Discovery and characterization of two highly divergent variants of a novel potyvirus species infecting Madagascar periwinkle (Catharanthus roseus L.)

During summer 2022, a cluster of Madagascar periwinkle plants with white and mauve flowers were observed with foliar mild yellow mosaic symptoms on a private property in Harlingen, Cameron County, Texas. The symptoms were reproduced on mechanically inoculated periwinkle and Nicotiana benthamiana plants. Virions of 776 to 849 nm in length and 11.7 to 14.8 nm in width were observed in transmission electron microscopy of leaf dip preparations made from symptomatic periwinkle leaves. Highthroughput sequencing (HTS) analysis of total RNA extracts from symptomatic leaves revealed the occurrence of two highly divergent variants of a novel Potyvirus species as the only virus-like sequences present in the sample. The complete genomes of both variants were independently amplified via RT-PCR, cloned, and Sanger sequenced. The 5' and 3' of the genomes were acquired using RACE methodology. The assembled virus genomes were 9,936 and 9,944 nucleotides (nt) long and they shared 99.9-100% identities with the respective HTS-derived genomes. Each genome encoded hypothetical polyprotein of 3,171 amino acids (aa) (362.6 kDa) and 3,173 aa (362.7 kDa), respectively, and they shared 77.3%/84.4% nt/aa polyproteins identities, indicating that they represent highly divergent variants of the same Potyvirus species. Both genomes also shared below species threshold polyprotein identity levels with the most closely phylogenetically related known potyviruses thus indicating that they belong to a novel species. The name periwinkle mild yellow mosaic virus (PwMYMV) is given to the potyvirus with complete genomes of 9,936 nt for variant 1 (PwMYMV-1) and 9,944 nt for variant 2 (PwMYMV-2). We propose that PwMYMV be assigned into the genus Potyvirus (family Potyviridae).

Correction: Haegeman et al. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. Plants 2023, 12, 2139

In the original publication [...].

High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus

This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.

Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests

High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.

High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw

Pawpaw (Asimina triloba) trees exhibiting stunting and foliar mosaic, chlorosis, or distortions were observed in New York. In 2021, leaf samples from two symptomatic trees and a sapling, as well as two asymptomatic trees, were tested for the presence of viruses and viroids by high-throughput sequencing (HTS) using total RNA after ribosomal RNA depletion. HTS sequence information revealed tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) in symptomatic but not in asymptomatic leaves. HTS reads and de novo-assembled contigs covering the genomes of both viruses were obtained, with a higher average read depth for RNA2 than RNA1. The occurrence of TRSV and ToRSV was confirmed in the original leaf samples used for HTS and 12 additional trees and saplings from New York and Maryland in 2022 by RT-PCR combined with Sanger sequencing, and DAS-ELISA. Single infections by TRSV in 11 of 14 trees and dual infections by TRSV and ToRSV in 3 of 14 trees were identified. The nucleotide sequence identity of partial gene fragments of TRSV and ToRSV was high among pawpaw isolates (94.9-100% and 91.8-100%, respectively) and between pawpaw isolates and isolates from other horticultural crops (93.6-100% and 71.3-99.3%, respectively). This study is the first to determine the virome of pawpaw.

Incidence and Genetic Diversity of Grapevine Virus G in Croatian Vineyards

Grapevine virus G (GVG) is a recently discovered vitivirus infecting grapevines. Historically, viruses in the genus Vitivirus have been associated with the grapevine rugose wood disease. Based on new and previously reported GVG isolates, primers and probes were developed for real-time RT-PCR. The developed assay successfully detected the virus in infected plants during dormancy and the growing season. A field study of 4327 grapevines from Croatian continental and coastal wine-growing regions confirmed the presence of GVG in 456 (~10.5%) grapevines from three collection plantations and 77 commercial vineyards, with infection rates ranging from 2% to 100%. Interestingly, the virus was confirmed only in vines considered to be Croatian autochthonous cultivars, but not in introduced cultivars. A 564-nucleotide long portion of the coat protein gene from previously known and newly characterized GVG isolates had nucleotide and amino acid identities ranging from 89% to 100% and from 96.8% to 100%, respectively. Phylogenetic analysis revealed five distinct groups, with isolates originating from the same site being close to each other, indicating possible local infection. The information presented in this manuscript sets the stage for future studies to better understand the ecology and epidemiology of GVG and the possible need for inclusion in certification schemes.

Virus and Virus-like Pathogens in the Grapevine Virus Collection of Croatian Autochthonous Grapevine Cultivars

Grapevine collections play an important role, especially in the study of viruses and virus-like pathogens. In 2009, after an initial ELISA screening for eight viruses (arabis mosaic virus, grapevine fanleaf virus, grapevine fleck virus, grapevine leafroll-associated viruses 1, 2, and 3, and grapevine viruses A and B), a collection of 368 grapevine accessions representing 14 different Croatian autochthonous cultivars and containing single or mixed infection of viruses was established to further characterize the viral pathogens. Subsequently, Western blot, RT-PCR, cloning, and sequencing revealed that grapevine rupestris stem pitting-associated virus was frequently found in accessions of the collection, with isolates showing substantial genetic diversity in the helicase and coat protein regions. High-throughput sequencing of 22 grapevine accessions provides additional insight into the viruses and viroids present in the collection and confirms the fact that Croatian autochthonous grapevine cultivars have high infection rates and high virome diversity. The recent spread of "flavescence dorée" phytoplasma in Europe has not spared the collection. After the first symptoms observed in 2020 and 2021, the presence of phytoplasma was confirmed by LAMP in six grapevine accessions and some of them were lost. Single or multiple viruses and viroids, as well as own rooted grapevines in the collection, make the plants susceptible to various abiotic factors, which, together with the recent occurrence of "flavescence dorée", makes the maintenance of the collection a challenge. Future efforts will be directed towards renewing the collection, as 56% of the original collection has been lost in the last 13 years.

Use of multiplate electrode aggregometry for personalisonalisation of antiplatelet therapy in left ventricular assisst device patients

Funding Acknowledgements

Type of funding sources: None.

Background

The use of Left Ventricular Assist Devices (LVAD) has noticeably improved the survival for patients with advanced heart failure.  However, this treatment is associated with significant adverse effects. Personalisation of antiplatelet therapy is a key in control and reduction of bleeding/thromboembolic complications of this treatment. However, ISHLT and the manufacturer still recommend unified treatment of 150 mg of acetylsalicylic acid for all LVAD patients. In our centre, we base the treatment decision on clinical picture and patient’s responsiveness to antiplatelet therapy. 

The treatment of choice is acetylsalicylic acid in doses 37.5 mg (1 patient), 75 mg (25 patients) and 150 mg (33 patients). For patients unresponsive or intolerant to acetylsalicylic acid we use 75 mg of clopidogrel, currently 9 patients.  1 patient receives both, 75 mg clopidogrel and 75 mg acetylsalicylic acid. 

Purpose

To gain a better understanding of the platelets function and patients" responses to antiplatelet therapy. In aim to reduce the prevalence of bleeding/thromboembolic related adverse events in LVAD patients, and therefore improve patients outcome.

Methods

In 2020, we decided to introduce a structured/test-based approach to antiplatelet therapy in this patients group. With the use of Multiplate Electrode Aggregometry (MEA) we have attempted to diagnose platelet disorders and monitor effectiveness of antiplatelet therapy. Based on MEA platlets inhibition test we were able to tailor the therapy. 

The retrospective audit was conducted with inclusion criteria;

1. Thromboembolic events include pump thrombosis and any other ischemic complications. Bleeding events contains gastrointestinal (GI) and central nervous system (CNS) events.

2. Any thromboembolic and bleeding events after starting antiplatelet therapy, in the first year after LVAD implantation

Results

The tables below presents reduction in both thromboembolic and bleeding complications.

Conclusion

Presented data can be interpreted that, the test-based approach to antiplatelet therapy may be beneficial in limiting the adverse effects of LVAD therapy. However, it needs to be acknowledged that the observation was carried out on a small group of the patients, over a short period of time. Therefore, an extended period of observation is recommended to obtain further data.

Identification and characterization of a novel virus associated with an eriophyid mite in extracts of fruit trees leaves

Eriophyid mites are commonly found on the leaf surface of different plant species. In the present study, a novel virus associated with an eriophyid mite species was detected using high-throughput sequencing (HTS) of total RNA from fruit tree leaves, primarily growing under greenhouse conditions. The complete genome sequence was characterized using rapid amplification of cDNA ends followed by Sanger sequencing, revealing a genome of 8885 nucleotides in length. The single positive-stranded RNA genome was predicted to encode typical conserved domains of members of the genus Iflavirus in the family Iflaviridae. Phylogenetic analysis showed this virus to be closely related to the unclassified iflavirus tomato matilda associated virus (TMaV), with a maximum amino acid sequence identity of 59% in the RNA-dependent RNA polymerase domain. This low identity value justifies the recognition of the novel virus as a potential novel iflavirus. In addition to a lack of graft-transmissibility evidence, RT-PCR and HTS detection of this virus in the putative host plants were not consistent through different years and growing seasons, raising the possibility that rather than a plant virus, this was a virus infecting an organism associated with fruit tree leaves. Identification of Tetra pinnatifidae HTS-derived contigs in all fruit tree samples carrying the novel virus suggested this mite as the most likely host of the new virus (p-value < 1e-11), which is tentatively named "eriophyid mite-associated virus" (EMaV). This study highlights the importance of a careful biological study before assigning a new virus to a particular plant host when using metagenomics data.

Incidence and risk factors for feline lymphoma in UK primary-care practice

Objectives

The study aimed to estimate the incidence and prevalence of feline lymphoma in cats attending primary‐care practices across the UK and to identify patient‐based and environmental (radon and pesticide exposure) risk factors.

Materials and Methods

Case records from the VetCompass programme from primary‐care veterinary practices in the UK were searched for a diagnosis of lymphoma in cats in 2016. Cases were required to have had an external laboratory confirmed diagnosis based on cytology and/or histopathology. A nested case–control study design was used to identify risk factors for lymphoma using multivariable logistic regression.

Results

From a cohort of 562,446 cats under veterinary care at VetCompass participating practices in 2016, a total of 271 lymphoma cases were identified (prevalence: 48/100,000, 95% confidence interval (CI) 44 to 56/100,000; incidence 32/100,000, 95% CI 26 to 35/100,000). There were 180 incident lymphoma cases and 803 controls, all aged 2 years and older. Male (odds ratio (OR) 1.7, 95% CI 1.2 to 2.4), insured (OR 3.6, 95% CI 2.3 to 5.6) and older cats (compared to cats 2 to <5 years, OR 5.0, 95% CI 2.8 to 8.8) were associated with increased odds of lymphoma diagnosis. Vaccinated cats were associated with decreased odds (OR 0.7, 95% CI 0.5 to 1.0) compared to unvaccinated cats, although the type of vaccination received was not statistically significant. Breed and environmental factors studied were not associated with a diagnosis of lymphoma.

Clinical Significance

This is the first study to estimate the frequency and report risk factors for lymphoma in cats attending UK primary‐care practice.

Transverse sectioning in the evaluation of skin biopsy specimens from alopecic dogs

OBJECTIVES

Transverse sectioning of skin biopsy specimens has revolutionised assessment of human alopecia by demonstration of every hair in each specimen, allowing quantitative evaluation of follicular activity. Since only vertical sectioning is performed routinely in veterinary laboratories, we aimed to determine whether transverse sectioning was a valuable technique in assessment of canine alopecia.

METHODS

Paired vertical and transverse sections of biopsy specimens from 31 alopecic dogs were examined independently in triplicate in random order and blinded to previous diagnosis using a standard check-list proforma. Assessments of key features (follicular activity [anagen/telogen], infundibular hyperkeratosis, sebaceous gland abnormalities, pigment clumping, dermal inflammation) by each sectioning method were compared.

RESULTS

In the 31 cases, (atrophic [n = 13], dysplastic [n = 12], inflammatory diseases [n = 6]), follicular inactivity scores (median, [lower-upper quartile]) in transverse sections significantly exceeded those in vertical sections (transverse 4 [3-5], vertical 3 [2-4]). Agreement between the two sectioning planes was moderate for infundibular hyperkeratosis (kappa = 0.5210) and dermal inflammation (0.4351), fair for sebaceous gland abnormalities (0.3966) and pigment clumping (0.2197), but slight for follicular activity (0.1041). Vertical sectioning demonstrated diagnostically important epidermal pathology (n = 2) and dermal thinning (n = 3) whereas transverse sectioning enhanced assessment of hair growth phase (n = 11), follicular structure and architecture (n = 11), and focal luminal or mural folliculitides (n = 3).

CLINICAL SIGNIFICANCE

Transverse sectioning confers significant benefits and complements traditional vertical sectioning in the histological assessment of canine hair follicle diseases, particularly when subtle abnormalities comprise distorted compound follicle architecture, hair cycle arrest or when relatively few adnexal structures are affected.

Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance

The genomic architecture and molecular mechanisms controlling variation in quantitative disease resistance loci are not well understood in plant species and have been barely studied in long-generation trees. Quantitative trait loci mapping and genome-wide association studies were combined to test a large single nucleotide polymorphism (SNP) set for association with quantitative and qualitative white pine blister rust resistance in sugar pine. In the absence of a chromosome-scale reference genome, a high-density consensus linkage map was generated to obtain locations for associated SNPs. Newly discovered associations for white pine blister rust quantitative disease resistance included 453 SNPs involved in wide biological functions, including genes associated with disease resistance and others involved in morphological and developmental processes. In addition, NBS-LRR pathogen recognition genes were found to be involved in quantitative disease resistance, suggesting these newly reported genes are qualitative genes with partial resistance, they are the result of defeated qualitative resistance due to avirulent races, or they have epistatic effects on qualitative disease resistance genes. This study is a step forward in our understanding of the complex genomic architecture of quantitative disease resistance in long-generation trees, and constitutes the first step towards marker-assisted disease resistance breeding in white pine species.

Evidence of Rubus Yellow Net Virus Integration into the Red Raspberry Genome

Rubus yellow net virus (RYNV) infects Rubus spp., causing a severe decline when present in mixed infections with other viruses. RYNV belongs to the family Caulimoviridae, also known as plant pararetroviruses, which can exist as episomal or integrated elements (endogenous). Most of integrated pararetroviruses are noninfectious; however, a few cases have been reported where they excised from the plant genome and formed infectious particles. Graft transmission onto indicator plants R. occidentalis "Munger" has been the standard test method for RYNV detection in certification programs. Previously, it was noticed that some RYNV PCR-positive plants did not induce symptoms on "Munger", suggesting an integration event. In this study, bio-indexing and different molecular techniques were employed to differentiate between integrated and episomal RYNV sequences. Reverse transcription-PCR using RYNV-specific oligonucleotides after DNase treatment generated positive results for the virus in graft transmissible isolates (episomal) only. To confirm these results, rolling circle amplification on DNA preparations from the same samples resulted in amplicons identified as RYNV only from plants with graft transmissible RYNV. High-throughput sequencing was used to identify the RYNV-like sequences present in the host DNA. These results indicate the integration of RYNV into the red raspberry genome and highlight the necessity to recognize this phenomenon (integration) in future Rubus quarantine and certification programs.

Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp

Viruses can cause economic losses in fruit trees, including Prunus spp., by reducing yield and marketable fruit. Given the genetic diversity of viruses, reliable diagnostic methods relying on PCR are critical in determining viral infection in fruit trees. This study evaluated the broad-range detection capacity of currently available real-time RT-PCR assays for Prunus-infecting viruses and developed new assays when current tests were inadequate or absent. Available assays for 15 different viruses were exhaustively evaluated in silico to determine their capacity to detect virus isolates deposited in GenBank. During this evaluation, several isolates deposited since the assay was designed exhibited nucleotide mismatches in relation to the existing assay’s primer sequences. In cases where updating an existing assay was impractical, we performed a redesign with the dual goals of assay compactness and comprehensive inclusion of genetic diversity. The efficiency of each developed assay was determined by a standard curve. To validate the assay designs, we tested them against a comprehensive set of 87 positive and negative Prunus samples independently analyzed by high throughput sequencing. As a result, all the real-time RT-PCR assays described herein successfully detected the different viruses and their corresponding isolates. To further validate the new and updated assays a Prunus germplasm collection was surveyed. The sensitive and reliable detection methods described here will be used for the large-scale pathogen testing required to maintain the highest quality nursery stock.

Continuous Free Cortisol Profiles-Circadian Rhythms in Healthy Men

CONTEXT

The pituitary-adrenal axis had historically been considered a representative model for circadian rhythms. A recently developed portable collection device has provided the opportunity to evaluate free cortisol profiles using the microdialysis approach in individuals free to conduct their day-to-day activities in their own surroundings.

METHODS

Two separate experiments were conducted in healthy male volunteers. The total and subcutaneous (SC) free cortisol levels were measured at 10-minute intervals for a 24-hour period in one experiment, and the SC free cortisol levels were measured at 20-minute interval for 72 consecutive hours in free-living individuals in the second experiment.

RESULTS

The characteristic circadian rhythm was evident in both serum total and SC free cortisol, with the lowest levels achieved and maintained in the hours surrounding sleep onset and the peak levels occurring in every individual around waking. In all free-living individuals, the circadian rhythm was consistent across the 72-hour period, despite a wide range of activities. All the participants also showed increased cortisol after the consumption of lunch. The lowest levels during all 24-hour periods were observed during the hours after lights off, at the onset of sleep.

CONCLUSIONS

To the best of our knowledge, the present study is the first to report up to three consecutive 24-hour measurements of SC free cortisol in healthy individuals. We believe our study is a landmark study that paves the way for ambulatory monitoring of free cortisol profiles continuously for a period of 72 hours in free-living individuals performing their day-to-day activities whether healthy or with diseases involving the hypothalamic-pituitary-adrenal axis.

Identification and genomic characterization of grapevine Kizil Sapak virus, a novel grapevine-infecting member of the family Betaflexiviridae

A novel virus with a (+) single-stranded RNA genome was detected by high-throughput sequencing (HTS) in a sample of grapevine (Vitis vinifera) cv. Kizil Sapak (sample/isolate 127) that originated from Turkmenistan. The complete genome of the virus, tentatively named "grapevine Kizil Sapak virus" (GKSV), is 7,604 nucleotides in length, excluding the poly(A) tail. The genome organization of GKSV, encoded genes, and sequence domains are typical for members of the family Betaflexiviridae, specifically those belonging to the subfamily Trivirinae. Phylogenetic analysis placed GKSV within the subfamily Trivirinae, in the same clade as fig latent virus 1 (FLV-1) but distinct from the clades formed by members of other genera. A comparative analysis of GKSV-127 with the HTS-derived sequences obtained from two additional isolates showed that they are genetic variants of the same virus species. Based on current ICTV species and genus demarcation criteria, and the results of the sequence and phylogenetic analyses, we propose that GKSV and FLV-1 represent a new genus within the subfamily Trivirinae.

A systematic review of the quality and scope of economic evaluations in child oral health research

BACKGROUND

Economic evaluations provide policy makers with information to facilitate efficient resource allocation. To date, the quality and scope of economic evaluations in the field of child oral health has not been evaluated. Furthermore, whilst the involvement of children in research has been actively encouraged in recent years, the success of this movement in dental health economics has not yet been explored. This review aimed to determine the quality and scope of published economic evaluations applied to children's oral health and to consider the extent of children's involvement.

METHODS

The following databases were searched: CINAHL, Cochrane Library, Econlit, EThOS, MEDLINE, NHS EED, OpenGrey, Scopus, Web of Science. Full economic evaluations, relating to any aspect of child oral health, published after 1997 were included and appraised against the Drummond checklist and the Consolidated Health Economic Evaluation Reporting Standards by a team of four calibrated reviewers. Data were also extracted regarding children's involvement and the outcome measures used.

RESULTS

Two thousand seven hundred fifteen studies were identified, of which 46 met the inclusion criteria. The majority (n = 38, 82%) were cost-effectiveness studies, with most focusing on the prevention or management of dental caries (n = 42, 91%). One study quantified outcomes in Quality Adjusted Life Years (QALYs), and one study utilised a child-reported outcome measure. The mean percentage of applicable Drummond checklist criteria met by the studies in this review was 48% (median = 50%, range = 0-100%) with key methodological weaknesses noted in relation to discounting of costs and outcomes. The mean percentage of applicable CHEERS criteria met by each study was 77% (median = 83%, range = 33-100%), with limited reporting of conflicts of interest. Children's engagement was largely overlooked.

CONCLUSIONS

There is a paucity of high-quality economic evaluations in the field of child oral health. This deficiency could be addressed through the endorsement of standardised economic evaluation guidelines by dental journals. The development of a child-centred utility measure for use in paediatric oral health would enable researchers to quantify outcomes in terms of quality adjusted life years (QALYs) whilst promoting child-centred research.

Genomic architecture of complex traits in loblolly pine

Dissecting the genetic and genomic architecture of complex traits is essential to understand the forces maintaining the variation in phenotypic traits of ecological and economical importance. Whole-genome resequencing data were used to generate high-resolution polymorphic single nucleotide polymorphism (SNP) markers and genotype individuals from common gardens across the loblolly pine (Pinus taeda) natural range. Genome-wide associations were tested with a large phenotypic dataset comprising 409 variables including morphological traits (height, diameter, carbon isotope discrimination, pitch canker resistance), and molecular traits such as metabolites and expression of xylem development genes. Our study identified 2335 new SNP × trait associations for the species, with many SNPs located in physical clusters in the genome of the species; and the genomic location of hotspots for metabolic × genotype associations. We found a highly polygenic basis of quantitative inheritance, with significant differences in number, effects size, genomic location and frequency of alleles contributing to variation in phenotypes in the different traits. While mutation-selection balance might be shaping the genetic variation in metabolic traits, balancing selection is more likely to shape the variation in expression of xylem development genes. Our work contributes to the study of complex traits in nonmodel plant species by identifying associations at a whole-genome level.

Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design

Grapevine leafroll-associated virus 3 (GLRaV-3) is the most widely prevalent and economically important of the complex of RNA viruses associated with grapevine leafroll disease (GLD). Phylogenetic studies have grouped GLRaV-3 isolates into nine different monophyletic groups and four supergroups, making GLRaV-3 a genetically highly diverse virus species. In addition, new divergent variants have been discovered recently around the world. Accurate identification of the virus is an essential component in the management and control of GLRaV-3; however, the diversity of GLRaV-3, coupled with the limited sequence information, have complicated the development of a reliable detection assay. In this study, GLRaV-3 sequence data available in GenBank and those generated at Foundation Plant Services, University of California-Davis, was used to develop a new RT-qPCR assay with the capacity to detect all known GLRaV-3 variants. The new assay, referred to as FPST, was challenged against samples that included plants infected with different GLRaV-3 variants and originating from 46 countries. The FPST assay detected all known GLRaV-3 variants, including the highly divergent variants, by amplifying a small highly conserved region in the 3' untranslated terminal region (UTR) of the virus genome. The reliability of the new RT-qPCR assay was confirmed by an enzyme linked immunosorbent assay (ELISA) that can detect all known GLRaV-3 variants characterized to date. Additionally, three new GLRaV-3 divergent variants, represented by four isolates, were identified using a hierarchical testing process involving the FPST assay, GLRaV-3 variant-specific assays and high-throughput sequencing analysis. These variants were distantly related to groups I, II, III, V, VI, VII and IX, but much similar to GLRaV-3 variants with no assigned group; thus, they may represent new clades. Finally, based on the phylogenetic analysis, a new GLRaV-3 subclade is proposed and named as group X.

Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing

Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of sequence information from 60 trees identified a novel virus, provisionally named "Pistachio ampelovirus A" (PAVA), in the NCGR that showed low amino acid sequence identity (approximately 42%) compared with members of the genus Ampelovirus (family Closteroviridae). A putative viroid, provisionally named "Citrus bark cracking viroid-pistachio" (CBCVd-pis), was also found in the NCGR and showed approximately 87% similarity to Citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 hybrid rootstock seedlings (P. atlantica × P. integerrima). A field survey of 123 trees from commercial orchards found no incidence of PAVA but five (4%) samples were infected with CBCVd-pis. Of 675 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (25.4%) were positive for CBCVd-pis by reverse-transcription polymerase chain reaction. Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families. These findings require further study and confirmation. This study establishes the occurrence of viral and viroid populations infecting pistachio trees.

Developing a questionnaire to determine the impact of self-management in diabetes: giving people with diabetes a voice

Background

The prevalence of diabetes mellitus (DM) is increasing dramatically, placing considerable financial burden on the healthcare budget of each country. Patient self-management is crucial for the control of blood glucose, which largely determines the chances of developing diabetes-related complications. Self-management interventions vary widely, and a method is required for assessing the impact of self-management. This paper describes the development of a questionnaire intended for use to measure the impact of self-management in diabetes.

Methods

An iterative development process was undertaken to identify the attributes of self-management using 5 steps. First, a literature review was undertaken to identify and understand themes relating to self-management of DM to inform a topic guide. Second, the topic guide was further refined following consultation with a Patient and Public Involvement group. Third, the topic guide was used to inform semi-structured interviews with patients with Type 1 DM (T1DM) and Type 2 DM (T2DM) to identify how self-management of DM affects individuals. Fourth, the research team considered potential attributes alongside health attributes from an existing measure (Diabetes Health Profile, DHP) to produce an instrument reflecting both health and self-management outcomes simultaneously. Finally, a draft instrument was tested in a focus group to determine the wording and acceptability.

Results

Semi-structured interviews were carried out with 32 patients with T1DM and T2DM. Eight potential attributes were identified: fear/worry/anxiety, guilt, stress, stigma, hassle, control, freedom, and feeling supported. Four of these self-management attributes were selected with four health attributes (mood, worry about hypos (hypoglycaemic episodes), vitality and social limitations) to produce the Health and Self-Management in Diabetes (HASMID^v1) questionnaire.

Conclusions

HASMID^v1 is a short questionnaire that contains eight items each with four response levels to measure the impact of self-management in diabetes for both T1DM and T2DM. The measure was developed using a mixed-methods approach that involved semi-structured interviews with people with diabetes. The measure has high face validity. Ongoing research is being undertaken to assess the validity of this questionnaire for measuring the impact of self-management interventions in economic evaluation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12955-017-0719-4) contains supplementary material, which is available to authorized users.

The FIELDS Instrument Suite for Solar Probe Plus: Measuring the Coronal Plasma and Magnetic Field, Plasma Waves and Turbulence, and Radio Signatures of Solar Transients

NASA's Solar Probe Plus (SPP) mission will make the first in situ measurements of the solar corona and the birthplace of the solar wind. The FIELDS instrument suite on SPP will make direct measurements of electric and magnetic fields, the properties of in situ plasma waves, electron density and temperature profiles, and interplanetary radio emissions, amongst other things. Here, we describe the scientific objectives targeted by the SPP/FIELDS instrument, the instrument design itself, and the instrument concept of operations and planned data products.

Development and Testing of a Cognitive Behavioral Therapy Resource for Children's Dental Anxiety

Cognitive Behavioral Therapy (CBT) is an evidence-based treatment for dental anxiety; however, access to therapy is limited. The current study aimed to develop a self-help CBT resource for reducing dental anxiety in children, and to assess the feasibility of conducting a trial to evaluate the treatment efficacy and cost-effectiveness of such an intervention. A mixed methods design was employed. Within phase 1, a qualitative "person-based" approach informed the development of the self-help CBT resource. This also employed guidelines for the development and evaluation of complex interventions. Within phase 2, children, aged between 9 and 16 y, who had elevated self-reported dental anxiety and were attending a community dental service or dental hospital, were invited to use the CBT resource. Children completed questionnaires, which assessed their dental anxiety and health-related quality of life (HRQoL) prior to and following their use of the resource. Recruitment and completion rates were recorded. Acceptability of the CBT resource was explored using interviews and focus groups with children, parents/carers and dental professionals. For this analysis, the authors adhered to the Mixed Methods Appraisal Tool criteria. There were 24 families and 25 dental professionals participating in the development and qualitative evaluation of the CBT resource for children with dental anxiety. A total of 56 children agreed to trial the CBT resource (66% response rate) and 48 of these children completed the study (86% completion rate). There was a significant reduction in dental anxiety (mean score difference = 7.7, t = 7.9, df = 45, P < 0.001, Cohen's d ES = 1.2) and an increase in HRQoL following the use of the CBT resource (mean score difference = -0.03, t = 2.14, df = 46, P < 0.05, Cohen's d ES = 0.3). The self-help approach had high levels of acceptability to stakeholders. These findings provide preliminary evidence for the effectiveness and acceptability of the resource in reducing dental anxiety in children and support the further evaluation of this approach in a randomized control trial. Knowledge Transfer Statement: This study details the development of a guided self-help Cognitive Behavioral Therapy resource for the management of dental anxiety in children and provides preliminary evidence for the feasibility and acceptability of this approach with children aged between 9 and 16 y. The results of this study will inform the design of a definitive trial to examine the treatment- and cost-effectiveness of the resource for reducing dental anxiety in children.

Statin-induced expression change of INSIG1 in lymphoblastoid cell lines correlates with plasma triglyceride statin response in a sex-specific manner

Statins are widely prescribed to lower plasma low-density lipoprotein (LDL) cholesterol levels. They also modestly reduce plasma triglyceride (TG), an independent cardiovascular disease risk factor, in most people. The mechanism and inter-individual variability of TG statin response is poorly understood. We measured statin-induced gene expression changes in lymphoblastoid cell lines derived from 150 participants of a simvastatin clinical trial and identified 23 genes (false discovery rate, FDR=15%) with expression changes correlated with plasma TG response. The correlation of insulin-induced gene 1 (INSIG1) expression changes with TG response (rho=0.32, q=0.11) was driven by men (interaction P=0.0055). rs73161338 was associated with INSIG1 expression changes (P=5.4 × 10⁻⁵) and TG response in two statin clinical trials (P=0.0048), predominantly in men. A combined model including INSIG1 expression level and splicing changes accounted for 29.5% of plasma TG statin response variance in men (P=5.6 × 10⁻⁶). Our results suggest that INSIG1 variation may contribute to statin-induced changes in plasma TG in a sex-specific manner.

Modelling the species jump: towards assessing the risk of human infection from novel avian influenzas

The scientific understanding of the driving factors behind zoonotic and pandemic influenzas is hampered by complex interactions between viruses, animal hosts and humans. This complexity makes identifying influenza viruses of high zoonotic or pandemic risk, before they emerge from animal populations, extremely difficult and uncertain. As a first step towards assessing zoonotic risk of influenza, we demonstrate a risk assessment framework to assess the relative likelihood of influenza A viruses, circulating in animal populations, making the species jump into humans. The intention is that such a risk assessment framework could assist decision-makers to compare multiple influenza viruses for zoonotic potential and hence to develop appropriate strain-specific control measures. It also provides a first step towards showing proof of principle for an eventual pandemic risk model. We show that the spatial and temporal epidemiology is as important in assessing the risk of an influenza A species jump as understanding the innate molecular capability of the virus. We also demonstrate data deficiencies that need to be addressed in order to consistently combine both epidemiological and molecular virology data into a risk assessment framework.

Perfect Phylogeny Problems with Missing Values

The perfect phylogeny problem is of central importance to both evolutionary biology and population genetics. Missing values are a common occurrence in both sequence and genotype data, but they make the problem of finding a perfect phylogeny NPhard even for binary characters. We introduce new and efficient perfect phylogeny algorithms for broad classes of binary and multistate data with missing values. Specifically, we address binary missing data consistent with the rich data hypothesis (RDH) introduced by Halperin and Karp and give an efficient algorithm for enumerating phylogenies. This algorithm is useful for computing the probability of data with missing values under the coalescent model. In addition, we use the partition intersection (PI) graph and chordal graph theory to generalize the RDH to multi-state characters with missing values. For a bounded number of states, we provide a fixed parameter tractable algorithm for the perfect phylogeny problem with missing data. Utilizing the PI graph, we are able to show that under multiple biologically motivated models for character data, our generalized RDH holds with high probability, and we evaluate our results with extensive empirical analysis.

Influenza at the animal–human interface: a review of the literature for virological evidence of human infection with swine or avian influenza viruses other than A(H5N1)

Factors that trigger human infection with animal influenza virus progressing into a pandemic are poorly understood. Within a project developing an evidence-based risk assessment framework for influenza viruses in animals, we conducted a review of the literature for evidence of human infection with animal influenza viruses by diagnostic methods used. The review covering Medline, Embase, SciSearch and CabAbstracts yielded 6,955 articles, of which we retained 89; for influenza A(H5N1) and A(H7N9), the official case counts of the World Health Organization were used. An additional 30 studies were included by scanning the reference lists. Here, we present the findings for confirmed infections with virological evidence. We found reports of 1,419 naturally infected human cases, of which 648 were associated with avian influenza virus (AIV) A(H5N1), 375 with other AIV subtypes, and 396 with swine influenza virus (SIV). Human cases naturally infected with AIV spanned haemagglutinin subtypes H5, H6, H7, H9 and H10. SIV cases were associated with endemic SIV of H1 and H3 subtype descending from North American and Eurasian SIV lineages and various reassortants thereof. Direct exposure to birds or swine was the most likely source of infection for the cases with available information on exposure.

Genomic variation in natural populations of Drosophila melanogaster

This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere- and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 5'- and 3'-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species.

Outcome of selective non-operative management of penetrating abdominal injuries from the North American National Trauma Database

BACKGROUND

The aim of this study was to investigate trends in the practice of selective non-operative management (SNOM) for penetrating abdominal injury (PAI) and to determine factors associated with its failure.

METHODS

The National Trauma Data Bank for 2002-2008 was reviewed. Patients with PAI were categorized as those who underwent successful SNOM (operative management not required) and those who failed SNOM (surgery required more than 4 h after admission). Yearly rates of SNOM versus non-therapeutic laparotomy (NTL) were plotted. Multivariable regression analysis was performed to identify factors associated with failed SNOM and mortality.

RESULTS

A total of 12 707 patients with abdominal gunshot and 13 030 with stab wounds were identified. Rates of SNOM were 22.2 per cent for gunshot and 33.9 per cent for stab wounds, and increased with time (P < 0.001). There was a strong correlation between the rise in SNOM and the decline in NTL (r = - 0.70). SNOM failed in 20.8 and 15.2 per cent of patients with gunshot and stab wounds respectively. Factors predicting failure included the need for blood transfusion (odds ratio (OR) 1.96, 95 per cent confidence interval 1.11 to 3.46) and a higher injury score. Failed SNOM was independently associated with mortality in both the gunshot (OR 4.48, 2.07 to 9.70) and stab (OR 9.83, 3.44 to 28.00) wound groups.

CONCLUSION

The practice of SNOM is increasing, with an associated decrease in the rate of NTL for PAI. In most instances SNOM is successful; however, its failure is associated with increased mortality. Careful patient selection and adherence to protocols designed to decrease the failure rate of SNOM are recommended.

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

Gene duplication via retrotransposition has been shown to be an important mechanism in evolution, affecting gene dosage and allowing for the acquisition of new gene functions. Although fixed retrotransposed genes have been found in a variety of species, very little effort has been made to identify retrogene polymorphisms. Here, we examine 37 Illumina-sequenced North American Drosophila melanogaster inbred lines and present the first ever data set and analysis of polymorphic retrogenes in Drosophila. We show that this type of polymorphism is quite common, with any two gametes in the North American population differing in the presence or absence of six retrogenes, accounting for ~13% of gene copy-number heterozygosity. These retrogenes were identified by a straightforward method that can be applied using any type of DNA sequencing data. We also use a variant of this method to conduct a genome-wide scan for intron presence/absence polymorphisms, and show that any two chromosomes in the population likely differ in the presence of multiple introns. We show that these polymorphisms are all in fact deletions rather than intron gain events present in the reference genome. Finally, by leveraging the known location of the parental genes that give rise to the retrogene polymorphisms, we provide direct evidence that natural selection is responsible for the excess of fixations of retrogenes moving off of the X chromosome in Drosophila. Further efforts to identify retrogene and intron presence/absence polymorphisms will undoubtedly improve our understanding of the evolution of gene copy number and gene structure.

Toxicological studies on 2,4,6-tribromoanisole

TBA, or 2,4,6-tribromoanisole, is a musty-smelling metabolite of 2,4,6-tribromophenol that is used as a flame retardant and an antifungal agent for wooden pallets and packaging materials. The compound can impart its peculiar, often offensive, odor on product packaging to the concern of consumers for the safety of the package contents. These studies were conducted to evaluate the safety of TBA to humans ingesting products tainted with TBA. In addition to the 28-day oral study, a bacterial reverse mutation study was conducted, and confirmed that TBA was not mutagenic. To evaluate oral safety, TBA was evaluated in single dose and 5-day and 4-week repeated dose oral toxicity studies in rats. The test article, administered in single gavage doses of 2000, 5000 and 7500 mg/kg body weight (bw), in 5 daily repeated doses of 1000, 2000 or 3000 mg/kg bw/day or in 28 daily oral gavage doses of 0 001, 0.01, 100, and 1000 mg/kg bw/day did not result in any deaths. Also, the single and repeat dose studies resulted in no significant differences between control and treated groups on body weight gain, food consumption, clinical observations, blood biochemical values, and hematology findings. Treatment-related adverse findings were only detected in male rats during repeated dose studies and were associated with high plasma concentrations of TBA. The test article-related finding of hyaline droplets in the cortical tubular epithelium of kidneys was associated with increases in α(2 μ)-globulin content in the kidneys as indicated by the intensity of immunohistochemical staining. These findings were correlated with an increased weight of kidneys in males administered 1000mg/kgbw/day for 28days. Chemical induction of hyaline droplets containing α(2μ)-globulin in the renal proximal tubule is a process unique to the male rat and is not relevant for human risk assessment. Findings of increased liver weight with minimal centrilobular to diffuse hepatocellular hypertrophy in males treated with TBA at 1000mg/kg bw/day for 28days were considered to be an adaptive metabolic response to xenobiotic administration. The increased volume of urine, noted in both males and females treated with 1000mg/kg bw/day was considered adaptive and necessary to excrete the high xenobiotic burden resulting from TBA administration. TBA appeared to be highly bioavailable since high concentrations of TBA were detected in plasma, at 1, 4 and 8h after administration of TBA at 100 and 1000mg/kg bw for 1 and 28days. Levels were dose-related but did not clarify the course of TBA elimination with time after administration. These studies indicate that TBA, administered orally to rats, produced male rat-specific, treatment-related toxicity at the highest orally administered dose in repeated dose (5-day at 3000mg/kg bw and 28-day at 1000mg/kg bw) studies. Therefore, the NOAEL for the 28-day oral study was determined to be 1000mg/kg bw/day for the rat.