A loop-mediated isothermal amplification assay for the visual detection of duck circovirus

BACKGROUND: Duck circovirus (DuCV) infection in farmed ducks is associated with growth problems or retardation syndromes. Rapid identification of DuCV infected ducks is essential to control DuCV effectively. Therefore(,) this study aims to develop of an assay for DuCV to be highly specific, sensitive, and simple without any specialized equipment. METHODS: A set of six specific primers was designed to target the sequences of the Rep gene of DuCV, and A loop-mediated isothermal amplification (LAMP) assay were developed and the reaction conditions were optimized for rapid detection of DuCV. RESULTS: The LAMP assay reaction was conducted in a 62°C water bath condition for 50 min. Then the amplification products were visualized directly for color changes. This LAMP assay is highly sensitive and able to detect twenty copies of DuCV DNA. The specificity of this LAMP assay was supported by no cross-reaction with other duck pathogens. CONCLUSION: This LAMP method for DuCV is highly specific and sensitive and can be used as a rapid and direct diagnostic assay for testing clinical samples

Reverse-transcription, loop-mediated isothermal amplification assay for the sensitive and rapid detection of H10 subtype avian influenza viruses

BACKGROUND: The H10 subtype avian influenza viruses (H10N4, H10N5 and H10N7) have been reported to cause disease in mammals, and the first human case of H10N8 subtype avian influenza virus was reported in 2013. Recently, H10 subtype avian influenza viruses (AIVs) have been followed more closely, but routine diagnostic tests are tedious, less sensitive and time consuming, rapid molecular detection assays for H10 AIVs are not available. METHODS: Based on conserved sequences within the HA gene of the H10 subtype AIVs, specific primer sets of H10 subtype of AIVs were designed and assay reaction conditions were optimized. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was established for the rapid detection of H10 subtype AIVs. The specificity was validated using multiple subtypes of AIVs and other avian respiratory pathogens, and the limit of detection (LOD) was tested using concentration gradient of in vitro-transcribed RNA. RESULTS: The established assay was performed in a water bath at 63 °C for 40 min, and the amplification result was visualized directly as well as under daylight reflections. The H10-RT-LAMP assay can specifically amplify H10 subtype AIVs and has no cross-reactivity with other subtypes AIVs or avian pathogens. The LOD of the H10-RT-LAMP assay was 10 copies per μL of in vitro-transcribed RNA. CONCLUSIONS: The RT-LAMP method reported here is demonstrated to be a potentially valuable means for the detection of H10 subtype AIV and rapid clinical diagnosis, being fast, simple, and low in cost. Consequently, it will be a very useful screening assay for the surveillance of H10 subtype AIVs in underequipped laboratories as well as in field conditions

The Mitochondrial Genome of Baylisascaris procyonis

BACKGROUND: Baylisascaris procyonis (Nematoda: Ascaridida), an intestinal nematode of raccoons, is emerging as an important helminthic zoonosis due to serious or fatal larval migrans in animals and humans. Despite its significant veterinary and public health impact, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. Mitochondrial (mt) genomes can provide a foundation for investigations in these areas and assist in the diagnosis and control of B. procyonis. In this study, the first complete mt genome sequence of B. procyonis was determined using a polymerase chain reaction (PCR)-based primer-walking strategy. METHODOLOGY/PRINCIPAL FINDINGS: The circular mt genome (14781 bp) of B. procyonis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes congruent with other chromadorean nematodes. Interestingly, the B. procyonis mtDNA featured an extremely long AT-rich region (1375 bp) and a high number of intergenic spacers (17), making it unique compared with other secernentean nematodes characterized to date. Additionally, the entire genome displayed notable levels of AT skew and GC skew. Based on pairwise comparisons and sliding window analysis of mt genes among the available 11 Ascaridida mtDNAs, new primer pairs were designed to amplify specific short fragments of the genes cytb (548 bp fragment) and rrnL (200 bp fragment) in the B. procyonis mtDNA, and tested as possible alternatives to existing mt molecular beacons for Ascaridida. Finally, phylogenetic analysis of mtDNAs provided novel estimates of the interrelationships of Baylisasaris and Ascaridida. CONCLUSIONS/SIGNIFICANCE: The complete mt genome sequence of B. procyonis sequenced here should contribute to molecular diagnostic methods, epidemiological investigations and ecological studies of B. procyonis and other related ascaridoids. The information will be important in refining the phylogenetic relationships within the order Ascaridida and enriching the resource of markers for systematic, population genetic and evolutionary biological studies of parasitic nematodes of socio-economic importance

Multi-objective optimization of water resources allocation in Han River basin (China) integrating efficiency, equity and sustainability

AbstractThe hydrological cycle, affected by climate change and rapid urbanization in recent decades, has been altered to some extent and further poses great challenges to three key factors of water resources allocation (i.e., efficiency, equity and sustainability). However, previous studies usually focused on one or two aspects without considering their underlying interconnections, which are insufficient for interaction cognition between hydrology and social systems. This study aims at reinforcing water management by considering all factors simultaneously. The efficiency represents the total economic interests of domesticity, industry and agriculture sectors, and the Gini coefficient is introduced to measure the allocation equity. A multi-objective water resources allocation model was developed for efficiency and equity optimization, with sustainability (the river ecological flow) as a constraint. The Non-dominated sorting genetic algorithm II (NSGA-II) was employed to derive the Pareto front of such a water resources allocation system, which enabled decision-makers to make a scientific and practical policy in water resources planning and management. The proposed model was demonstrated in the middle and lower Han River basin, China. The results indicate that the Pareto front can reflect the conflicting relationship of efficiency and equity in water resources allocation, and the best alternative chosen by cost performance method may provide rich information as references in integrated water resources planning and management.</jats:p

Comprehensive Evaluation of Water Resources Carrying Capacity in the Han River Basin

As one of the most crucial indices of sustainable development and water security, water resources carrying capacity (WRCC) has been a pivotal and hot-button issue in water resources planning and management. Quantifying WRCC can provide useful references on optimizing water resources allocation and guiding sustainable development. In this study, the WRCCs in both current and future periods were systematically quantified using set pair analysis (SPA), which was formulated to represent carrying grade and explore carrying mechanism. The Soil and Water Assessment Tool (SWAT) model, along with water resources development and utilization model, was employed to project future water resources scenarios. The proposed framework was tested on a case study of China’s Han River basin. A comprehensive evaluation index system across water resources, social economy, and ecological environment was established to assess the WRCC. During the current period, the WRCC first decreased and then increased, and the water resources subsystem performed best, while the eco-environment subsystem achieved inferior WRCC. The SWAT model projected that the amount of the total water resources will reach about 56.9 billion m3 in 2035s, and the water resources development and utilization model projected a rise of water consumption. The declining WRCC implies that the water resources are unable to support or satisfy the demand of ecological and socioeconomic development in 2035s. The study furnishes abundant and valuable information for guiding water resources planning, and the core idea of this model can be extended for the assessment, prediction, and regulation of other systems

Comprehensive Evaluation of Water Resources Carrying Capacity in the Han River Basin

As one of the most crucial indices of sustainable development and water security, water resources carrying capacity (WRCC) has been a pivotal and hot-button issue in water resources planning and management. Quantifying WRCC can provide useful references on optimizing water resources allocation and guiding sustainable development. In this study, the WRCCs in both current and future periods were systematically quantified using set pair analysis (SPA), which was formulated to represent carrying grade and explore carrying mechanism. The Soil and Water Assessment Tool (SWAT) model, along with water resources development and utilization model, was employed to project future water resources scenarios. The proposed framework was tested on a case study of China’s Han River basin. A comprehensive evaluation index system across water resources, social economy, and ecological environment was established to assess the WRCC. During the current period, the WRCC first decreased and then increased, and the water resources subsystem performed best, while the eco-environment subsystem achieved inferior WRCC. The SWAT model projected that the amount of the total water resources will reach about 56.9 billion m3 in 2035s, and the water resources development and utilization model projected a rise of water consumption. The declining WRCC implies that the water resources are unable to support or satisfy the demand of ecological and socioeconomic development in 2035s. The study furnishes abundant and valuable information for guiding water resources planning, and the core idea of this model can be extended for the assessment, prediction, and regulation of other systems.</jats:p