scholarly journals Spatial Sampling to Detect an Invasive Pathogen Outside of an Eradication Zone

2011 ◽  
Vol 101 (6) ◽  
pp. 725-731 ◽  
Author(s):  
I. Demon ◽  
N. J. Cunniffe ◽  
B. P. Marchant ◽  
C. A. Gilligan ◽  
F. van den Bosch
Keyword(s):  
Plant Pathology ◽  
Sampling Methods ◽  
Optimization Method ◽  
Spatial Sampling ◽  
Effective Control ◽  
Spatially Explicit ◽  
Invasive Pathogens ◽  
Invasive Pathogen ◽  
Optimum Sample ◽  
Spatial Simulated Annealing

Invasive pathogens are known to cause major damage to the environments they invade. Effective control of such invasive pathogens depends on early detection. In this paper we focus on sampling with the aim of detecting an invasive pathogen. To that end, we introduce the concept of optimized spatial sampling, using spatial simulated annealing, to plant pathology. It has been mathematically proven (15) that this optimization method converges to the optimum allocation of sampling points that give the largest detection probability. We show the benefits of the method to plant pathology by (i) first illustrating that optimized spatial sampling can easily be applied for disease detection, and then we show that (ii) combining it with a spatially explicit epidemic model, we can develop optimum sample schemes, i.e., optimum locations to sample that maximize the probability of detecting an invasive pathogen. This method is then used as baseline against which other sampling methods can be tested for their accuracy. For the specific example case of this paper, we test (i) random sampling, (ii) stratified sampling as well as (iii) sampling based on the output of the simulation model (using the most frequently infected hosts as sample points), and (iv) sampling the hosts closest to the outbreak point.

Emergence and populations genomics of the highly invasive chestnut blight pathogen

2020 ◽  
Author(s):  
◽  
Lea Stauber
Keyword(s):  
Mating Type ◽  
Fungal Genome ◽  
Chestnut Blight ◽  
Mixed Mating ◽  
Large Set ◽  
Pathogen Evolution ◽  
Invasive Pathogens ◽  
Invasive Pathogen ◽  
Genome Wide

Invasive pathogens are a threat to forest and agroecosystems, as well as animal and human health. Identifying genomic determinants of pathogen evolution, as well as investigations into the genetic structure of invasive pathogen populations provide fundamental insights to why species can emerge as invasive pathogens. In this PhD project I investigated the emergence and population genomics of the invasive chestnut blight fungus Cryphonectria parasitica, using comparative and population genomic approaches. C. parasitica recently emerged as an invasive bark pathogen on non-Asian Castanea species in North America and Europe. In the first chapter, I investigated genomic determinants of lifestyle transitions in the genus Cryphonectria, by genome comparisons of C. parasitica and its sister species. The study uncovered a striking loss of genes associated with carbohydrate metabolism in the invasive pathogen C. parasitica, which may have promoted its pathogenicity on Castanea species. The second chapter explores the emergence and diversification of a highly invasive chestnut blight lineage across south-eastern Europe. By analyzing the genome-wide diversity of a large set of C. parasitica isolates of predominantly European origin, the study showed that a highly successful clonal pathogen lineage can emerge from a recombinant bridgehead population within Europe. Interestingly, the emergence of this clonal lineage was accompanied by an evolutionary transition from mixed mating type populations to single mating type outbreak populations. Lastly, in the third chapter I investigated temporal changes in genetic diversity of established C. parasitica populations in southern Switzerland, as well as potential links between the presence of the deleterious hyperparasitic mycovirus Cryphonectria hypovirus 1 (CHV1) and fungal genome-wide diversity. The results indicate increased mating among related fungal individuals, resulting in high genetic similarity of genotypes and facilitated CHV1 transmission. There were no substantial changes in fungal population structure and after ˜30 years and no detectable impact of CHV1 presence on fungal genome-wide diversity. Although our results show stable CHV1 incidence in fungal populations over three decades, the short-term interaction dynamics are likely highly volatile. The overall findings of this PhD thesis highlight the relevance of genomic determinants facilitating pathogen emergence and invasions. C. parasitica is a useful model to study fundamental questions of pathogen evolution and invasive processes, as well as antagonistic pathogen-hyperparasite interactions.

scholarly journals Invasive snake causes massive reduction of all endemic herpetofauna on Gran Canaria

2021 ◽  
Vol 288 (1964) ◽  
Author(s):  
Julien C. Piquet ◽  
Marta López-Darias
Keyword(s):  
Sampling Methods ◽  
Distance Sampling ◽  
The Other ◽  
Spatially Explicit ◽  
Negative Consequences ◽  
Gran Canaria ◽  
Island Biodiversity ◽  
Capture Recapture ◽  
The Impact ◽  
Number Of Individuals

Invasive snakes represent a serious threat to island biodiversity, being responsible for far-reaching impacts that are noticeably understudied, particularly regarding native reptiles. We analysed the impact of the invasive California kingsnake, Lampropeltis californiae —recently introduced in the Canary Islands—on the abundance of all endemic herpetofauna of the island of Gran Canaria. We quantified the density in invaded and uninvaded sites for the Gran Canaria giant lizard, Gallotia stehlini , the Gran Canaria skink, Chalcides sexlineatus , and Boettger's wall gecko, Tarentola boettgeri . We used spatially explicit capture-recapture and distance-sampling methods for G. stehlini and active searches under rocks for the abundance of the other two reptiles. The abundance of all species was lower in invaded sites, with a reduction in the number of individuals greater than 90% for G. stehlini , greater than 80% for C. sexlineatus and greater than 50% for T. boettgeri in invaded sites. Our results illustrate the severe impact of L. californiae on the endemic herpetofauna of Gran Canaria and highlight the need for strengthened measures to manage this invasion. We also provide further evidence of the negative consequences of invasive snakes on island reptiles and emphasize the need for further research on this matter on islands worldwide.

scholarly journals Anti-Foc RT4 Activity of a Newly Isolated Streptomyces sp. 5–10 From a Medicinal Plant (Curculigo capitulata)

2021 ◽  
Vol 11 ◽  
Author(s):  
Tianyan Yun ◽  
Miaoyi Zhang ◽  
Dengbo Zhou ◽  
Tao Jing ◽  
Xiaoping Zang ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Medicinal Plant ◽  
Fermentation Broth ◽  
Membrane Integrity ◽  
Morphological Characteristics ◽  
Gene Clusters ◽  
Optimization Method ◽  
Effective Control ◽  
Multidrug Resistance Gene ◽  
Irreversible Damage

Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense (Foc) is a disastrous soil-borne fungal disease. Foc tropical race 4 (Foc TR4) can infect almost all banana cultivars. Until now, there is a shortage of safety and effective control methods and commercial banana cultivars with a resistance against Foc TR4. Biocontrol using environmentally friendly microbes is a promising strategy for the management of Foc TR4. Here, a strain 5–10, newly isolated from a medicinal plant (Curculigo capitulata), exhibited a high antifungal activity against Foc TR4. Combing the morphological characteristics and molecular identification, strain 5–10 was classified as a Streptomyces genus. The sequenced genome revealed that more than 39 gene clusters were involved in the biosynthesis of secondary metabolites. Some multidrug resistance gene clusters were also identified such as mdtD, vatB, and vgaE. To improve the anti-Foc TR4 activity of the strain 5–10 extracts, an optimization method of fermentation broth was established. Antifungal activity increased by 72.13% under the fermentation system containing 2.86 g/L of NaCl and 11.57% of inoculation amount. After being treated with the strain 5–10 extracts, the Foc TR4 hyphae shrinked, deformed, and ruptured. The membrane integrity and cell ultrastructure incurred irreversible damage. Streptomyces sp. 5–10 extracts play a fungicidal role in Foc TR4. Hence, Streptomyces sp. 5–10 will be a potential biocontrol agent to manage fungal diseases by exploring the microbial fertilizer.

scholarly journals An Improved Parallelized Multi-Objective Optimization Method for Complex Geographical Spatial Sampling: AMOSA-II

2020 ◽  
Vol 9 (4) ◽  
pp. 236
Author(s):  
Xiaolan Li ◽  
Bingbo Gao ◽  
Zhongke Bai ◽  
Yuchun Pan ◽  
Yunbing Gao
Keyword(s):  
Markov Chains ◽  
Optimization Problems ◽  
Optimization Method ◽  
Spatial Sampling ◽  
Computational Time ◽  
Test Problems ◽  
Optimal Solutions ◽  
Multi Objective Optimization ◽  
Nsga Ii ◽  
Multi Objective

Complex geographical spatial sampling usually encounters various multi-objective optimization problems, for which effective multi-objective optimization algorithms are much needed to help advance the field. To improve the computational efficiency of the multi-objective optimization process, the archived multi-objective simulated annealing (AMOSA)-II method is proposed as an improved parallelized multi-objective optimization method for complex geographical spatial sampling. Based on the AMOSA method, multiple Markov chains are used to extend the traditional single Markov chain; multi-core parallelization technology is employed based on multi-Markov chains. The tabu-archive constraint is designed to avoid repeated searches for optimal solutions. Two cases were investigated: one with six typical traditional test problems, and the other for soil spatial sampling optimization applications. Six performance indices of the two cases were analyzed—computational time, convergence, purity, spacing, min-spacing and displacement. The results revealed that AMOSA-II performed better which was more effective in obtaining preferable optimal solutions compared with AMOSA and NSGA-II. AMOSA-II can be treated as a feasible means to apply in other complex geographical spatial sampling optimizations.

Design Method of Assembly Accuracy Repeatability of Heavy Duty Machine Tool

2014 ◽  
Vol 800-801 ◽  
pp. 516-520
Author(s):  
Bin Jiang ◽  
Jia Xue Zhao ◽  
Shou Zheng Sun ◽  
Yi Fei Wang ◽  
Ying Li
Keyword(s):  
Machine Tool ◽  
Design Method ◽  
Optimization Method ◽  
Differential Method ◽  
Effective Control ◽  
Assembly Process ◽  
Heavy Duty ◽  
Assembly Accuracy ◽  
Heavy Machine ◽  
Machine Assembly

Focus on the problems that heavy duty machine tool lack of fault samples and process information in repetitive assembly, result in the existing assembly process method can’t meet the repetitive assembly accuracy. According to characteristics of local machine assembly process, propose its assembly repeatability evaluation indexes. Establish the mapping relation among machine performance, assembly accuracy and structure, and built a hierarchical model of assembly process, obtain the process optimal design scheme of assembly accuracy repeatability. Use the multivariate function differential method, propose a calculation method of heavy machine assembly accuracy, and verify applicability of the method, depend on the machine loads and structure criterions, propose heavy machine assembly accuracy repeatability optimization method, example analysis shows that: the servo effect of repetitive assembly accuracy in new process is obvious, simultaneously stress field magnitude and stability of new technology is better than the original, realize effective control of the machine tool assembly accuracy repeatability.

scholarly journals Genetic Variability of Isolates of Ramulispora sorghi From Cáceres-MT, Brazil

2019 ◽  
Vol 11 (10) ◽  
pp. 250
Author(s):  
A. V. M. Duarte ◽  
C. L. Correa ◽  
M. A. A. Barelli ◽  
B. W. Zago ◽  
N. L. Sander ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Relevant Information ◽  
Optimization Method ◽  
Control Measures ◽  
Effective Control ◽  
Breeding Programs ◽  
Mato Grosso ◽  
Average Value

Among the most produced cereals worldwide, sorghum (Sorghum bicolor (L.) Moench), presents low productivity in Brazil, mainly due to the occurrence of diseases, with a prominence of sooty stripe, caused by the fungus Ramulispora sorghi, until then considered a secondary disease, has increased its incidence and severity, especially in conditions of high humidity and temperature. The most efficient means of control is the use of resistant cultivars, in this sense, studies on the genetic variability of the fungus through molecular markers are of great importance for the breeding programs of sorghum. The objective of this work was to evaluate the genetic variability in isolates of Ramulispora sorghi belonging to the mycoteca of the Laboratory of Genetic Resources & Biotechnology of the Universidade do Estado de Mato Grosso, campus of Cáceres, via molecular markers of the ISSR type. The results indicate the existence of genetic variability among the isolates of R. sorghi. The Polymorphic Information Content (PIC) showed that the primers were classified as medium informational with an average value of 0.27. 71 polymorphic fragments were formed considering the 40 isolates of R. sorghi, which presented the value of k = 2, represent the differentiation of the isolates into two distinct clusters. The genetic dissimilarity measures were estimated by the Coefficient of Nei and Li, where the combination between the isolates B107/16 (15) and B103/15 (16) obtained the smallest magnitude (0,12) and the combinations between isolates B111/16 (2) and S114/15 (33), S316/15 (3) and S114/15 (33), B115/16 (4) and S114/15 (33), B118/16 (6) and S114/15 (33) were more dissimilar (1,00). The “UPGMA” method provided a breakdown of the 40 isolates into 4 distinct groups. The Cophenetic Correlaction Coefficient (CCC) presented significant value with r = 0,84. The Tocher’s optimization method allowed the 40 isolates to be distributed in 10 different groups. These results provide relevant information on the genetic variability among the 40 isolates of R. sorghi analyzed. In addition, they indicate that fungus have a wide genetic diversity, and have been recurring in different regions of Brazil and the world, and thus, larger studies become essential for more effective control measures.

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