Development and evaluation of one-step RT-qPCR TaqMan multiplex panels applied to six viruses occurring in lily and tulip bulbs.

One-step RT-qPCR TaqMan assays have been developed for six plant viruses with considerable economic impact in the growing of tulip and lily bulbs: lily mottle virus, lily symptomless virus, lily virus X, Plantago asiatica mosaic virus, tulip breaking virus and tulip virus X. To enhance efficacy and cost-efficiency these assays were combined into multiplex panels. Four different multiplex panels were designed, each consisting of three virus assays and an adapted assay for the housekeeping gene nad5 of lilies and tulips, that acts as an internal amplification control. To eliminate false negative results due to variation in the viral genome sequences, for each target virus two assays were developed on distinct conserved genomic regions. Specificity, PCR efficiency and compatibility of primers and probes were tested using gBlock constructions. Diagnostic samples were used to evaluate the strategy. High Throughput Sequencing of a set of the diagnostic samples, further verified the presence or absence of the viruses in the RNA samples and sequence variations in the target genes. This interchangeable multiplex panel strategy may be a valuable tool for the detection of viruses in certification, surveys and virus diagnostics.

Impact of Hydrocodone Rescheduling on Dental Prescribing of Opioids.

INTRODUCTION: In the United States, dentists frequently prescribe hydrocodone. In October 2014, the US Drug Enforcement Administration rescheduled hydrocodone from controlled substance schedule III to II, introducing more restricted prescribing and dispensing regulations, which may have changed dental prescribing of opioids. OBJECTIVE: The study aim was to evaluate the impact of the hydrocodone rescheduling on dental prescribing of opioids in the United States. METHODS: This was a cross-sectional study of opioids prescribed by dentists between October 2012 and October 2016, using the IQVIA Longitudinal Prescription Dataset. Monthly dentist-based opioid prescribing rate (opioid prescription [Rx]/1,000 dentists) and monthly average opioid dosages per prescription (mean morphine milligram equivalent per day [MME/d]) were measured in the 24 mo before and after hydrocodone rescheduling in October 2014 (index or interruption). An interrupted time-series analysis was conducted using segmented ordinary least square regression models, with Newey-West standard errors to handle autocorrelation. RESULTS: Dentists prescribed 50,412,942 opioid prescriptions across the 49 mo. Hydrocodone was the most commonly prescribed opioid pre- and postindex (74.9% and 63.8%, respectively), followed by codeine (13.8% and 21.6%), oxycodone (8.1% and 9.5%), and tramadol (2.9% and 4.8%). At index, hydrocodone prescribing immediately decreased by -834.8 Rx/1,000 dentists (95% confidence interval [CI], -1,040.2 to -629.4), with increased prescribing of codeine (421.9; 95% CI, 369.7-474.0), oxycodone (85.3; 95% CI, 45.4-125.2), and tramadol (111.8; 95% CI, 101.4-122.3). The mean MME increased at index for all opioids except for hydrocodone, and dosages subsequently decreased during the postindex period. CONCLUSION: Following the rescheduling, dentist prescribing of hydrocodone declined while prescribing of nonhydrocodone opioids increased. Understanding the impact of this regulation informs strategies to ensure appropriate prescribing of opioids for dental pain. KNOWLEDGE TRANSFER STATEMENT: The study findings can be used by policy makers to make informed decisions in developing future risk mitigation strategies aimed to regulate opioid prescribing behaviors. Furthermore, dentist-specific resources and guidelines are needed subsequent to these policies in order to meet the dental population needs.

Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates.

To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named "Stralarivirus". Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

An Alternative Bioassay for Synchytrium endobioticum Demonstrates the Expression of Potato Wart Resistance in Aboveground Plant Parts.

The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently, 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here, we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing but not in fully expanded aboveground organs. Colonization of the host by S. endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan polymerase chain reaction and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in axillary buds and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed in both etiolated "belowground" sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared with resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant-pathogen interaction. Because wart resistance is active in both below- and aboveground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs because it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding. Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Occurrence of Fusarium Head Blight species and Fusarium mycotoxins in winter wheat in the Netherlands in 2009.

Most recent information on the occurrence of Fusarium Head Blight species and related mycotoxins in wheat grown in the Netherlands dates from 2001. This aim of this study was to investigate the incidence and levels of Fusarium Head Blight species and Fusarium mycotoxins, as well as their possible relationships, in winter wheat cultivated in the Netherlands in 2009. Samples were collected from individual fields of 88 commercial wheat growers. Samples were collected at harvest from 86 fields, and 2 weeks before the expected harvest date from 21 fields. In all, 128 samples, the levels of each of seven Fusarium Head Blight species and of 12 related mycotoxins were quantified. The results showed that F. graminearum was the most frequently observed species at harvest, followed by F. avenaceum and M. nivale. In the pre-harvest samples, only F. graminearum and M. nivale were relevant. The highest incidence and concentrations of mycotoxins were found for deoxynivalenol, followed by zearalenone and beauvericin, both pre-harvest and at harvest. Other toxins frequently found--for the first time in the Netherlands--included T-2 toxin, HT-2 toxin, and moniliformin. The levels of deoxynivalenol were positively related to F. graminearum levels, as well as to zearalenone levels. Other relationships could not be established. The current approach taken in collecting wheat samples and quantifying the presence of Fusarium Head Blight species and related mycotoxins is an efficient method to obtain insight into the occurrence of these species and toxins in wheat grown under natural environmental conditions. It is recommended that this survey be repeated for several years to establish inter-annual variability in both species composition and mycotoxin occurrence.

Population dynamics of Phytophthora infestans in the Netherlands reveals expansion and spread of dominant clonal lineages and virulence in sexual offspring.

For a comprehensive survey of the structure and dynamics of the Dutch Phytophthora infestans population, 652 P. infestans isolates were collected from commercial potato fields in the Netherlands during the 10-year period 2000-2009. Genotyping was performed using 12 highly informative microsatellite markers and mitochondrial haplotypes. In addition, for each isolate, the mating type was determined. STRUCTURE analysis grouped the 322 identified genotypes in three clusters. Cluster 1 consists of a single clonal lineage NL-001, known as "Blue_13"; all isolates in this cluster have the A2 mating type and the Ia mitochondrial haplotype. Clusters 2 and 3 display a more elaborate substructure containing many unique genotypes. In Cluster 3, several distinct clonal lineages were also identified. This survey witnesses that the Dutch population underwent dramatic changes in the 10 years under study. The most notable change was the emergence and spread of A2 mating type strain NL-001 (or "Blue_13"). The results emphasize the importance of the sexual cycle in generating genetic diversity and the importance of the asexual cycle as the propagation and dispersal mechanism for successful genotypes. Isolates were also screened for absence of the Avrblb1/ipiO class I gene, which is indicative for virulence on Rpi-blb1. This is also the first report of Rpi-blb1 breakers in the Netherlands. Superimposing the virulence screening on the SSR genetic backbone indicates that lack the Avrblb1/ipiO class I gene only occurred in sexual progeny. So far, the asexual spread of the virulent isolates identified has been limited.

Prioritizing comparative-effectiveness research topics via stakeholder involvement: an application in COPD.

A major priority for funding agencies and researchers involved in comparative-effectiveness research (CER) is to ensure that research questions will produce findings that are relevant and feasible to implement. In this article, we describe a process for involving experts and stakeholders in identifying and prioritizing CER studies, as illustrated by our experience in chronic obstructive pulmonary disease (COPD).

Skeletal health in men with chronic lung disease: rates of testing, treatment, and fractures.

UNLABELLED: To advance our understanding of the burden of fractures among men, we studied a group of men at high risk for low bone strength due to lung disease. We found high rates of fractures but low rates of bone density testing that could predict fracture before it occurs. INTRODUCTION: To advance understanding of the burden of fragility fractures and attention to bone health among men with chronic obstructive lung disease (COPD), we quantified rates of fragility fracture, bone density testing, and anti-resorptive treatment and calculated the number needed to screen (NNS) to prevent one hip fracture in a cohort of men with COPD. METHODS: Veterans Administration (VA) and VA-Medicare administrative data permitted a retrospective cohort study of 87,360 men aged 50 and older, newly diagnosed with COPD between 1999 and 2003. Logistic regression models including patient characteristics, morbidities, and medication use assessed the effect of covariates on fracture and probability of testing or treatment. RESULTS: Mean age was 66.8. Hip and wrist fracture rates were 3.99 and 1.31 per 1,000 person years, respectively. Mean follow-up was 2.67 years; 4.4% underwent bone densitometry; 2.8% filled anti-resorptive prescriptions. Age, white race/ethnicity, more COPD exacerbations, barbiturate use, and anti-Parkinson's drug use were significantly associated with fracture. Age, and systemic corticosteroids were most significantly associated with testing or treatment. Based on published adherence and treatment effects, the cohort's calculated NNS to prevent one hip fracture is 432. CONCLUSIONS: Fracture rate was high and testing and treatment uncommon. The NNS of 432 to prevent one hip fracture is smaller than 731, the NNS for women aged 65-69 for whom universal screening is recommended. Attention to the bone health of this population is warranted. Future research must determine how testing and treatment impact overall quality of life and mortality of men with COPD.

Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp).

We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units. Five VNTR markers showing multiple alleles were validated with a reference set of isolates from different parts of the world and a population from a banana plantation in Costa Rica. Polymorphism information content values varied from 0.6414 to 0.7544 for the reference set and from 0.0400 and 0.7373 for the population set. Eighty percent of the polymorphism information content values were above 0.60, indicating that the markers are highly informative. These markers allowed robust scoring of agarose gels and proved to be useful for variability and population genetics studies. In conclusion, the strategy we developed to identify and validate VNTR markers is an efficient means to incorporate markers that can be used for fungicide resistance management and to develop breeding strategies to control banana black leaf streak disease. This is the first report of VNTR-minisatellites from the M. fijiensis genome sequence.

Present and future costs of COPD in Iceland and Norway: results from the BOLD study.

The Burden of Obstructive Lung Disease (BOLD) initiative provides standardised estimates of the burden of chronic obstructive pulmonary disease (COPD) worldwide. We estimate the current and future economic burden of COPD in Reykjavik, Iceland and Bergen, Norway using data from the BOLD initiative. Data on utilisation of healthcare resources were gathered from the BOLD survey, existing literature and unit costs from national sources. Economic data were applied to a Markov model using transition probabilities derived from Framingham data. Sensitivity analyses were conducted varying unit costs, utilisation and prevalence of disease. The cost of COPD was 478 euro per patient per yr in Iceland and 284 euro per patient per yr in Norway. The estimated cumulative costs of COPD for the population aged > or = 40 yrs, were 130 million euro and 1,539 million euro for the following 10 yrs in Iceland and Norway, respectively. Costs of COPD accounted for 1.2 and 0.7% of healthcare budgets in Iceland and Norway, respectively. Sensitivity analyses showed estimates were most sensitive to changes in exacerbation frequency. COPD has a significant economic burden in both Iceland and Norway and will grow in the future. Interventions aimed at avoiding exacerbations will have the most impact on costs of COPD over the next 20 yrs.

Pathogenic relevance of Lactobacillus: a retrospective review of over 200 cases.

Given that Lactobacillus has been reported to be the causative pathogen in many types of infection despite debate regarding the organism's clinical significance, a literature review was conducted to investigate the treatments and outcomes of Lactobacillus infections reported to date. In this article, the characteristics of over 200 reported cases of Lactobacillus-associated infections are summarized. Lactobacillus was found to be frequently associated with endocarditis and bacteremia. Lactobacillus was also associated with a variety of other infections including, but not limited to, peritonitis, abscesses, and meningitis. The species casei and rhamnosus were the most common. The isolates tended to be most sensitive to erythromycin and clindamycin and most resistant to vancomycin. The species that was most sensitive to vancomycin was acidophilus. The overall mortality rate was nearly 30%. There was a significant association between mortality and polymicrobial infection (P=0.004). In the subset of patients with bacteremia, increased mortality was associated with inadequate treatment (P=0.001) and polymicrobial bacteremia (P=0.044).

An automated overlying water-renewal system for sediment toxicity studies.

An automated water-renewal toxicity test system is described for exposing benthic invertebrates to whole sediments. The system will intermittently deliver laboratory or on-site water for overlying water replacement in sediment exposures. A range of cycle rates can be used to produce different volume additions of overlying water per day to exposure chambers. The system can be used with six different treatments and eight replicates per treatment producing 48 exposure chambers. Three formulated sediments with variable organic carbon (1.5%, 7.5%) and sand (14%, 63%) content were prepared to test the system exposing amphipods, Hyalella azteca and midges, Chironomus tentans in 10 day whole sediment tests. Intermittent water flow was used with a 90 min cycle time to create two volume additions of laboratory water per 24 h in exposure chambers (180 ml sediment, 320 ml water). Overlying water quality conditions, and survival and growth of both species were consistent and within acceptable limits for the testing requirements of the U.S. EPA guidelines for sediments with freshwater invertebrates.

Meloidogyne haplanaria n. sp. (Nematoda: Meloidogynidae), a Root-knot Nematode Parasitizing Peanut in Texas.

Meloidogyne haplanaria n. sp. is described and illustrated from specimens parasitizing peanut in Texas. The perineal pattern of the female is rounded to oval with a dorsal arch that is high and rounded except for striae near the vulva, which are low with rounded shoulders. The striae are distinctly forked in the lateral field, and punctations often occur as a small group near the tail tip and singly within the whole perineal pattern. The female stylet is 13-16 microm long and has broad, distinctly set-off knobs. The excretory pore opens 40-118 microm from the head, approximately halfway between the anterior end and the metacorpus. Males are 1.2-2.4 microm in length and have a high, wide head cap that slopes posteriorly. The labial disc and medial lips are partially fused to form an elongated lip structure. In some specimens the labial disk is distinctly separated from the lips by a groove. The stylet is 17-22 microm long and has wide knobs that are rounded and distinctly set off from the shaft. Mean second-stage juvenile length is 419 microm. The head region is not annulated, and the large labial disc and crescent-shaped medial lips are fused to form a dumbbell-shaped head cap. The stylet is 9-12 microm long and has rounded, posteriorly sloping knobs. The slender tail, 58-74 microm long, has a distinct, inflated rectum and a slightly rounded tip. The hyaline tail terminus is 11-16 microm long. The isozyme phenotypes for esterase and malic dehydrogenase do not correspond to any other recognized Meloidogyne species. Tomato and peanut are good hosts; corn and wheat are very poor hosts; and cotton, tobacco, pepper, and watermelon are nonhosts.

Ubiquitin junction, what's your function?

A report on the Ubiquitin and Intracellular Protein Degradation FASEB summer conference, Saxtons River, USA, 23-28 June 2001.

Economic evaluation of systemic treatments for cytomegalovirus retinitis in patients with AIDS.

OBJECTIVE: To determine the cost of using systemic therapy to treat newly diagnosed cytomegalovirus (CMV) retinitis in persons with AIDS. DESIGN: Incidence-based simulation model of CMV treatment from a government payer perspective. SETTING: Swiss healthcare system. PATIENTS AND PARTICIPANTS: Patients with AIDS and newly diagnosed CMV retinitis. INTERVENTIONS: Patients were assigned to 1 of 4 treatment regimens for induction and maintenance therapy: (i) intravenous (IV) cidofovir induction and maintenance (cidofovir IV/IV); (ii) IV foscarnet induction and maintenance (foscarnet IV/IV); (iii) IV ganciclovir induction and maintenance (ganciclovir IV/IV); and (iv) IV ganciclovir induction and oral (PO) ganciclovir maintenance (ganciclovir IV/PO). Following a second relapse, patients were assigned to one of the other regimens. MAIN OUTCOME MEASURES: Time to first and subsequent progression, duration of maintenance treatment and direct medical expenditures [1998 Swiss francs (SwF)] . RESULTS: The median time to first progression was longest for cidofovir IV/IV, followed by foscarnet IV/IV, ganciclovir IV/IV and ganciclovir IV/PO. Mean survival was 13 months and mean costs for this period in the base case were lowest in those initially treated with cidofovir (SwF146,742), followed by initial treatment with foscarnet IV/IV (SwF194,809), ganciclovir IV/PO (SwF195,190) and ganciclovir IV/IV (SwF243,964). Costs were most sensitive to changes in efficacy estimates. CONCLUSIONS: Of the regimens studied, initiation of treatment with systemic cidofovir appears least costly over a 13-month period.