipeline called “Alpaca” that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation.

Results

Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies.

Conclusion

Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3927-8) contains supplementary material, which is available to authorized users.

Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid

The CP 96-1252 cultivar of sugarcane is a complex hybrid of commercial importance. DNA was extracted from lab-grown leaf tissue and sequenced. The raw Illumina DNA sequencing results provide 101 Gbp of genome sequence reads. The dataset is available from https://www.ncbi.nlm.nih.gov/bioproject/PRJNA345486/.

Maximizing Information Yield From Pheromone-Baited Monitoring Traps: Estimating Plume Reach, Trapping Radius, and Absolute Density of Cydia pomonella (Lepidoptera: Tortricidae) in Michigan Apple

Novel methods of data analysis were used to interpret codling moth (Cydia pomonella) catch data from central-trap, multiple-release experiments using a standard codlemone-baited monitoring trap in commercial apple orchards not under mating disruption. The main objectives were to determine consistency and reliability for measures of: 1) the trapping radius, composed of the trap's behaviorally effective plume reach and the maximum dispersive distance of a responder population; and 2) the proportion of the population present in the trapping area that is caught. Two moth release designs were used: 1) moth releases at regular intervals in the four cardinal directions, and 2) evenly distributed moth releases across entire approximately 18-ha orchard blocks using both high and low codling moth populations. For both release designs, at high populations, the mean proportion catch was 0.01, and for the even release of low populations, that value was approximately 0.02. Mean maximum dispersive distance for released codling moth males was approximately 260 m. Behaviorally effective plume reach for the standard codling moth trap was < 5 m, and total trapping area for a single trap was approximately 21 ha. These estimates were consistent across three growing seasons and are supported by extraordinarily high replication for this type of field experiment. Knowing the trapping area and mean proportion caught, catch number per single monitoring trap can be translated into absolute pest density using the equation: males per trapping area = catch per trapping area/proportion caught. Thus, catches of 1, 3, 10, and 30 codling moth males per trap translate to approximately 5, 14, 48, and 143 males/ha, respectively, and reflect equal densities of females, because the codling moth sex ratio is 1:1. Combined with life-table data on codling moth fecundity and mortality, along with data on crop yield per trapping area, this fundamental knowledge of how to interpret catch numbers will enable pest managers to make considerably more precise projections of damage and therefore more precise and reliable decisions on whether insecticide applications are justified. The principles and methods established here for estimating absolute codling moth density may be broadly applicable to pests generally and thereby could set a new standard for integrated pest management decisions based on trapping.

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

BACKGROUND

Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome.

RESULTS

Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable - estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.

CONCLUSIONS

Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8.2. These advances result from new overlapping and assembly algorithms, including an adaptive overlapping strategy based on tf-idf weighted MinHash and a sparse assembly graph construction that avoids collapsing diverged repeats and haplotypes. We demonstrate that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either Pacific Biosciences (PacBio) or Oxford Nanopore technologies and achieves a contig NG50 of >21 Mbp on both human and Drosophila melanogaster PacBio data sets. For assembly structures that cannot be linearly represented, Canu provides graph-based assembly outputs in graphical fragment assembly (GFA) format for analysis or integration with complementary phasing and scaffolding techniques. The combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex genomes.

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

BACKGROUND

The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.

RESULTS

By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual.

CONCLUSIONS

The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery

ThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant Arabidopsis thaliana. The data collection currently includes the latest structural and functional annotation from the Araport11 update, the Col-0 genome sequence, RNA-seq and array expression, co-expression, protein interactions, homologs, pathways, publications, alleles, germplasm and phenotypes. The data are collected from a wide variety of public resources. Users can browse gene-specific data through Gene Report pages, identify and create gene lists based on experiments or indexed keywords, and run GO enrichment analysis to investigate the biological significance of selected gene sets. Developed by the Arabidopsis Information Portal project (Araport, https://www.araport.org/), ThaleMine uses the InterMine software framework, which builds well-structured data, and provides powerful data query and analysis functionality. The warehoused data can be accessed by users via graphical interfaces, as well as programmatically via web-services. Here we describe recent developments in ThaleMine including new features and extensions, and discuss future improvements. InterMine has been broadly adopted by the model organism research community including nematode, rat, mouse, zebrafish, budding yeast, the modENCODE project, as well as being used for human data. ThaleMine is the first InterMine developed for a plant model. As additional new plant InterMines are developed by the legume and other plant research communities, the potential of cross-organism integrative data analysis will be further enabled.

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

Alightment of Spotted Wing Drosophila (Diptera: Drosophilidae) on Odorless Disks Varying in Color

Methods for trapping spotted wing drosophila, Drosophila suzukii (Matsmura) (Diptera: Drosophilidae), have not yet been optimized for detecting this devastating pest of soft-skinned fruits. Here, we report outcomes of choice and no-choice laboratory bioassays quantifying the rates of spotted wing drosophila alightment on 5-cm-diameter sticky disks of various colors, but no fruit odors. Red, purple, and black disks captured the most spotted wing drosophila when presented against a white background. Male and female spotted wing drosophila responded identically in these tests. Significantly more D. suzukii were captured on the red and yellow disks than those presenting the corresponding grayscale for that color, proving that D. suzukii perceives colors and not just the level of target brightness. Fluorescent red is the best candidate for trap color, while clear and white are the least desirable. However, when the background was switched to black, all nonfluorescent colors were equally acceptable to spotted wing drosophila, suggesting that background must be specified when reporting spotted wing drosophila color preference. Additional spotted wing drosophila research is justified on the effects of target color against natural backgrounds.

Association of Vitamin D With Stress Fractures: A Retrospective Cohort Study

Vitamin D is an essential, fat-soluble nutrient that is a key modulator of bone health. Despite the gaining popularity throughout published medical studies, no consensus has been reached regarding a serum vitamin D level that will guarantee adequate skeletal health in a patient with an increased functional demand. The purpose of the present investigation was to examine the serum concentrations of vitamin D in patients with confirmed stress fractures. A total of 124 patients were included in our retrospective cohort study. Of the 124 patients, 53 had vitamin D levels measured within 3 months of diagnosis. An association was seen in patients with a stress fracture and vitamin D level measured, as 44 (83.02%) of the 53 patients had a serum 25-hydroxyvitamin D level <40 ng/mL. Although an association was seen at our institution in patients with stress fractures and a serum vitamin D concentration <40 ng/mL, a larger and prospective investigation is warranted to further understand the effect of vitamin D level and stress fracture prevention in an active, nonmilitary population.

Lyme Disease Manifestations in the Foot and Ankle: A Retrospective Case Series

Lyme disease is the result of Borrelia burgdorferi bacterial infection after exposure from a tick bite. A pathognomonic finding in early-stage Lyme disease is an expanding, red macular ring known as erythema migrans. Lyme arthritis is a late-stage manifestation of this disease, affecting the large, weightbearing joints with intermittent pain and swelling. The existing data on Lyme disease and subsequent arthritis have reported manifestations in the lower extremity, primarily in the knee and ankle and less commonly the small joints of the foot. We present a retrospective case series of 11 cases of painful arthritis in the foot and ankle with confirmatory Lyme disease testing.

Divergent host preferences of above- and below-ground Culex pipiens mosquitoes and their hybrid offspring

Culex pipiens form pipiens and Cx. pipiens form molestus (Diptera: Culicidae) belong to a cosmopolitan taxonomic group known as the Pipiens Assemblage. Hybridization between these forms is thought to contribute to human transmission of West Nile virus (WNV) in North America. Complementary choice and no-choice landing assays were developed to examine host acceptance by North American Cx. pipiens in the laboratory. Populations collected from above- and below-ground sites in suburban Chicago were identified as forms pipiens and molestus using a polymerase chain reaction-based assay. Avian and human host acceptance was then quantified for the two populations, as well as for their hybrid and backcross offspring. No-choice tests were used to demonstrate that both the pipiens and molestus forms were capable of feeding on human and avian hosts. Choice tests were used to demonstrate that form pipiens females were strongly avian-seeking; an individual's probability of accepting the chick host was 85%. Form molestus females were more likely to accept the human host (87%). Rates of host acceptance by F1 and backcross progeny were intermediate to those of their parents. The results suggest that host preferences in Cx. pipiens are genetically determined, and that ongoing hybridization between above- and below-ground populations is an important contributor to epizootic transmission of WNV in North America.

Araport: the Arabidopsis information portal

The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release ‘modules’ that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts ‘science apps,’ developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community.

Production of onion fly attractants and ovipositional stimulants by bacterial isolates cultured on onion

Decomposing onions at certain microbial successional stages produce potent volatile attractants and ovipositional stimulants of the onion fly,Delia antiqua (Diptera: Anthomyiidae). A reproducible source of these compounds was obtained by culturingErwinia carotovora var.carotovora (EC) on sterile onion tissue. In laboratory choice tests, EC-inoculated onion was more attractive thanKlebsiella pneumoniae (KP) cultured on onion, EC cultured on potato (a nonhost of onion fly), or the chemical synthetic baits dipropyl disulfide and an aqueous solution of 2-phenylethanol and pentanoic acid. Onion flies were mildly attracted to potato after inoculation with EC, but females did not accept EC-inoculated potato for oviposition. This work emphasizes that sources of semiochemicals may need to be defined microbiologically as well as physically and chemically.

Stimulo-deterrent diversion: A concept and its possible application to onion maggot control

Considerable basic information has been gathered on the interaction between the onion fly (Delia antiqua) and its host plant, the onion (Allium cepa). An attempt is underway to manipulate ovipositional behavior of this pest by treating onion seedlings with chemical deterrents while simultaneously providing deeply planted onion culls on which onion flies prefer to lay. This bipolar strategy of behavioral manipulation, termed "stimulo-deterrent diversion" (SDD), has the advantages of: (1) avoiding severe pest deprival and concomitant overriding of deterrents, (2) combining the effects of "push" and "pull" multiplicatively, and (3) providing opportunities for enhanced biological control in sites where the pest becomes concentrated. The suggestion is made that using SDD along with soil insecticide might relax or even reverse selection for physiological resistance ofD. antiqua to insecticides. As tools of molecular biology open new possibilities for manipulating plants and their allelochemicals, applied chemical ecologists should consider arranging situations where the allelochemicals have clear and adaptive messages for the pest. By combining toxins and deterrents at sites where feeding should be prevented, while simultaneously expediting use of alternative plants or plant parts, it might be possible to guide pest evolution toward paths of less conflict with human interest.

Cinnamyl derivatives and monoterpenoids as nonspecific ovipositional deterrents of the onion fly

Laboratory dose-response choice tests and discriminate-dosage bioassays revealed wide variation in the effectiveness of cinnamyl, cinnamoyl, monoterpene, and phenethyl alcohol derivatives as ovipositional deterrents toDelia antiqua (Meigen), the onion fly. (E)-Cinnamic acids were not detectably deterrent. When formulated in particles of polyethylene glycol, (E)-cinnamaldehyde had a BR90 (concentration eliciting 90% deterrency) of 1.0% and (E)-4-methoxycinnamaldehyde had a BR90 of 0.38%. Among nine monoterpenoids tested,p-cymene was inactive, citronellal had a BR90 of 3.7%, and terpinene-4-ol had a BR90 of 0.46%. Para-substituted phenethyl alcohols gave increasing deterrence in the order: -NO2, CH3O-, -Cl, -CH3, -H. Wide varieties of structures were deterrent: C-8 to C-13, intermediate in polarity, and possessing either oxygen-containing or nitrile functional groups. The air concentration of (E)-cinnamaldehyde at its BR90 was 1.7 ng/ml. This relatively high concentration, the diversity in deterrent structures, and the lack of differences in deterrency among positional and optical isomers suggest that ovipositional deterrency in onion flies is mediated by receptors broadly tuned for detecting phenylpropenoid, phenolic, monoterpenoid, and perhaps other classes of allelochemicals.

Predicting the functional effect of amino acid substitutions and indels

As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. Frameshifts and non-sense mutations are likely to cause a negative effect on protein function. Existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. Our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for UniProt non-human protein variations. In our approach, the area under the receiver operating characteristic curve (AUC) for the human and non-human protein variation datasets is ∼0.85. We also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. In summary, we have developed a new algorithm, PROVEAN (Protein Variation Effect Analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. The PROVEAN tool is available online at http://provean.jcvi.org.

The bonobo genome compared with the chimpanzee and human genomes

Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.

A vertebrate case study of the quality of assemblies derived from next-generation sequences

The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references.

New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information

Background

In order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research. For this reason, after five years from the initial submission of the Entamoeba histolytica draft genome publication, we have re-examined the original 23 Mb assembly and the annotation of the predicted genes.

Principal Findings

The evaluation of the genomic sequence led to the identification of more than one hundred artifactual tandem duplications that were eliminated by re-assembling the genome. The reannotation was done using a combination of manual and automated genome analysis. The new 20 Mb assembly contains 1,496 scaffolds and 8,201 predicted genes, of which 60% are identical to the initial annotation and the remaining 40% underwent structural changes. Functional classification of 60% of the genes was modified based on recent sequence comparisons and new experimental data. We have assigned putative function to 3,788 proteins (46% of the predicted proteome) based on the annotation of predicted gene families, and have identified 58 protein families of five or more members that share no homology with known proteins and thus could be entamoeba specific. Genome analysis also revealed new features such as the presence of segmental duplications of up to 16 kb flanked by inverted repeats, and the tight association of some gene families with transposable elements.

Significance

This new genome annotation and analysis represents a more refined and accurate blueprint of the pathogen genome, and provides an upgraded tool as reference for the study of many important aspects of E. histolytica biology, such as genome evolution and pathogenesis.

Entamoeba histolytica is an anaerobic parasitic protozoan that causes amoebic dysentery. The parasites colonize the large intestine, but under some circumstances may invade the intestinal mucosa, enter the bloodstream and lead to the formation of abscesses such amoebic liver abscesses. The draft genome of E. histolytica, published in 2005, provided the scientific community with the first comprehensive view of the gene set for this parasite and important tools for elucidating the genetic basis of Entamoeba pathogenicity. Because complete genetic knowledge is critical for drug discovery and potential vaccine development for amoebiases, we have re-examined the original draft genome for E. histolytica. We have corrected the sequence assembly, improved the gene predictions and refreshed the functional gene assignments. As a result, this effort has led to a more accurate gene annotation, and the discovery of novel features, such as the presence of genome segmental duplications and the close association of some gene families with transposable elements. We believe that continuing efforts to improve genomic data will undoubtedly help to identify and characterize potential targets for amoebiasis control, as well as to contribute to a better understanding of genome evolution and pathogenesis for this parasite.

Assembly algorithms for next-generation sequencing data

The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.

Toxicity of bloodmeals from ivermectin-treated cattle to Anopheles gambiae s.l

Two anthelmintic drugs used as cattle dewormers, ivermectin and moxidectin, were tested for their lethal and sublethal effects on the malarial vectors Anopheles gambiae s.s. and An. arabiensis. In the laboratory, direct addition of ivermectin to bovine blood reduced the survivorship and fecundity of mosquitoes fed on the blood. The median lethal concentration (LC(50)) of ivermectin in the bloodmeal, for the laboratory populations of An. gambiae s.l., was 19.8 ppb. In the field, commercially available formulations containing ivermectin or moxidectin were injected into cattle at three times the recommended dose. Most (90%) of the An. gambiae s.s. that fed on the ivermectin-treated cattle within 2 weeks of treatment failed to survive more than 10 days post-bloodmeal. No eggs were deposited by An. gambiae s.s. that fed on ivermectin-treated cattle within 10 days of treatment. In contrast, the survivorship and egg production of the mosquitoes that fed on the moxidectin-treated cattle were no different from those feeding on untreated cattle. These results indicate that treatment of cattle with ivermectin could be used, as part of an integrated control programme, to reduce the zoophilic vector populations that contribute to the transmission of the parasites responsible for human malaria.

Designation of chemicals in terms of the locomotor responses they elicit from insects: an update of Dethier et al. (1960)

A scheme updating that of Dethier et al. (1960) (J. Econ. Entomol. 53: 134-136) for chemicals influencing insect locomotor behavior is introduced. Attractant, repellent, and arrestant retain their previous definitions. However, attractants or repellents are now recognized to operate both by kinetic and tactic mechanisms. Locomotor initiator is a new term for stimuli that activate normal levels of kinetic locomotion. Locomotor stimulant is reserved for activation of abnormally high kinetic locomotion, like that arising upon sublethal exposure to certain insecticides. The new terms engagent and disengagent apply to chemicals that, by their effects on locomotion, increase or decrease interaction with the source of stimulation, respectively. With these clarifications, insect behavioral terms unique to medical entomology but contradicting Dethier et al.'s classical scheme can be reconciled with the vocabulary of formal behavioral science.

Charcot-Marie-Tooth type 1A with a pes planovalgus foot type: a case report

The classic foot type of Charcot-Marie-Tooth type 1A is pes cavovarus with associated digital contractures. In this article, we describe a painful pes planovalgus foot type in a 10-year-old child with progressive Charcot-Marie-Tooth type 1A polyneuropathy. The authors discuss possible etiologies and treatment options in this isolated case. The value of gait analysis in preoperative planning and postoperative surveillance are also discussed.

LEVEL OF CLINICAL EVIDENCE

4.

Aggressive assembly of pyrosequencing reads with mates

MOTIVATION

DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a 'hybrid' approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data.

RESULTS

Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data.

AVAILABILITY

The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License.

Alcohol consumption among recreational boaters: factors for intervention

Recreational boating is a popular leisure time activity in many countries. It is estimated that, in Australia, boating incidents cause more harm than rail and air crashes combined and, in terms of transport, are second only to motor vehicle crashes as a cause of serious injury. The consumption of alcohol among recreational boaters is considered an important risk factor for fatalities and injuries among both operators and passengers. Using a database of all recreational vessels registered in Western Australia (WA), a sample of 500 adult boaters was recruited to participate in a telephone survey. The effects of demographic variables and boating characteristics upon the use of alcohol among recreational boaters on their last trip were explored using logistic regression. The odds of not having a drink were associated, after adjusting for age, with having completed a boating education course and with carrying children less than 12 years on board. The use of alcohol was not found to be prevalent among WA recreational boat owners. Based on these findings, it is recommended that efforts to decrease boating-related incidents, such as through education and legislation measures, be monitored over time to determine the effects of these strategies upon safety behaviours.

Parkour: a new extreme sport and a case study

Parkour is an extreme sport that has been popular in Europe for a few years. This sport has now made it across the Atlantic and is quickly gaining popularity in the United States. Participants of this activity, known as parkouristes, try to overcome obstacles in their environment in the most efficient manner possible. This can be accomplished by simply jumping or scaling an obstacle, but sometimes this is done in a very acrobatic manner. The sport had a longtime underground following but has now gained media exposure through various television advertisements, and it has even been featured in recent blockbuster films. As a result, many amateurs are attempting to recreate these dangerous stunts without proper protection or guidance. We will review the case of an 18-year-old male who sustained multiple fracture/dislocations of his left foot while practicing parkour. ACFAS Level of Clinical Evidence: 4.

Genome sequence of Aedes aegypti, a major arbovirus vector

We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.

Differentiation of competitive vs. non-competitive mechanisms mediating disruption of moth sexual communication by point sources of sex pheromone (part I): Theory

This study establishes a theoretical framework for differentiating among possible behavioral mechanisms whereby sexual communication of moths is disrupted in crops treated with point sources of pheromone. The major mechanisms recognized in the mating disruption literature fall into two main categories: competitive (competitive attraction = false-plume-following) and non-competitive (camouflage, desensitization, and sensory imbalance). Each disruption mechanism has been precisely defined verbally, and then the distinguishing characteristics of the two categories were defined mathematically. The sets of predictions associated with each category were visualized by graphical plots of mathematical simulations. Profiles of simulated male visitation rates to pheromone-baited traps deployed in pheromone-treated crops were graphed against density of pheromone dispensers by using various types of axes. Key traits of non-competitive attraction are as follows: concave profiles on untransformed axes, with an asymptotic approach to zero catch of male moths in traps; a straight line with positive slope when 1/catch is plotted against dispenser density (Miller-Gut plot); and a straight line with negative slope when catch is plotted against dispenser density * catch (Miller-de Lame plot). Key traits of non-competitive disruption profiles include: an initial linear disruption profile on untransformed axes; a concave Miller-Gut plot; and a recurving Miller-de Lame plot. These differences in profiles provide a basis for distinguishing competitive from non-competitive mechanisms when analyzing disruption profiles from field experiments. Slopes and intercepts of these secondary plots can also reveal both male and female moth densities, if the relative attractiveness of traps, females, and dispensers is known. The absolute value of the slope of the Miller-de Lame plot is a measure of each dispenser's activity (D(a)) for suppressing catch of male moths in traps. An application activity (D(Aa)) for a given dispenser can be calculated by multiplying D(a) by the number of such dispensers applied per hectare of crop.

Linked selected and neutral loci in heterogeneous environments

We analyze a system of ordinary differential equations modeling haplotype frequencies at a physically linked pair of loci, one selected and one neutral, in a population consisting of two demes with divergent selection regimes. The system is singularly perturbed, with the migration rate m between the demes serving as a small parameter. We use geometric singular perturbation theory to show that when m is sufficiently small, each solution not initially fixed for the same selected allele in both demes approaches one of a 1-dimensional continuum of equilibria. We then obtain asymptotic expansions of the solutions and show their validity on arbitrarily long finite time intervals. From these expansions we obtain formulas for the transient dynamics of F(ST) (a measure of population structure) at both loci, as well as for the rate of genotyping error if the allelic state at the selected locus is inferred from that at the neutral (marker) locus. We examine two cases in detail, one modeling two populations in secondary contact after a period of evolution in allopatry, and the other modeling the origination and spread of a resistance allele.

Differentiation of competitive vs. non-competitive mechanisms mediating disruption of moth sexual communication by point sources of sex pheromone (part 2): Case studies

Eleven out of 13 disruption profiles (plots of dispenser density vs. male catch) from moth sex pheromone literature were consistent with a competitive-attraction mechanism, in which dispensers attract males and thereby divert them from females. Mean dispenser activity (D(a)) across all competitive-attraction cases was 0.04 +/- 0.06 (SD); values ranged from 0.0005 for a tiny laminated flake dispenser of racemic disparlure targeting gypsy moth to 0.2 for polyethylene tube dispensers used against lightbrown apple moth. A dispenser application activity (D(Aa)) can be calculated by multiplying D(a) by the number of such dispensers applied per hectare of crop. The highest dispenser application activity (D(Aa)) values approached 200 and corresponded to >99% inhibition of catches of male moths in monitoring traps. Relative to the D(Aa) scale, % inhibition of catches of male moths compressed and obscured large differences in D(Aa) when % disruption exceeded 90%. For cases of competitive attraction, these two efficacy scales can be interconverted by using the formula: D(Aa) approximately = 100/(100 minus % disruption). When disruptive point sources of pheromone were directly observed, male moths were seen approaching pheromone dispensers whose disruption profiles matched competitive attraction. Two cases fit non-competitive disruption mechanisms, which include camouflage, desensitization (adaptation and/or habituation), and sensory imbalance. In these cases, pheromone was released at rates higher than for cases of disruption by competitive attraction. Practical ramifications of the finding that competitive attraction appears to be the prevalent mechanism for moth mating disruption by pheromone point sources are listed. We believe that the congruence of diverse sets of mating disruption field data with explicit a priori predictions validates competitive-attraction theory. The analytical tools and principles governing competitive attraction that were uncovered during this study of mating disruption of moths should be generally applicable to competitive-attraction phenomena.

Mechanized applicator for large-scale field deployment of paraffin-wax dispensers of pheromone for mating disruption in tree fruit

A tractor-mounted mechanized applicator was developed for large-scale deployment of paraffin-wax dispensers of pheromone for mating disruption of oriental fruit moth, Grapholita molesta (Busck). The wax formulation was mostly water and emulsified paraffin wax containing 5% (by weight) pheromone [93:6:1 blend of (Z)-8-dodecen-1-yl-acetate:(E)-8-dodecen-1-yl-acetate: (Z)-8-dodecen-1-ol]. Ten milliliters of wax was applied per tree as approximately 160 deposits (0.04 ml of wax per drop). An average of 23 min was required to treat 1 ha of crop. Disruption efficacy of mechanically applied wax was measured relative to an untreated control in replicated 0.4-ha blocks within a recently abandoned apple orchard. From 6 May to 27 June, 100% disruption of tethered virgin females and 97% inhibition of pheromone traps was achieved for 52 d with two applications of wax. However, during mid- to late summer (July-August), this level of efficacy was maintained for only approximately 1 wk after each of two applications. Higher temperatures later in the season may have accounted for abbreviated efficacy of the applied small drops. Mechanically applied paraffin-wax technology may increase adoption of mating disruption given that a higher level of efficacy was achieved despite deploying less active ingredient per hectare relative to that used with reservoir dispensers. The savings in labor by not requiring hand application of reservoir dispensers could be directed toward cost of machinery. However, the short duration of efficacy obtained with the current wax formulation and mechanical applicator is judged uneconomical given the eight or more applications that would have been required for high-performance disruption over the full season. Larger drops with lower surface area-to-volume ratios are expected to prolong pheromone release for extended efficacy and desirable overall economics.

Higher densities of distributed pheromone sources provide disruption of codling moth (Lepidoptera: Tortricidae) superior to that of lower densities of clumped sources

Field experiments quantified the effect of synthetic pheromone release-site density and distribution on 1) orientational disruption of male codling moths, Cydia pomonella (L.) (Lepidoptera: Tortricidae), to pheromone-baited traps; and 2) fruit injury. A clustering test varied pheromone release-site density from 0 to 1,000 Isomate-C Plus dispensers per ha while maintaining the total number of dispensers at 1,000. Percentage of orientational disruption of pheromone-baited traps increased significantly as a function of increasing density of release sites. Fruit injury decreased as the density of release sites increased and was lowest in plots treated with Isomate-C Plus dispensers distributed as 1,000 point sources per ha. We also manipulated point source density of 0.1-ml paraffin-wax drops containing 5% codlemone [(E,E)-8,10-dodecadien-1-ol], and thus the total amount of pheromone deployed per hectare. The percentage of disruption of traps baited with either 1.0- or 0.1-mg codlemone lures increased with increasing density of wax drops deployed. Both trapping and field observations confirmed that wax drops were attractive to male codling moths, suggesting that disruption was mediated by competitive attraction. Development of dispensers that can be mechanically applied at high densities has potential to improve the efficacy and economics of codling moth disruption at high population densities.