Quantification of Temporal and Spatial Dynamics of Bean pod mottle virus at Different Spatial Scales

Bean pod mottle virus (BPMV) is the most prevalent virus infecting soybean (Glycine max) in the United States; however, the temporal and spatial dynamics in BPMV at varying spatial scales has not been elucidated. To quantify the temporal and spatial dynamics of BPMV at a field scale, a quadrat-based method was developed in which six soybean rows, each consisting of 30-cm-long quadrats, were established within soybean cv. NE3001 field plots (i.e., 150 quadrats per plot) in BPMV-inoculated and non-inoculated plots. Quadrats were sampled by selecting the youngest fully expanded leaflet from each of four plants within each quadrat beginning 25 days after planting, and continued at 8- to 11- day intervals until crop senescence. Leaf sap was extracted from each 4-leaflet (bulked) sample (from each quadrat), and tested for presence of the BPMV by ELISA. Quadrat position (plot, row, and quadrat number) and the date of sampling that each quadrat first tested positive for BPMV was recorded and mapped. The rate of BPMV incidence in 2006 ranged from 0.09 to 0.12 logits/day, indicating that BPMV incidence was doubling every 5.3 to 7.7 days in 2006. Doubling times for BPMV incidence in 2007 were slower, ranging from 17.3 to 34.7 days. Analysis of spatial patterns using ordinary runs revealed that BPMV-infected quadrats were predominantly clustered within both BPMV-inoculated and non-inoculated plots throughout both growing seasons. In addition to within field plot studies, a threeyear statewide disease survey (2005-2007) was conducted in Iowa to quantify county and field scale BPMV prevalence and incidence by systematically selecting 30 plants/soybean field (8 to 16 soybean fields per county). Leaf samples were then tested for BPMV by ELISA and county-level BPMV incidence maps were generated using ArcGIS software. End-of-season BPMV prevalence was 39/96 counties in 2005 (40%), 90/99 counties in 2006 (90.1%), and 74/99 counties in 2007 (74.7%). The incidence of BPMV within Iowa counties ranged from 0 to 100% and BPMV incidence significantly increased statewide from north to south. Spatial autocorrelation (dependence) analysis using Moran’s I revealed clustering for BPMV incidence among Iowa counties, indicating that BPMV incidence among counties was not random. The elucidation of the within-field temporal and spatial dynamics of BPMV and the statewide geographic distribution of BPMV in Iowa has important implications with regards to sampling, plant disease forensics, BPMV management, and risk prediction of BPMV

Quantifying the Within-Field Temporal and Spatial Dynamics of Bean pod mottle virus in Soybean

The prevalence and incidence of Bean pod mottle virus (BPMV) have been reported to be on the increase in the United States but little is known about the temporal and spatial dynamics of this virus within soybean (Glycine max) fields. A quadrat-based sampling method was developed to quantify the within-field spread of BPMV in soybean in 2006 and 2007. Twenty-five 30-cm-long quadrats were established within each row of soybean in field plots consisting of six rows, each 7.6 m long and spaced 0.76 m apart. Four treatments were used to influence the temporal and spatial dynamics of BPMV epidemics. Treatments were: (i) establishment of a point source of BPMV inoculum within soybean plots; (ii) lambda-cyhalothrin insecticide applied at the V1 and R2 growth stages; (iii) establishment of a BPMV inoculum point source, plus the application of foliar insecticide sprays at the V1 and R2 growth stages; and (iv) a nontreated, noninoculated control. All quadrats (census) were sampled beginning 25 days after planting; sampling continued every 8 to 11 days until plants were senescent. Sap from leaf samples was extracted and tested for BPMV by enzyme-linked immunosorbent assay. The incidence of BPMV per treatment was plotted against time to produce BPMV incidence curves for temporal analyses. In addition, positions of BPMV-positive quadrats were mapped for spatial analyses. BPMV was detected within soybean plots on the first sampling date in 2006 (30 May) and on the second sampling date in 2007 (21 June). The rate of BPMV temporal spread within treatments ranged from 0.11 to 0.13 logits/day in 2006 and from 0.05 to 0.07 logits/day in 2007. Doubling times for BPMV incidence among treatments ranged from 5.4 to 6.4 days in 2006 and from 10.0 to 14.1 days in 2007. Soybean plots that had the earliest dates of BPMV detection within quadrats (x) also had the highest BPMV incidence (y) at the end of the growing season (R2 = 66.5 and 70.4% for 2006 and 2007, respectively). Spatial analyses using ordinary runs, black-white join-counts, and spatial autocorrelation revealed highly aggregated spatial patterns of BPMV-infected quadrats over time. Bean leaf beetle population densities were linearly related to BPMV incidence (P \u3c 0.0001) in both years, indicating that BPMV epidemics were greatly influenced by bean leaf beetle population density. To our knowledge, this is the first study to quantify the seasonal temporal and spatial dynamics of BPMV spread within soybean

Prevalence, Incidence, and Spatial Dependence of Soybean mosaic virus in Iowa

The prevalence of soybean fields with plants infected with Soybean mosaic virus (SMV) in Iowa is assumed to be random, because the primary source of the virus is SMV-infected seed. Data collected from 2,500 soybean fields sampled over a 3-year period as part of the Iowa Soybean Disease Survey (2005 to 2007) were used to evaluate this assumption. SMV was first detected in early June of each year but counties in which it was first detected varied among years. Prevalence at the county scale at end of season was 32.3, 27.3, and 89.9% in 2005, 2006, and 2007, respectively. End-of-season incidence of SMV within SMV-positive counties was 1.5 to 25.0, 1.7 to 24, and 1.8 to 58% in 2005, 2006, and 2007, respectively. The number of fields in which plants infected with SMV were detected increased at the linear rate of approximately one new field every 2 days in 2007, compared with one new field every 22 days (2005) and 21 days (2006), with coefficients of determination (R2) of 93.2 to 96.8% using the linear model. Weak spatial dependence for end-of-season SMV incidence was detected using Moran\u27s Index, indicating that the risk for SMV incidence at the county scale within Iowa at the end of the growing season is not random

Quantifying the Effect of Pyraclostrobin on Grainfill Period and Kernel Dry Matter Accumulation in Maize

Strobilurin fungicides are effective against a wide range of foliar fungal diseases on several crops and may offer additional physiological benefits, including plants staying green longer than normal (the stay-green effect ). It has been hypothesized that the stay-green effect may extend the grain fill period leading to increased grain yield due to a longer period of dry matter accumulation. We investigated the effect of pyraclostrobin fungicide applied at tasseling on foliar disease suppression, stalk rot severity, the stay-green effect of leaves in the upper canopy, dry matter accumulation, time at physiological maturity, grain yield, and moisture at harvest in maize from 2008 through 2010 in Iowa at six location years. Foliar disease severity was0.1) between pyraclostrobin-treated and non-treated maize in all location years, treated plots tended to have higher yield and grain moisture. Time at physiological maturity did not differ between pyraclostrobin-treated and nontreated plots (P \u3e 0.1). Although we demonstrated an application of pyraclostrobin to maize delayed senescence of the leaves thus contributing to the stay-green effect, our data did not show grain-fill period extension

Evaluating the Importance of Stem Canker of Soybean in Iowa

The relative importance of stem canker of soybean in Iowa compared with other soybean diseases present in the state was assessed using data collected from over 3,400 soybean fields sampled in the Iowa Soybean Disease Survey that was conducted from 2005 to 2007. Symptomatic plant tissues from soybean plants with stem canker symptoms were cultured on acidified potato dextrose agar. The prevalence of stem canker on soybean in 2005 in Iowa was 2.6%; the disease was not detected in 2006 and 2007. In 2005, 63 isolates with Diaporthe/Phomopsis characteristics were collected. To identify isolates to fungal species and variety, single-spored isolates were subjected to polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and sequencing of the internal transcribed spacer (ITS) region. Fourteen isolates were identified as D. phaseolorum var. caulivora (northern stem canker) and 49 as Phomopsis longicolla. To quantify and compare the aggressiveness of D. phaseolorum var. caulivora isolates collected in Iowa, nine isolates were arbitrarily selected for components analysis. Incubation period, rate of lesion expansion, final lesion length, and time to plant death for each isolate were quantified. Significant differences in components of aggressiveness were detected among the nine isolates. Results from this work suggest stem canker is a minor disease of soybean in Iowa

A Review of the Toxicity and Phytochemistry of Medicinal Plant Species Used by Herbalists in Treating People Living With HIV/AIDS in Uganda

Introduction: Despite concerns about toxicity, potentially harmful effects and herb-drug interactions, the use of herbal medicines remains widely practiced by people living with HIV/AIDS (PLHIV) in Uganda. Objective: The objective of the paper was to comprehensively review the literature on the toxicity and chemical composition of commonly used medicinal plant species in treating PLHIV in Uganda. Methods: We reviewed relevant articles and books published over the last sixty years on ethnobotany, antiviral/anti-HIV activity, toxicity, phytochemistry of Vachellia hockii, Albizia coriaria, Bridelia micrantha, Cryptolepis sanguinolenta, Erythrina abyssinica, Gardenia ternifolia, Gymnosporia senegalensis, Psorospermum febrifugium, Securidaca longipendunculata, Warburgia ugandensis and Zanthoxylum chalybeum and their synonyms. We searched PubMed, Web of Science, Scopus, Science Direct and Google Scholar. Discussion: Most of the plant species reviewed apart from P. febrifugium, S. longipedunculata and C. sanguinolenta lacked detailed phytochemical analyses as well as the quantification and characterization of their constituents. Crude plant extracts were the most commonly used. However, purified/single component extracts from different plant parts were also used in some studies. The U87 human glioblastoma was the most commonly used cell line. Water, ethanol, methanol and DMSO were the commonest solvents used. In some instances, isolated purified compounds/extracts such as Cryptolepine and Psorospermin were used. Conclusion: Cytotoxicity varied with cell type, solvent and extract type used making it difficult for direct comparison of the plant species. Five of the eleven plant species namely, A. coriaria, C. sanguinolenta, G. ternifolia, P. febrifugium and Z. chalybeum had no cytotoxicity studies in animal models. For the remaining six plant species, the crude aqueous and ethanol extracts were mainly used in acute oral toxicity studies in mice. Herbalists reported only A. coriaria and W. ugandensis to cause toxic side effects in humans. However, selective cytotoxic plant extracts can potentially be beneficial as anticancer or anti-tumour drugs

Successful interruption of the transmission of Onchocerca volvulus in Mpamba-Nkusi focus, Kibaale district, mid-western Uganda

Background: The Mpamba-Nkusi onchocerciasis focus is situated in the mid-western part of Uganda. It has an area of 300 km2 and used to have Simulium neavei as the vector which develops in a phoretic association on freshwater crabs. Ground larviciding with temephos (Abate EC500) was initiated in June 2002. All the 330 communities in this focus have undergone annual treatment with ivermectin since 1995 and were later shifted to semi-annual treatment in 2009.Objective: To establish the impact of mass drug administration in combination with larviciding on the interruption of O. volvulus transmission.Design: Longitudinal studySetting: Rural areas in Mpamba-Nkusi focus, Kibaale district.Subjects: Individuals five years and above living in the focus.Interventions: Annual and semi-annual treatment with ivermectin supplemented by vector elimination were used. Epidemiological, entomological and serological assessments were conducted.Results: Freshwater crabs (n = 14,391) caught from monitoring sites (n = 41) since 2008 were negative for immature stages of S. neavei. The S.neavei population was reduced following trial and initiation of ground larviciding. No adult S. neavei has been caught in the focus for over five years. Parasitological examination of individuals residing in the focus revealed a microfilaria (mf) prevalence of 0.3% (95% CI 0 – 0.65%; n = 732) in 2012. Serological assays testing for Onchocerca volvulus antibodies conducted on 3351 children <15 years in 2009 indicated point prevalence of 0.6% , (95% CI, 0.3-0.8%) while in 2012 another survey conducted among 3,407 children, only 1/3407 (0.03%, 95% CI, 0-0.09%) individual was positive for O. volvulus antibodies.Conclusions: Epidemiological and entomological findings suggest that interruption of transmission has been achieved

Diagnostic accuracy of Xpert MTB/RIF Ultra for tuberculous meningitis in HIV-infected adults: a prospective cohort study.

BACKGROUND: WHO recommends Xpert MTB/RIF as initial diagnostic testing for tuberculous meningitis. However, diagnosis remains difficult, with Xpert sensitivity of about 50-70% and culture sensitivity of about 60%. We evaluated the diagnostic performance of the new Xpert MTB/RIF Ultra (Xpert Ultra) for tuberculous meningitis. METHODS: We prospectively obtained diagnostic cerebrospinal fluid (CSF) specimens during screening for a trial on the treatment of HIV-associated cryptococcal meningitis in Mbarara, Uganda. HIV-infected adults with suspected meningitis (eg, headache, nuchal rigidity, altered mental status) were screened consecutively at Mbarara Regional Referral Hospital. We centrifuged CSF, resuspended the pellet in 2 mL of CSF, and tested 0·5 mL with mycobacteria growth indicator tube culture, 1 mL with Xpert, and cryopreserved 0·5 mL, later tested with Xpert Ultra. We assessed diagnostic performance against uniform clinical case definition or a composite reference standard of any positive CSF tuberculous test. FINDINGS: From Feb 27, 2015, to Nov 7, 2016, we prospectively evaluated 129 HIV-infected adults with suspected meningitis for tuberculosis. 23 participants were classified as probable or definite tuberculous meningitis by uniform case definition, excluding Xpert Ultra results. Xpert Ultra sensitivity was 70% (95% CI 47-87; 16 of 23 cases) for probable or definite tuberculous meningitis compared with 43% (23-66; 10/23) for Xpert and 43% (23-66; 10/23) for culture. With composite standard, we detected tuberculous meningitis in 22 (17%) of 129 participants. Xpert Ultra had 95% sensitivity (95% CI 77-99; 21 of 22 cases) for tuberculous meningitis, which was higher than either Xpert (45% [24-68]; 10/22; p=0·0010) or culture (45% [24-68]; 10/22; p=0·0034). Of 21 participants positive by Xpert Ultra, 13 were positive by culture, Xpert, or both, and eight were only positive by Xpert Ultra. Of those eight, three were categorised as probable tuberculous meningitis, three as possible tuberculous meningitis, and two as not tuberculous meningitis. Testing 6 mL or more of CSF was associated with more frequent detection of tuberculosis than with less than 6 mL (26% vs 7%; p=0·014). INTERPRETATION: Xpert Ultra detected significantly more tuberculous meningitis than did either Xpert or culture. WHO now recommends the use of Xpert Ultra as the initial diagnostic test for suspected tuberculous meningitis. FUNDING: National Institute of Neurologic Diseases and Stroke, Fogarty International Center, National Institute of Allergy and Infectious Disease, UK Medical Research Council/DfID/Wellcome Trust Global Health Trials, Doris Duke Charitable Foundation

Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-Associated Bacteroidetes for Microbial Source Tracking across Sixteen Countries on Six Continents

Numerous quantitative PCR assays for microbial fecal source tracking (MST) have been developed and evaluated in recent years. Widespread application has been hindered by a lack of knowledge regarding the geographical stability and hence applicability of such methods beyond the regional level. This study assessed the performance of five previously reported quantitative PCR assays targeting human-, cattle-, or ruminant-associated Bacteroidetes populations on 280 human and animal fecal samples from 16 countries across six continents. The tested cattle-associated markers were shown to be ruminant-associated. The quantitative distributions of marker concentrations in target and nontarget samples proved to be essential for the assessment of assay performance and were used to establish a new metric for quantitative source-specificity. In general, this study demonstrates that stable target populations required for marker-based MST occur around the globe. Ruminant-associated marker concentrations were strongly correlated with total intestinal Bacteroidetes populations and with each other, indicating that the detected ruminant-associated populations seem to be part of the intestinal core microbiome of ruminants worldwide. Consequently tested ruminant-targeted assays appear to be suitable quantitative MST tools beyond the regional level while the targeted human-associated populations seem to be less prevalent and stable, suggesting potential for improvements in human-targeted methods