Sampling strategies for the detection of grapevine fanleaf virus and the grapevine strain of tomato ringspot virus

This study was conducted to determine the influence of season, host genotype virus isolate and sample tissue on ELISA detection of the two nepoviruses. Enzyme-linked immunosorbent assay (ELISA) readily detects grapevine fanleaf virus (GFLV) and the causal agent of grapevine yellow vein, tomato ringspot virus (TomRSV) in infected grapevines. Three serologically identical isolates of GFLV (fanleaf deformation, vein-banding and yellow mosaic) were examined in one cultivar of Vitis rupestris SCHEELE and in three cultivars of V.. vinifera L. TomRSV was examined in V. vinifera cv. Carignane. The tissues tested included: shoot tips, mature leaves and cambial scrapings. The following tissues taken from GFLV-infected dormant canes were also tested: sawdust, cambial scrapings, dormant buds, and induced shoots, roots and callus. There were no differences in GFLV ELISA results when different cultivars and virus isolates were compared. However, seasonal differences in ELISA detection of GFLV were observed. Shoot tip values went from a high of > 4.00 OD450nm in May to a low of 0.05 OD450nm in September. 'Mature leaves also gave the highest values in May and rapidly decreased to relatively low and constant levels throughout the rest of the season. ELISA values from cambial scrapings were moderately high and relatively constant throughout the season. When GFLV-infected dormant canes were tested, induced actively growing tissues gave the highest ELISA values. TomRSV ELISA values were relatively constant over the season and shoot tips, mature leaves and cambial scrapings produced similar ELISA values.Strategien der Probenahme zur Feststellung des Grapevine fanleaf-Virus und des Tomato ringspot-Virus der RebeDas Ziel der vorliegenden Untersuchung war es, den Einfluß der Jahreszeit, des Wirtsgenotyps, des Virusisolates und des Pflanzengewebes auf den Nachweis zweier Nepoviren durch ELISA zu bestimmen. Das Virus der Reisigkrankheit (GFLV} und der Erreger der Adernvergilbung bei Reben, das Tomatenringfleckenvirus (TomRSV}, können durch Enzyme-linked immunosorbent assay (ELISA) leicht nachgewiesen werden. Drei serologisch identische Isolate von GFLV (verantwortlich für Fächerblättrigkeit, Adernaufhellung und Panaschüre) wurden an einer Sorte von Vitis rupestris SCHEELE und drei Sorten von V. vinifera L., TomRSV wurde an V. vinifera cv. Carignane getestet. Hierbei wurden Triebspitzen, ausgewachsene Blätter und Kambiumschabsel geprüft. Von dormantem GFLV-infiziertem Rebholz wurden untersucht: Sägemehl, Kambiumschabsel, Ruheknospen, sowie aus dem Holz entstandene Triebe, Wurzeln und Kallusgewebe. Die Ergebnisse des ELISA-Tests wurden weder durch die Testrebensorte noch durch das Virusisolat beeinflußt. Mittels ELISA konnten jedoch jahreszeitlich bedingte Unterschiede im GFLV-Titer nachgewiesen werden. Bei den Triebspitzen sanken die Werte von einem Maximum > 4.00 OD450nm im Mai auf ein Minimum von 0.05 OD450nm im September. Auch ausgewachsene Blätter zeigten im Mai die höchsten Werte, die dann rasch auf ein relativ niedriges und gleichbleibendes Niveau zurückgingen. Die ELISA-Werte des Kambiumschabsels blieben während der ganzen Vegetationsperiode relativ hoch und stabil. Beim Test von GFLV-infiziertem dormantem Schnittholz zeigten die induzierten, wachsenden Gewebe die höchsten ELISA-Werte. Die ELISA-Werte für TomRSV blieben während der Vegetationsperiode relativ konstant, und es gab kaum Unterschiede zwischen Triebspitzen, ausgewachsenen Blättern und Kambiumschabsel

Syrah decline: viral or non-viral?

Declining young grapevine plants of V. vinifera variety Syrah suggesting a unique problem for this popular variety. Generally the affected vines show red canopy symptoms starting from early to late summer due to the stress caused by affecting factors

Serological detection of Grapevine rupestris stem pitting-associated virus (GRSPa V) by a polyclonal antiserum to recombinant virus coat protein

The coat protein gene of Grapevine rupestris stem pitting-associated virus (GRSPaV) was amplified with primers based on the completely sequenced Californian GRSPaV isolate, The protein expressed in Escherichia coli was used to raise an antiserum in rabbit. This antiserum was successfully used to detect virus coat protein in infected grapevine extracts either spotted on polyvinyl difluoride membranes (dot immunobinding) or blotted on membranes after gel separation (Western blot). The antiserum titre was 1:5,000 in Western blot. GRSPaV was detected in leaf petioles and cortical scrapings from dormant canes during the whole vegetative season. Several accessions of Vitis rupestris, currently used as presumptive virus-free indicators of Rupestris stem pitting, were found to be infected by this virus. While the application of the antiserum in ELISA was ineffective, the availability of similarly simple and effective serological tools, such as dot immunobinding, may allow a wide survey for GRSPaV

Local species assemblages are influenced more by past than current dissimilarities in photosynthetic activity

Most land on Earth has been changed by humans and past changes of land can have lasting influences on current species assemblages. Yet few globally representative studies explicitly consider such influences even though auxiliary data, such as from remote sensing, are readily available. Time series of satellite-derived data have been commonly used to quantify differences in land-surface attributes such as vegetation cover, which will among other things be influenced by anthropogenic land conversions and modifications. Here we quantify differences in current and past (up to five years before sampling) vegetation cover, and assess whether such differences differentially influence taxonomic and functional groups of species assemblages between spatial pairs of sites. Specifically, we correlated between-site dissimilarity in photosynthetic activity of vegetation (the Enhanced Vegetation Index) with the corresponding dissimilarity in local species assemblage composition from a global database using a common metric for both, the Bray-Curtis index. We found that dissimilarity in species assemblage composition was on average more influenced by dissimilarity in past than current photosynthetic activity, and that the influence of past dissimilarity increased when longer time periods were considered. Responses to past dissimilarity in photosynthetic activity also differed among taxonomic groups (plants, invertebrates, amphibians, reptiles, birds and mammals), with reptiles being among the most influenced by more dissimilar past photosynthetic activity. Furthermore, we found that assemblages dominated by smaller and more vegetation-dependent species tended to be more influenced by dissimilarity in past photosynthetic activity than prey-dependent species. Overall, our results have implications for studies that investigate species responses to current environmental changes and highlight the importance of past changes continuing to influence local species assemblage composition. We demonstrate how local species assemblages and satellite-derived data can be linked and provide suggestions for future studies on how to assess the influence of past environmental changes on biodiversity

Molecular analysis of a California strain of Rupestris stem pitting-associated virus isolated from declining Syrah grapevines

The sequence of the genome of a Rupestris stem pitting-associated virus (RSPaV) isolated from a declining Syrah grapevine in California, designated the Syrah strain (RSPaV-SY) was determined. The genome of this strain had an overall nucleotide identity os 77% in comparison with RSPaV sequences in GenBank; the coat protein was the most conservd gene among RSPaV sequences among replicase was the least conserved gene. Phylogenetic analysis of partial coat protein and replicase gene sequences showed RSPaV-SY clustrd independently from the majority of RSPaV isolates

Open Science in Software Engineering

Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other scientific disciplines, in software engineering, we are still struggling in adapting open science to the particularities of our discipline, rendering progress in our scientific community cumbersome. In this chapter, we reflect upon the essentials in open science for software engineering including what open science is, why we should engage in it, and how we should do it. We particularly draw from our experiences made as conference chairs implementing open science initiatives and as researchers actively engaging in open science to critically discuss challenges and pitfalls, and to address more advanced topics such as how and under which conditions to share preprints, what infrastructure and licence model to cover, or how do it within the limitations of different reviewing models, such as double-blind reviewing. Our hope is to help establishing a common ground and to contribute to make open science a norm also in software engineering.Comment: Camera-Ready Version of a Chapter published in the book on Contemporary Empirical Methods in Software Engineering; fixed layout issue with side-note

Soot structure and flow characteristics in turbulent non-premixed methane flames stabilised on a bluff-body

The soot properties of methane in turbulent regimes are not well characterised but are highly desirable. Methane is the main constituent of natural gas that is broadly used in many industrial combustors. Investigation of turbulent methane flames under well-defined boundary conditions is therefore useful for interpreting soot formation in practical burners and can be used for further model development. This study presents a joint experimental and numerical study of a series of turbulent non-premixed bluff-body flames fuelled with pure methane for three values of the momentum flux ratio of fuel jet to co-flowing air. Soot volume fraction (SVF) and flowfield are measured simultaneously using planar laser-induced incandescence (P-LII) and 2D-polarised particle image velocimetry (P-PIV). Additionally, time-averaged temperature, mixture fraction, OH and C2H2 concentrations are estimated numerically using RANS models. The global flame structure for all three flames features a recirculation zone with a double-vortex structure, a jet-propagating zone, and a neck zone connecting the two regions. The soot distribution within the recirculation zone shows clear distinct features, which is attributed to the mean mixture fraction distribution in this zone. Increasing the momentum flux ratio shifts the location of the mean stoichiometric mixture fraction to the rich inner vortex core, leading to a distinct peak of the total integrated soot in the inner vortex of the recirculation zone that is not observed in other cases. Also, it is deduced that the soot inception starts earlier in the recirculation zone for the flame with the highest momentum flux ratio and in the jet zone for the other two flames. Much higher soot concentration and lower intermittency are found with ethylene-based flames stabilised on the same burner and with the same operating conditions. In addition, the study has generated a database of soot and flowfield results, which can be helpful for future model validations.Amir Rowhani, Zhiwei Sun, Alfonso Chinnici, Paul R. Medwell, Graham J. Nathan, Bassam B. Dall

Urban agriculture: a global analysis of the space constraint to meet urban vegetable demand

Urban agriculture (UA) has been drawing a lot of attention recently for several reasons: the majority of the world population has shifted from living in rural to urban areas; the environmental impact of agriculture is a matter of rising concern; and food insecurity, especially the accessibility of food, remains a major challenge. UA has often been proposed as a solution to some of these issues, for example by producing food in places where population density is highest, reducing transportation costs, connecting people directly to food systems and using urban areas efficiently. However, to date no study has examined how much food could actually be produced in urban areas at the global scale. Here we use a simple approach, based on different global-scale datasets, to assess to what extent UA is constrained by the existing amount of urban space. Our results suggest that UA would require roughly one third of the total global urban area to meet the global vegetable consumption of urban dwellers. This estimate does not consider how much urban area may actually be suitable and available for UA, which likely varies substantially around the world and according to the type of UA performed. Further, this global average value masks variations of more than two orders of magnitude among individual countries. The variations in the space required across countries derive mostly from variations in urban population density, and much less from variations in yields or per capita consumption. Overall, the space required is regrettably the highest where UA is most needed, i.e., in more food insecure countries. We also show that smaller urban clusters (i.e., <100 km2 each) together represent about two thirds of the global urban extent; thus UA discourse and policies should not focus on large cities exclusively, but should also target smaller urban areas that offer the greatest potential in terms of physical space

A retrospective time trend study of firearm and nonfirearm homicide in Cape Town from 1994 to 2013

Background. Gunshot injuries from interpersonal violence are a major cause of mortality. In South Africa (SA), the Firearms Control Act of 2000 sought to address firearm violence by removing illegally owned firearms from circulation, stricter regulation of legally owned firearms, and stricter licensing requirements. Over the last few years, varied implementation of the Act and police corruption have increased firearm availability.Objectives. To investigate whether changes in firearm availability in SA were associated with changes in firearm homicide rates.Methods. This was a retrospective time trend study (1994 - 2013) using postmortem data. Time trends of firearm and non-firearm homicide rates were analysed with generalised linear models. Distinct time periods for temporal trends were assigned based on a priori assumptions regarding changes in the availability of firearms.Results. Firearm and non-firearm homicide rates adjusted for age, sex and race exhibited different temporal trends. Non-firearm homicide rates either decreased or remained stable over the entire period. Firearm homicide increased at 13% annually from 1994 through 2000, and decreased by 15% from 2003 through 2006, corresponding with changes in firearm availability in 2001, 2003, 2007 and 2011. A 21% annual increase in firearm homicide after 2010 coincided with police fast-tracking new firearm licence applications. Cape Town’s coloured population experienced a significantly greater increase than other population groups following additional exposure to illegal firearms from 2007.Conclusions. The strong association between firearm availability and homicide, and the reversal of a decreasing firearm homicide trend during a period of lax enforcement, provide further support for the association between reduced firearm homicide and stricter regulation

Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses

We have characterized the virome in single grapevines by 454 high-throughput sequencing of double-stranded RNA recovered from the vine stem. The analysis revealed a substantial set of sequences similar to those of fungal viruses. Twenty-six putative fungal virus groups were identified from a single plant source. These represented half of all known mycoviral families including the Chrysoviridae, Hypoviridae, Narnaviridae, Partitiviridae, and Totiviridae. Three of the mycoviruses were associated with Botrytis cinerea, a common fungal pathogen of grapes. Most of the rest appeared to be undescribed. The presence of viral sequences identified by BLAST analysis was confirmed by sequencing PCR products generated from the starting material using primers designed from the genomic sequences of putative mycoviruses. To further characterize these sequences as fungal viruses, fungi from the grapevine tissue were cultured and screened with the same PCR probes. Five of the mycoviruses identified in the total grapevine extract were identified again in extracts of the fungal cultures