hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean

Phytophthora sojae is a significant pathogen of soybean worldwide. Pathotype surveys for Phytophthora sojae are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for P. sojae or other gene-for-gene pathosystem studies

Ecologies of co-production in the Anthropocene

The urgency, uncertainty and unevenness of the Anthropocene has foregrounded the spatial and temporal multiplicity of co-production between science and society. In this article, we draw together work in geography, science and technology studies and cognate disciplines concerned with ‘co-producing’ knowledge for environmental governance, and with the ‘co-production’ of science and politics. Yet these existing studies and approaches have tended to focus on discrete moments of co-production within bounded time-spaces. Building on work associated with ecologies of participation and geographies of science, we introduce the notion of ‘ecologies of co-production’ as a way to more faithfully attend to multiple co-existing co-productions and the interrelations between them. We define this as diverse interrelating practices and spaces of co-production which intermingle and are co-produced with(in) wider systems and political cultures in which they are situated. We set out how this opens up new ways of thinking about and attending to the spaces and interrelations, diversities and exclusions, histories and constitutions, and responsibilities and affects of co-productions between science and society in the Anthropocene. We suggest that this approach can make a difference in how we do co-production, how we analyse co-production and how we live, act and figure in an Anthropocene world

Comparing different pneumoperitoneum (12 vs. 15 mmHg) pressures with cytokine analysis to evaluate clinical outcomes in patients undergoing robotic‐assisted laparoscopic radical cystectomy and intracorporeal robotic urinary diversion

© 2023 The Authors. BJUI Compass published by John Wiley & Sons Ltd on behalf of BJU International Company. This is an open access article under the terms of the Creative Commons Attribution License. https://creativecommons.org/licenses/by/4.0/Background: Robotic cystectomy is the mainstay surgical intervention for treatment‐refractory non muscle‐invasive and muscle‐invasive bladder cancer. However, paralytic ileus may complicate the postoperative recovery and may be a consequence of an inflammatory response associated with transient gut ischaemia. We have therefore investigated clinical, operative and inflammatory biomarker associations between paralytic ileus in the context of robotic cystectomy and intracorporeal ileal conduit urinary diversion. Methods: Prospective consecutive patients referred for robotic cystectomy were consented and included in the study, while patients >75 years old and converted to open procedure were excluded. The pneumoperitoneum pressure (PP) for carbon dioxide insufflation required to perform the procedure efficiently and safely was recorded (12 or 15 mmHg). We also recorded the postoperative days patients passed flatus and stools, whether they developed ileus, as well as other standard clinical and demographic data. The expression of select proinflammatory and anti‐inflammatory cytokines was determined by multiplex analysis using a cytometric bead array with changes in profiles correlated with the pressures applied and with the existence of an ileus. Results: Twenty‐seven patients were recruited, but only 20 were used in the study with 10 patients in each PP group. Seven patients were excluded all of whom had an extracorporeal ileal conduit formation. There were differences in the 40‐min shorter operative time and 1 day shorter length of stay, as well as passing flatus 1 day and stools 1.5 days earlier in the 12 mmHg compared with the 15 mmHg group. More patients had ileus in the 15 mmHg group vs 12 mmHg group (30% vs. 10.0%). These were not statistically significant. Similarly, there were no statistical differences in the expression of proinflammatory cytokines at the two different pressures or between patient groups, but there were outliers, with the median indicating nonsymmetrical distribution. By comparison, anti‐inflammatory cytokines showed some significant differences between groups, with IL‐6 and IL‐10 showing elevated levels post surgery. No statistical difference was observed between pressures or the existence of an ileus, but the maximum levels of IL‐6 and IL‐10 detected in some patients reflect a pressure difference. Conclusions: The initial findings of this novel scientific study indicated a higher risk of paralytic ileus postrobotic cystectomy and robotic intracorporeal urinary diversion when a higher pressure of 15 mmHg is used compared with 12 mmHg. Although further studies are required to establish the linkage between cytokine profile expression, pressure and ileus, our initial data reinforces the advantages of lower pressure robotic cystectomy and intracorporeal urinary diversion in patient outcomes.Peer reviewe

Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia

Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate

Meta-analysis of yield response of foliar fungicide-treated hybrid corn in the United States and Ontario, Canada

Foliar fungicide applications to corn (Zea mays L.) occur at one or more application timings ranging from early vegetative growth stages to mid-reproductive stages. Previous studies indicated that fungicide applications are profitable under high disease pressure when applied during the tasseling to silking growth stages. Few comprehensive studies in corn have examined the impact of fungicide applications at an early vegetative growth stage (V6) compared to late application timings (VT) for yield response and return on fungicide investment (ROI) across multiple locations

Economics methods in Cochrane systematic reviews of health promotion and public health related interventions.

Peer reviewedPublisher PD

Meta-analysis of yield response of foliar fungicide-treated hybrid corn in the United States and Ontario, Canada

Background Foliar fungicide applications to corn (Zea mays L.) occur at one or more application timings ranging from early vegetative growth stages to mid-reproductive stages. Previous studies indicated that fungicide applications are profitable under high disease pressure when applied during the tasseling to silking growth stages. Few comprehensive studies in corn have examined the impact of fungicide applications at an early vegetative growth stage (V6) compared to late application timings (VT) for yield response and return on fungicide investment (ROI) across multiple locations. Objective Compare yield response of fungicide application timing across multiple fungicide classes and calculate the probability of positive ROI. Methods Data were collected specifically for this analysis using a uniform protocol conducted in 13 states in the United States and one province in Canada from 2014–2015. Data were subjected to a primary mixed-model analysis of variance. Subsequent univariate meta-analyses, with and without moderator variables, were performed using standard meta-analytic procedures. Follow-up power and prediction analyses were performed to aid interpretation and development of management recommendations. Results Fungicide application resulted in a range of yield responses from -2,683.0 to 3,230.9 kg/ha relative to the non-treated control, with 68.2% of these responses being positive. Evidence suggests that all three moderator variables tested (application timing, fungicide class, and disease base level), had some effect (α = 0.05) on the absolute difference in yield between fungicide treated and non-treated plots (). Application timing influenced , with V6 + VT and the VT application timings resulting in greater yield responses than the V6 application timing alone. Fungicide formulations that combined demethylation inhibitor and quinone outside inhibitor fungicides significantly increased yield response. Conclusion Foliar fungicide applications can increase corn grain yield. To ensure the likelihood of a positive ROI, farmers should focus on applications at VT and use fungicides that include a mix of demethylation inhibitor and quinone outside inhibitor active ingredients

Ecology and diversity of culturable fungal species associated with soybean seedling diseases in the Midwestern United States

Aims: To isolate and characterize fungi associated with diseased soybean seedlings in Midwestern soybean production fields and to determine the influence of environmental and edaphic factors on their incidence. Methods and Results: Seedlings were collected from fields with seedling disease history in 2012 and 2013 for fungal isolation. Environmental and edaphic data associated with each field was collected. 3036 fungal isolates were obtained and assigned to 76 species. The most abundant genera recovered were Fusarium (73%) and Trichoderma (11.2%). Other genera included Mortierella, Clonostachys, Rhizoctonia, Alternaria, Mucor, Phoma, Macrophomina and Phomopsis. Most recovered species are known soybean pathogens. However, non-pathogenic organisms were also isolated. Crop history, soil density, water source, precipitation and temperature were the main factors influencing the abundance of fungal species. Conclusion: Key fungal species associated with soybean seedling diseases occurring in several US production regions were characterized. This work also identified major environment and edaphic factors affecting the abundance and occurrence of these species. Significance and Impact of the Study: The identification and characterization of the main pathogens associated with seedling diseases across major soybean-producing areas could help manage those pathogens, and devise more effective and sustainable practices to reduce the damage they cause