Cultural adaptation to Bolivian Quechua and psychometric analysis of the Patient Health Questionnaire PHQ-9.

OBJECTIVE: Cultural adaptation of the Patient Health Questionnaire-PHQ-9 to Bolivian Quechua and analysis of the internal structure validity, reliability, and measurement invariance by sociodemographic variables. METHODS: The PHQ-9 was translated and back-translated (English-Quechua-English) to optimise translation. For the cultural adaptation, experts, and people from the target population (e.g., in focus groups) verified the suitability of the translated PHQ-9. For the psychometric analysis, we performed a Confirmatory Factor Analysis (CFA) to evaluate internal validity, calculated α and ω indices to assess reliability, and performed a Multiple Indicator, Multiple Cause (MIMIC) model for evaluating measurement invariance by sex, age, marital status, educational level and residence. We used standard goodness-of-fit indices to interpret both CFA results. RESULTS: The experts and focus groups improved the translated PHQ-9, making it clear and culturally equivalent. For the psychometric analysis, we included data from 397 participants, from which 73.3% were female, 33.0% were 18-30 years old, 56.7% reported primary school studies, 63.2% were single, and 62.0% resided in urban areas. In the CFA, the single-factor model showed adequate fit (Comparative Fit Index = 0.983; Tucker-Lewis Index = 0.977; Standardized Root Mean Squared Residual = 0.046; Root Mean Squared Error of Approximation = 0.069), while the reliability was optimal (α = 0.869-0.877; ω = 0.874-0.885). The invariance was confirmed across all sociodemographic variables (Change in Comparative Fit Index (delta) or Root Mean Square Error of Approximation (delta) < 0.01). CONCLUSIONS: The PHQ-9 adapted to Bolivian Quechua offers a valid, reliable and invariant unidimensional measurement across groups by sex, age, marital status, educational level and residence.

Cultural adaptation to quechua and psychometric analysis of the patient health questionnaire (PHQ-9) in a peruvian population. / Adaptación cultural al Quechua y análisis psicométrico del Patient Health Questionnaire (PHQ-9) en población peruana.

OBJECTIVE: . To translate and culturally adapt the Patient Health Questionnaire (PHQ-9) to three varieties of Quechua and analyse their validity, reliability, and measurement invariance. MATERIALS AND METHODS: . 1) Cultural adaptation phase: the PHQ-9 was translated from English into three variants of Quechua (Central, Chanca, Cuzco-Collao) and translated again into English. Then, experts and focus groups allowed the translations to be culturally adapted. 2) Psychometric phase: the unidimensionality of the adapted PHQ-9 was evaluated by using Confirmatory Factor Analysis (CFA), reliability was evaluated by internal consistency (Alpha and Omega), and measurement invariance according to Quechua varieties and sociodemographic variables was evaluated by using CFA, multigroups and MIMIC models (Multiple Indicator Multiple Cause). RESULTS: . Each of the adaptations of the PHQ-9 to the three Quechua varieties reported clear and culturally equivalent items. Subsequently, data from 970 Quechua-speaking adult men and women were analyzed. The general one-dimensional model reported an adequate fit (Comparative fit index = 0.990, Tucker-Lewis index = 0.987, Standardized root mean squared residual= 0.048, Root mean squared error of approximation=0.071); each of the Quechua varieties also showed an adequate fit. Reliability was high for all varieties (α = 0.865 - 0.915; ω = 0.833 - 0.881). The results of the multigroup CFA and MIMIC models confirmed measurement invariance according to Quechua variant, sex, residence, age, marital status and educational level. CONCLUSIONS: . The PHQ-9 adaptations to Central Quechua, Chanca and Cuzco-Collao offer a valid, reliable and invariant measurement, confirming that comparisons can be made between the evaluated groups. Its use will benefit mental health research and care for Quechua-speaking populations.

OBJETIVO: . Traducir y adaptar culturalmente el Patient Health Questionnaire (PHQ-9) a tres variedades del quechua y analizar su validez, confiabilidad e invarianza. MATERIALES Y MÉTODOS: . 1) Fase de adaptación cultural: el PHQ-9 fue traducido del inglés a tres variantes del quechua (Central, Chanca, Cuzco-Collao) y traducido nuevamente al inglés, posteriormente expertos y grupos focales permitieron adaptar culturalmente las traducciones. 2) Fase psicométrica: se evaluó la uni-dimensionalidad del PHQ-9 adaptado mediante un Análisis Factorial Confirmatorio (CFA), la confiabilidad se evaluó mediante consistencia interna (Alpha y Omega), y la invarianza de medida según variedades del quechua y variables sociodemográficas se evaluó empleando CFA multigrupos y modelos MIMIC (Múltiples Indicadores y Múltiples Causas). RESULTADOS: . Cada una de las adaptaciones del PHQ-9 a las tres variedades de quechua reportaron ítems claros y culturalmente equivalentes. Posteriormente, con 970 datos de quechuahablantes adultos varones y mujeres, el modelo general unidimensional reportó un ajuste adecuado (índice de ajuste comparativo: 0,990, índice de Tucker-Lewis: 0,987, residuo estandarizado cuadrático medio: 0,048, raíz del error cuadrático medio de aproximación: 0,071), lo mismo ocurrió para cada variedad del quechua. La confiabilidad fue alta para todas las variedades (α = 0,865 - 0,915; ω = 0,833 - 0,881). Los resultados del CFA multigrupos y modelos MIMIC confirmaron invarianza de medida según variante del quechua, sexo, residencia, edad, estado civil y nivel educativo. CONCLUSIONES: . Las adaptaciones del PHQ-9 a Quechua Central, Chanca y Cuzco-Collao ofrecen una medición válida, confiable e invariante, confirmando que se pueden hacer comparaciones en los grupos evaluados. Su uso beneficiará a la investigación y a la atención en salud mental de poblaciones quechuahablantes.

Quantitative microbial spoilage risk assessment caused by fungi in sports drinks through multilevel modelling.

The risk of fungal spoilage of sports drinks produced in the beverage industry was assessed using quantitative microbial spoilage risk assessment (QMSRA). The most relevant pathway was the contamination of the bottles during packaging by mould spores in the air. Mould spores' concentration was estimated by longitudinal sampling for 6 years (936 samples) in different production areas and seasons. This data was analysed using a multilevel model that separates the natural variability in spore concentration (as a function of sampling year, season, and area) and the uncertainty of the sampling method. Then, the expected fungal contamination per bottle was estimated by Monte Carlo simulation, considering their settling velocity and the time and exposure area. The product's shelf life was estimated through the inoculation of bottles with mould spores, following the determination of the probability of visual spoilage as a function of storage time at 20 and 30 °C using logistic regression. The Monte Carlo model estimated low expected spore contamination in the product (1.7 × 10-6 CFU/bottle). Nonetheless, the risk of spoilage is still relevant due to the large production volume and because, as observed experimentally, even a single spore has a high spoilage potential. The applicability of the QMSRA during daily production was made possible through the simplification of the model under the hypothesis that no bottle will be contaminated by more than one spore. This simplification allows the calculation of a two-dimensional performance objective that combines the spore concentration in the air and the exposure time, defining "acceptable combinations" according to an acceptable level of spoilage (ALOS; the proportion of spoiled bottles). The implementation of the model at the operational level was done through the representation of the simplified model as a two-dimensional diagram that defines acceptable and unacceptable areas. The innovative methodology employed here for defining and simplifying QMSRA models can be a blueprint for future studies aiming to quantify the risk of spoilage of other beverages with a similar scope.

Automation of an atomic force microscope via Arduino.

The Atomic Force Microscopy is a very versatile technique that allows to characterize surfaces by acquiring topographies with sub-nanometer resolution. This technique often overcomes the problems and capabilities of electron microscopy when characterizing few nanometers thin coatings over solid substrates. They are expensive, in the half million dollar range for standard units, and therefore it is often difficult to upgrade to new units with improved characteristics. One of these improvements, motorization and automation of the measurements is very interesting to sample different parts of a substrate in an unattended way. Here we report a low cost upgrade under 60 $ to a Dimension 3000 AFM based on a control unit using an Arduino Leonardo. It enables to acquire dozens or hundreds of images automatically by mimicking keyboard shortcuts and interfacing the AFM PCI card.

Adaptación cultural al Quechua y análisis psicométrico del Patient Health Questionnaire (PHQ-9) en población peruana / Cultural adaptation to Quechua and psychometric analysis of the Patient Health Questionnaire PHQ-9 in a peruvian population

Objetivo . Traducir y adaptar culturalmente el Patient Health Questionnaire (PHQ-9) a tres variedades del quechua y analizar su validez, confiabilidad e invarianza. Materiales y métodos . 1) Fase de adaptación cultural: el PHQ-9 fue traducido del inglés a tres variantes del quechua (Central, Chanca, Cuzco-Collao) y traducido nuevamente al inglés, posteriormente expertos y grupos focales permitieron adaptar culturalmente las traducciones. 2) Fase psicométrica: se evaluó la uni-dimensionalidad del PHQ-9 adaptado mediante un Análisis Factorial Confirmatorio (CFA), la confiabilidad se evaluó mediante consistencia interna (Alpha y Omega), y la invarianza de medida según variedades del quechua y variables sociodemográficas se evaluó empleando CFA multigrupos y modelos MIMIC (Múltiples Indicadores y Múltiples Causas). Resultados . Cada una de las adaptaciones del PHQ-9 a las tres variedades de quechua reportaron ítems claros y culturalmente equivalentes. Posteriormente, con 970 datos de quechuahablantes adultos varones y mujeres, el modelo general unidimensional reportó un ajuste adecuado (índice de ajuste comparativo: 0,990, índice de Tucker-Lewis: 0,987, residuo estandarizado cuadrático medio: 0,048, raíz del error cuadrático medio de aproximación: 0,071), lo mismo ocurrió para cada variedad del quechua. La confiabilidad fue alta para todas las variedades (α = 0,865 - 0,915; ω = 0,833 - 0,881). Los resultados del CFA multigrupos y modelos MIMIC confirmaron invarianza de medida según variante del quechua, sexo, residencia, edad, estado civil y nivel educativo. Conclusiones . Las adaptaciones del PHQ-9 a Quechua Central, Chanca y Cuzco-Collao ofrecen una medición válida, confiable e invariante, confirmando que se pueden hacer comparaciones en los grupos evaluados. Su uso beneficiará a la investigación y a la atención en salud mental de poblaciones quechuahablantes.

Objective . To translate and culturally adapt the Patient Health Questionnaire (PHQ-9) to three varieties of Quechua and analyse their validity, reliability, and measurement invariance. Materials and methods . 1) Cultural adaptation phase: the PHQ-9 was translated from English into three variants of Quechua (Central, Chanca, Cuzco-Collao) and translated again into English. Then, experts and focus groups allowed the translations to be culturally adapted. 2) Psychometric phase: the unidimensionality of the adapted PHQ-9 was evaluated by using Confirmatory Factor Analysis (CFA), reliability was evaluated by internal consistency (Alpha and Omega), and measurement invariance according to Quechua varieties and sociodemographic variables was evaluated by using CFA, multigroups and MIMIC models (Multiple Indicator Multiple Cause). Results . Each of the adaptations of the PHQ-9 to the three Quechua varieties reported clear and culturally equivalent items. Subsequently, data from 970 Quechua-speaking adult men and women were analyzed. The general one-dimensional model reported an adequate fit (Comparative fit index = 0.990, Tucker-Lewis index = 0.987, Standardized root mean squared residual= 0.048, Root mean squared error of approximation=0.071); each of the Quechua varieties also showed an adequate fit. Reliability was high for all varieties (α = 0.865 - 0.915; ω = 0.833 - 0.881). The results of the multigroup CFA and MIMIC models confirmed measurement invariance according to Quechua variant, sex, residence, age, marital status and educational level. Conclusions . The PHQ-9 adaptations to Central Quechua, Chanca and Cuzco-Collao offer a valid, reliable and invariant measurement, confirming that comparisons can be made between the evaluated groups. Its use will benefit mental health research and care for Quechua-speaking populations.

Horn fly transcriptome data of ten populations from the southern United States with varying degrees and molecular mechanisms of pesticide resistance.

Haematobia irritans irritans (Linnaeus, 1758: Diptera: Muscidae), the horn fly, is an external parasite of penned and pastured livestock that causes a major economic impact on cattle production worldwide. Pesticides such as synthetic pyrethroids and organophosphates are routinely used to control horn flies; however, resistance to these chemicals has become a concern in several countries. To further elucidate the molecular mechanisms of resistance in horn fly populations, we sequenced the transcriptomes of ten populations of horn flies from the southern US possessing varying degrees of pesticide resistance levels to pyrethroids, organophosphates, and endosulfans. We employed an Illumina paired end HiSeq approach, followed by de novo assembly of the transcriptomes using CLC Genomics Workbench 8.0.1 De Novo Assembler using multiple kmers, and annotation using Blast2GO PRO version 5.2.5. The Gene Ontology biological process term Response to Insecticide was found in all the populations, but at an increased frequency in the populations with higher levels of insecticide resistance. The raw sequence reads are archived in the Sequence Read Archive (SRA) and assembled population transcriptomes in the Transcriptome Shotgun Assembly (TSA) at the National Center for Biotechnology Information (NCBI).

Biochemical characterisation of Cytochrome P450 oxidoreductase from the cattle tick, Rhipicephalus microplus, highlights potential new acaricide target.

Management of the cattle tick, Rhipicephalus microplus, presents a challenge because some populations of this cosmopolitan and economically important ectoparasite are resistant to multiple classes of acaricides. Cytochrome P450 oxidoreductase (CPR) is part of the cytochrome P450 (CYP450) monooxygenases that are involved in metabolic resistance by their ability to detoxify acaricides. Inhibiting CPR, the sole redox partner that transfers electrons to CYP450s, could overcome this type of metabolic resistance. This report represents the biochemical characterisation of a CPR from ticks. Recombinant CPR of R. microplus (RmCPR), minus its N-terminal transmembrane domain, was produced in a bacterial expression system and subjected to biochemical analyses. RmCPR displayed a characteristic dual flavin oxidoreductase spectrum. Incubation with nicotinamide adenine dinucleotide phosphate (NADPH) lead to an increase in absorbance between 500 and 600 nm with a corresponding appearance of a peak absorbance at 340-350 nm indicating functional transfer of electrons between NADPH and the bound flavin cofactors. Using the pseudoredox partner, kinetic parameters for both cytochrome c and NADPH binding were calculated as 26.6 ± 11.4 µM and 7.03 ± 1.8 µM, respectively. The turnover, Kcat, for RmCPR for cytochrome c was calculated as 0.08 s-1 which is significantly lower than the CPR homologues of other species. IC50 (Half maximal Inhibitory Concentration) values obtained for the adenosine analogues 2', 5' ADP, 2'- AMP, NADP+and the reductase inhibitor diphenyliodonium were: 140, 82.2, 24.5, and 75.3 µM, respectively. Biochemically, RmCPR resembles CPRs of hematophagous arthropods more so than mammalian CPRs. These findings highlight the potential of RmCPR as a target for the rational design of safer and potent acaricides against R. microplus.

The adult horn fly transcriptome and its complement of transcripts encoding cytochrome P450s, glutathione S-transferases, and esterases.

The horn fly, Haematobia irritans, is a blood-feeding parasitic fly with a global distribution that includes Europe, Africa, Asia, and the Americas. The fly has a major detrimental economic impact upon cattle production, with losses estimated at over $800 million annually in the United States and $2.5 billion in Brazil alone. Insecticide resistance in specific horn fly populations has been a problem for many years and there are several mechanisms whereby resistance develops. Little is known about the complement of metabolic enzymes encoded by the horn fly's genome that might provide the fly with detoxification or sequestration pathways to survive insecticide treatments. The cytochrome P450, glutathione S-transferase, and esterase enzyme families contain members that are capable of sequestering and/or detoxifying xenobiotic molecules such as insecticides. We sought to develop a comprehensive dataset of metabolic enzyme-encoding transcript sequences from the adult horn fly, as this is the life stage whose actions directly impose the economic costs to cattle producers. We used an Illumina paired-end read RNA-Seq approach to determine the adult horn fly transcriptomes from laboratory and field populations of horn flies with varying levels of pesticide resistance, including untreated and pyrethroid-treated newly eclosed adult flies. We followed with bioinformatic analyses to discern sequences putatively encoding cytochrome P450, esterase, and GST enzymes. We utilized read-mapping of RNA-Seq data and quantitative real-time polymerase chain reaction (qRT-PCR) to examine gene expression levels of specific P450 transcripts in several fly populations with varying degrees of pesticide resistance.

Identification of anti-horn fly vaccine antigen candidates using a reverse vaccinology approach.

BACKGROUND: The horn fly, Haematobia irritans irritans, causes significant production losses to the cattle industry. Horn fly control relies on insecticides; however, alternative control methods such as vaccines are needed due to the fly's capacity to quickly develop resistance to insecticides, and the pressure for eco-friendly options. METHODS: We used a reverse vaccinology approach comprising three vaccine prediction and 11 annotation tools to evaluate and rank 79,542 translated open reading frames (ORFs) from the horn fly's transcriptome, and selected 10 transcript ORFs as vaccine candidates for expression in Pichia pastoris. The expression of the 10 selected transcripts and the proteins that they encoded were investigated in adult flies by reverse transcription polymerase chain reaction (RT-PCR) and mass spectrometry, respectively. Then, we evaluated the immunogenicity of a vaccine candidate in an immunization trial and the antigen's effects on horn fly mortality and fecundity in an in vitro feeding assay. RESULTS: Six of the ten vaccine candidate antigens were successfully expressed in P. pastoris. RT-PCR confirmed the expression of all six ORFs in adult fly RNA. One of the vaccine candidate antigens, BI-HS009, was expressed in sufficient quantity for immunogenicity and efficacy trials. The IgG titers of animals vaccinated with BI-HS009 plus adjuvant were significantly higher than those of animals vaccinated with buffer plus adjuvant only from days 42 to 112, with a peak on day 56. Progeny of horn flies feeding upon blood from animals vaccinated with BI-HS009 plus adjuvant collected on day 56 had 63% lower pupariation rate and 57% lower adult emergence than the control group (ANOVA: F (1, 6) = 8.221, P = 0.028 and F (1, 6) = 8.299, P = 0.028, respectively). CONCLUSIONS: The reverse vaccinology approach streamlined the discovery process by prioritizing possible vaccine antigen candidates. Through a thoughtful process of selection and in vivo and in vitro evaluations, we were able to identify a promising antigen for an anti-horn fly vaccine.

Factors That Affect the Microbiological Stability of Chicha Morada during Its Production on an Industrial Scale: A Review.

ABSTRACT: Chicha morada, also known as purple corn drink (PCD), is a traditional noncarbonated beverage commonly prepared at homes and restaurants in Peru. However, in recent years, it is being produced at an industrial scale aiming to extend its shelf life, expand its marketing, and make it known worldwide. Traditionally, this beverage, whose main component is purple corn (Zea mays L.), was made and consumed quickly and in some cases, stored under refrigeration until consumption, but never beyond 24 to 48 h. With its industrialization, factories are presented with challenges to design and provide adequate protection of the beverage, assuring its quality and safety. Although its production at an industrial level is similar to that of other noncarbonated drinks containing fruit juice, several processing factors could affect the microbiological stability desired for this beverage, such as the storage of the purple corn drink extract. In this document, a critical review of the production process (raw materials, production stages, and forms of commercialization) that can directly affect the contamination of the beverage is made. Recommendations are made for improving the control points in the industrial process and to avoid potential microbiological problems.

Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus.

Ticks from the genus Rhipicephalus have enormous global economic impact as ectoparasites of cattle. Rhipicephalus microplus and Rhipicephalus annulatus are known to harbor infectious pathogens such as Babesia bovis, Babesia bigemina, and Anaplasma marginale. Having reference quality genomes of these ticks would advance research to identify druggable targets for chemical entities with acaricidal activity and refine anti-tick vaccine approaches. We sequenced and assembled the genomes of R. microplus and R. annulatus, using Pacific Biosciences and HiSeq 4000 technologies on very high molecular weight genomic DNA. We used 22 and 29 SMRT cells on the Pacific Biosciences Sequel for R. microplus and R. annulatus, respectively, and 3 lanes of the Illumina HiSeq 4000 platform for each tick. The PacBio sequence yields for R. microplus and R. annulatus were 21.0 and 27.9 million subreads, respectively, which were assembled with Canu v. 1.7. The final Canu assemblies consisted of 92,167 and 57,796 contigs with an average contig length of 39,249 and 69,055 bp for R. microplus and R. annulatus, respectively. Annotated genome quality was assessed by BUSCO analysis to provide quantitative measures for each assembled genome. Over 82% and 92% of the 1066 member BUSCO gene set was found in the assembled genomes of R. microplus and R. annulatus, respectively. For R. microplus, only 189 of the 1066 BUSCO genes were missing and only 140 were present in a fragmented condition. For R. annulatus, only 75 of the BUSCO genes were missing and only 109 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information.

Sex Chromosome Evolution in Muscid Flies.

Sex chromosomes and sex determining genes can evolve fast, with the sex-linked chromosomes often differing between closely related species. Population genetics theory has been developed and tested to explain the rapid evolution of sex chromosomes and sex determination. However, we do not know why the sex chromosomes are divergent in some taxa and conserved in others. Addressing this question requires comparing closely related taxa with conserved and divergent sex chromosomes to identify biological features that could explain these differences. Cytological karyotypes suggest that muscid flies (e.g., house fly) and blow flies are such a taxonomic pair. The sex chromosomes appear to differ across muscid species, whereas they are conserved across blow flies. Despite the cytological evidence, we do not know the extent to which muscid sex chromosomes are independently derived along different evolutionary lineages. To address that question, we used genomic and transcriptomic sequence data to identify young sex chromosomes in two closely related muscid species, horn fly (Haematobia irritans) and stable fly (Stomoxys calcitrans). We provide evidence that the nascent sex chromosomes of horn fly and stable fly were derived independently from each other and from the young sex chromosomes of the closely related house fly (Musca domestica). We present three different scenarios that could have given rise to the sex chromosomes of horn fly and stable fly, and we describe how the scenarios could be distinguished. Distinguishing between these scenarios in future work could identify features of muscid genomes that promote sex chromosome divergence.

Small-Molecule Inhibitors of Inward Rectifier Potassium (Kir) Channels Reduce Bloodmeal Feeding and Have Insecticidal Activity Against the Horn Fly (Diptera: Muscidae).

Bloodmeal feeding by the horn fly, Haematobia irritans (L.), is associated with reduced milk production and blood loss that ultimately prevents weight gain of calves and yearlings. Thus, blood feeding by H. irritans causes significant economic losses in several continents. As with other arthropods, resistance to the majority of commercialized insecticides reduces the efficacy of current control programs. Thus, innovative technologies and novel biochemical targets for horn fly control are needed. Salivary gland and Malpighian tubule function are critical for H. irritans survivorship as they drive bloodmeal acquisition and maintain ion- and fluid homeostasis during bloodmeal processing, respectively. Experiments were conducted to test the hypothesis that pharmacological modulation of H. irritans inward rectifier potassium (Kir) channels would preclude blood feeding and induce mortality by reducing the secretory activity of the salivary gland while simultaneously inducing Malpighian tubule failure. Experimental results clearly indicate structurally diverse Kir channel modulators reduce the secretory activity of the salivary gland by up to fivefold when compared to control and the reduced saliva secretion was highly correlated to a reduction in bloodmeal acquisition in adult flies. Furthermore, adult feeding on blood treated with Kir channel modulators resulted in significant mortality. In addition to validating the Kir channels of H. irritans as putative insecticide targets, the knowledge gained from this study could be applied to develop novel therapeutic technologies targeting salivary gland or Malpighian tubule function to reduce the economic burden of horn fly ectoparasitism on cattle health and production.

The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901.

The longhorned tick, Haemaphysalis longicornis, feeds upon a wide range of bird and mammalian hosts. Mammalian hosts include cattle, deer, sheep, goats, humans, and horses. This tick is known to transmit a number of pathogens causing tick-borne diseases, and was the vector of a recent serious outbreak of oriental theileriosis in New Zealand. A New Zealand-USA consortium was established to sequence, assemble, and annotate the genome of this tick, using ticks obtained from New Zealand's North Island. In New Zealand, the tick is considered exclusively parthenogenetic and this trait was deemed useful for genome assembly. Very high molecular weight genomic DNA was sequenced on the Illumina HiSeq4000 and the long-read Pac Bio Sequel platforms. Twenty-eight SMRT cells produced a total of 21.3 million reads which were assembled with Canu on a reserved supercomputer node with access to 12 TB of RAM, running continuously for over 24 days. The final assembly dataset consisted of 34,211 contigs with an average contig length of 215,205 bp. The quality of the annotated genome was assessed by BUSCO analysis, an approach that provides quantitative measures for the quality of an assembled genome. Over 95% of the BUSCO gene set was found in the assembled genome. Only 48 of the 1066 BUSCO genes were missing and only 9 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information.

Gene expression during the early stages of host perception and attachment in adult female Rhipicephalus microplus ticks.

The cattle tick, Rhipicephalus microplus, is a serious pest of cattle, with significant economic consequences to the livestock industries of tropical and semitropical countries. Rhipicephalus microplus belongs to the Metastriata group of the Ixodidae family known as hard ticks. When adult hard ticks feed, mating has not yet occurred and an initial host attachment phase of 1-2 days is followed by a slow feeding phase that can last several days. Once mating occurs, feeding concludes with a rapid engorgement phase that is completed in 12-36 h. Our group's interest in mining the genome and transcriptome of R. microplus for novel targets for development of tick control technologies led us to investigate the early transcriptional events occurring upon tick attachment and subsequent feeding. We placed newly molted unfed adult R. microplus females upon a bovine host and harvested the attached ticks after 3, 6, 12, and 24 h. We also placed a group of these ticks in a gas-permeable tube taped onto the side of the bovine host. These ticks were able to sense the host but unable to penetrate the tube to begin attachment and were ultimately harvested after 3 h. This study produced a comprehensive transcriptome from newly molted adult ticks and will provide a useful resource for studies of tick feeding and host perception and also assist genome annotation refinements.

Impacts of long-term insecticide treatment regimes on skdr and kdr pyrethroid resistance alleles in horn fly field populations.

We evaluated the effects of four different 6-year duration control strategies on the resistance levels and frequency of the pyrethroid target site resistance alleles, superkdr (skdr) and kdr, at four field populations of Haematobia irritans irritans (Linnaeus, 1758) (Diptera: Muscidae) in Louisiana, USA. Consecutive use of pyrethroid ear tags for 6 years caused a significant increase in the resistance ratio to pyrethroids as well as the frequencies of both skdr and kdr resistance alleles. After 3 years of consecutive use of pyrethroid ear tags, followed by 1 year with no treatment, and followed by 2 years with organophosphate ear tags, the resistance ratio for pyrethroid was not significantly affected, the %R-skdr significantly dropped while the %R-kdr allele remained relatively high and stable. Similar results were observed when pyrethroid ear tags were used for three consecutive years, followed by 1 year with no treatment, and followed by 2 years with endosulfan ear tags; however, this treatment resulted in a slight increase in the resistance ratio for pyrethroids. In a mosaic, the resistance ratio for pyrethroids showed a 2.5-fold increase but the skdr-kdr genetic profiles did not change, as the %R alleles (skdr and kdr) remained low and stable through the 6 years. Lack of exposure to pyrethroid insecticides for 3 years significantly affected the skdr mutation but not the kdr mutation, preventing re-establishment of susceptibility to pyrethroids. SS-SR (skdr-kdr) individuals were responsible for the maintenance of the kdr mutation in two of the populations studied, and fitness cost seems to strongly affect the SR-RR genotype. None of the four treatment regimens evaluated in the study had satisfactory results for the management of kdr resistance alleles.

Prevalence of Ehrlichia canis (Rickettsiales: Ehrlichieae) DNA in Tissues From Rhipicephalus sanguineus (Acari: Ixodidae) Ticks in Areas Endemic for Canine Monocytic Ehrlichiosis in Brazil.

Canine monocytic ehrlichiosis (CME) is a disease caused by the obligate intracellular bacterium Ehrlichia canis. Tropical lineages of Rhipicephalus sanguineus ticks play an essential role in the transmission of this pathogen. The aim of the present study was to evaluate the prevalence of E. canis DNA in tissue from R. sanguineus ticks in areas endemic for CME in Brazil and quantify levels of E. canis DNA in dissected tissues from these samples. A total of 720 ticks were collected from 72 dogs (36 dogs from the city Araçatuba in São Paulo state and 36 from Campo Grande in the state of Mato Grosso do Sul). Ticks were dissected to collect the guts, ovaries and salivary gland. A quantitative polymerase chain reaction (qPCR) targeting the disulphide bond formation (dsb) protein gene was performed to quantify the level of E. canis infection. The E. canis dsb-qPCR assay was positive for 31.9, 10, and 15.2% of the gut, ovary, and salivary glands, respectively. The average gut, ovary, and salivary gland bacterial load estimated by qPCR was 1.21 × 103, 2.60 × 103, and 4.92 × 103 gene copies/µl, respectively. This is the first report of E. canis DNA in ovaries of R. sanguineus ticks parasitizing dogs in these CME-endemic areas. These observations raise the possibility of E. canis trans-ovarial transmission.

The assembled transcriptome of the adult horn fly, Haematobia irritans.

The horn fly, Haematobia irritans irritans (Linnaeus, 1758; Diptera: Muscidae), a hematophagous external parasite of cattle, causes considerable economic losses to the livestock industry worldwide. This pest is mainly controlled with insecticides; however, horn fly populations from several countries have developed resistance to many of the products available for their control. In an attempt to better understand the adult horn fly and the development of resistance in natural populations, we used an Illumina paired-end read HiSeq and GAII approach to determine the transcriptomes of untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males from a Louisiana population of horn flies with a moderate level of pyrethroid resistance. A total of 128,769,829, 127,276,458, 67,653,920, and 64,270,124 quality-filtered Illumina reads were obtained for untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males, respectively. The de novo assemblies using CLC Genomics Workbench 8.0.1 yielded 15,699, 11,961, 2672, 7278 contigs (≥ 200 nt) for untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males, respectively. More than 56% of the assembled contigs of each data set had significant hits in the BlastX (UniProtKB/Swiss-Prot database) (E <0.001). The number of contigs in each data set with InterProScan, GO mapping, Enzyme codes and KEGG pathway annotations were: Untreated Control Adult Females - 10,331, 8770, 2963, 2183; Untreated control adult males - 8392, 7056, 2449, 1765; Permethrin-treated surviving adult males - 1992, 1609, 641, 495; Permethrin + PBO-treated killed adult males - 5561, 4463, 1628, 1211.

Molecular Characterization of the 2016 New World Screwworm (Diptera: Calliphoridae) Outbreak in the Florida Keys.

New World screwworm (NWS), Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a myiasis-causing fly that can be a serious threat to the health of livestock, wildlife, and humans. Its progressive eradication from the southern United States, Mexico, and Central America from the 1950s to 2000s is an excellent example of successful pest management using sterile insect technique (SIT). In late 2016, autochthonous NWS were detected in the Florida Keys, representing this species' first invasion in the United States in >30 yr. Rapid use of quarantine and SIT was successful in eliminating the infestation by early 2017; however, the geographic source of this infestation remains unknown. Here, we use amplicon sequencing to generate mitochondrial and nuclear sequence data representing all confirmed cases of NWS from this infestation, and compare these sequences to preexisting data sets sampling the native distribution of NWS. We ask two questions regarding the FL Keys outbreak. First, is this infestation the result of a single invasion from one source, or multiple invasions from different sources? And second, what is the geographic origin of this invasion? We found virtually no sequence variation between specimens collected from the FL Keys outbreak, which is consistent with a single source of introduction. However, we also found very little geographic resolution in any of the data sets, which precludes identification of the source of this outbreak. Our lack of success in answering our second question speaks to the need for finer-scale genetic or genomic assessments of NWS population structure, which would facilitate source determination of potential future outbreaks.

A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination.

Haematobia irritans, commonly known as the horn fly, is a globally distributed blood-feeding pest of cattle that is responsible for significant economic losses to cattle producers. Chemical insecticides are the primary means for controlling this pest but problems with insecticide resistance have become common in the horn fly. To provide a foundation for identification of genomic loci for insecticide resistance and for discovery of new control technology, we report the sequencing, assembly, and annotation of the horn fly genome. The assembled genome is 1.14 Gb, comprising 76,616 scaffolds with N50 scaffold length of 23 Kb. Using RNA-Seq data, we have predicted 34,413 gene models of which 19,185 have been assigned functional annotations. Comparative genomics analysis with the Dipteran flies Musca domestica L., Drosophila melanogaster, and Lucilia cuprina, show that the horn fly is most closely related to M. domestica, sharing 8,748 orthologous clusters followed by D. melanogaster and L. cuprina, sharing 7,582 and 7,490 orthologous clusters respectively. We also identified a gene locus for the sodium channel protein in which mutations have been previously reported that confers target site resistance to the most common class of pesticides used in fly control. Additionally, we identified 276 genomic loci encoding members of metabolic enzyme gene families such as cytochrome P450s, esterases and glutathione S-transferases, and several genes orthologous to sex determination pathway genes in other Dipteran species.