Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Abstract Background The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of “two-speed” genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. Results We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. Conclusion This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.

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Large-scale transcriptomics to dissect two years of the life of a fungal phytopathogen interacting with its host plant

10.1101/2020.10.13.331520 ◽

2020 ◽

Author(s):

Elise J. Gay ◽

Jessica L. Soyer ◽

Nicolas Lapalu ◽

Juliette Linglin ◽

Isabelle Fudal ◽

...

Keyword(s):

Gene Expression ◽

Life Cycle ◽

Host Plant ◽

Large Scale ◽

Plant Disease ◽

Leptosphaeria Maculans ◽

Plant Infection ◽

Effector Genes ◽

Plant Disease Control ◽

Durable Disease Resistance

AbstractThe fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of “two-speed” genome organisms in which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are located in regions enriched in heterochromatin, either constitutive or facultative. These findings provide support for the hypothesis that fungal genes involved in niche adaptation are located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.Author SummaryFungi are extremely important organisms in the global ecosystem. Some are damaging plant pathogens that threaten global food security. A knowledge of their biology and pathogenic cycle is vital for the design of environmentally-friendly control strategies. Unfortunately, many parts of their life cycle remain unknown, due to the complexity of their life-cycles and technical limitations. Here, we use a rapeseed pathogen, Leptosphaeria maculans, which has a particularly complex life-cycle, to show that large-scale RNA-Seq analyses of fungal gene expression can decipher all stages of the fungal cycle over two years of interaction with living or dead hosts, in laboratory and agricultural conditions. We found that the fungus uses about 9% of the genes of its genome specifically during interactions with the plant, and observed waves of extremely tight, complex regulation during the colonization of specific tissues and specific parts of the life-cycle. Our findings highlight the importance of genes encoding effectors, small secreted proteins manipulating the host. This work opens up new avenues for plant disease control through the identification of stage-specific effectors leading to the discovery of novel durable disease resistance genes, or the analysis of epigenetic regulation, which could be manipulated to interfere with effector gene expression.

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Synchronization in 5G networks: a hybrid Bayesian approach toward clock offset/skew estimation and its impact on localization

EURASIP Journal on Wireless Communications and Networking ◽

10.1186/s13638-021-01963-x ◽

2021 ◽

Vol 2021 (1) ◽

Author(s):

Meysam Goodarzi ◽

Darko Cvetkovski ◽

Nebojsa Maletic ◽

Jesús Gutiérrez ◽

Eckhard Grass

Keyword(s):

Bayesian Approach ◽

Large Scale ◽

Hybrid Approach ◽

Position Estimation ◽

5G Networks ◽

Clock Skew ◽

Depth Analysis ◽

The Impact ◽

Mean Square Errors ◽

Clock Offset

AbstractClock synchronization has always been a major challenge when designing wireless networks. This work focuses on tackling the time synchronization problem in 5G networks by adopting a hybrid Bayesian approach for clock offset and skew estimation. Furthermore, we provide an in-depth analysis of the impact of the proposed approach on a synchronization-sensitive service, i.e., localization. Specifically, we expose the substantial benefit of belief propagation (BP) running on factor graphs (FGs) in achieving precise network-wide synchronization. Moreover, we take advantage of Bayesian recursive filtering (BRF) to mitigate the time-stamping error in pairwise synchronization. Finally, we reveal the merit of hybrid synchronization by dividing a large-scale network into local synchronization domains and applying the most suitable synchronization algorithm (BP- or BRF-based) on each domain. The performance of the hybrid approach is then evaluated in terms of the root mean square errors (RMSEs) of the clock offset, clock skew, and the position estimation. According to the simulations, in spite of the simplifications in the hybrid approach, RMSEs of clock offset, clock skew, and position estimation remain below 10 ns, 1 ppm, and 1.5 m, respectively.

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Large-Scale Landslide Displacement Rate Prediction Based on Multi-Factor Support Vector Regression Machine

Applied Sciences ◽

10.3390/app11041381 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1381

Author(s):

Xiuzhen Li ◽

Shengwei Li

Keyword(s):

Support Vector Regression ◽

Water Level ◽

Large Scale ◽

Displacement Rate ◽

Support Vector ◽

Single Factor ◽

Reservoir Water ◽

Reservoir Water Level ◽

Depth Analysis ◽

Three Factor

Forecasting the development of large-scale landslides is a contentious and complicated issue. In this study, we put forward the use of multi-factor support vector regression machines (SVRMs) for predicting the displacement rate of a large-scale landslide. The relative relationships between the main monitoring factors were analyzed based on the long-term monitoring data of the landslide and the grey correlation analysis theory. We found that the average correlation between landslide displacement and rainfall is 0.894, and the correlation between landslide displacement and reservoir water level is 0.338. Finally, based on an in-depth analysis of the basic characteristics, influencing factors, and development of landslides, three main factors (i.e., the displacement rate, reservoir water level, and rainfall) were selected to build single-factor, two-factor, and three-factor SVRM models. The key parameters of the models were determined using a grid-search method, and the models showed high accuracies. Moreover, the accuracy of the two-factor SVRM model (displacement rate and rainfall) is the highest with the smallest standard error (RMSE) of 0.00614; it is followed by the three-factor and single-factor SVRM models, the latter of which has the lowest prediction accuracy, with the largest RMSE of 0.01644.

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Development and Testing of an Unmanned Aerial Vehicle for Large Scale Particle Image Velocimetry

Volume 3: Industrial Applications; Modeling for Oil and Gas, Control and Validation, Estimation, and Control of Automotive Systems; Multi-Agent and Networked Systems; Control System Design; Physical Human-Robot Interaction; Rehabilitation Robotics; Sensing and Actuation for Control; Biomedical Systems; Time Delay Systems and Stability; Unmanned Ground and Surface Robotics; Vehicle Motion Controls; Vibration Analysis and Isolation; Vibration and Control for Energy Harvesting; Wind Energy ◽

10.1115/dscc2014-5838 ◽

2014 ◽

Cited By ~ 4

Author(s):

Christopher Pagano ◽

Flavia Tauro ◽

Salvatore Grimaldi ◽

Maurizio Porfiri

Keyword(s):

Particle Image Velocimetry ◽

Large Scale ◽

Field Experiments ◽

Particle Image ◽

Low Cost ◽

Surface Flow ◽

Natural Environments ◽

Natural Stream ◽

Image Velocimetry ◽

Scale Particle

Large scale particle image velocimetry (LSPIV) is a nonintrusive environmental monitoring methodology that allows for continuous characterization of surface flows in natural catchments. Despite its promise, the implementation of LSPIV in natural environments is limited to areas accessible to human operators. In this work, we propose a novel experimental configuration that allows for unsupervised LSPIV over large water bodies. Specifically, we design, develop, and characterize a lightweight, low cost, and stable quadricopter hosting a digital acquisition system. An active gimbal maintains the camera lens orthogonal to the water surface, thus preventing severe image distortions. Field experiments are performed to characterize the vehicle and assess the feasibility of the approach. We demonstrate that the quadricopter can hover above an area of 1×1m2 for 4–5 minutes with a payload of 500g. Further, LSPIV measurements on a natural stream confirm that the methodology can be reliably used for surface flow studies.

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Measuring ignitability for in situ burning of oil spills weathered under Arctic conditions: From laboratory studies to large-scale field experiments

Marine Pollution Bulletin ◽

10.1016/j.marpolbul.2011.05.020 ◽

2011 ◽

Vol 62 (8) ◽

pp. 1780-1785 ◽

Cited By ~ 27

Author(s):

Janne Fritt-Rasmussen ◽

Per Johan Brandvik

Keyword(s):

Large Scale ◽

Field Experiments ◽

Oil Spills ◽

Laboratory Studies ◽

Scale Field ◽

Arctic Conditions ◽

Large Scale Field

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Mechanics Research on Rock Stress and Deformation of Lancang River Canyon's Large - Scale Dumping Deformation

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.353-356.318 ◽

2013 ◽

Vol 353-356 ◽

pp. 318-323

Author(s):

Song Ye ◽

Yu Sheng Li ◽

Qian Guo

Keyword(s):

Large Scale ◽

Geological Structure ◽

Deformation Characteristics ◽

Deep Part ◽

Trailing Edge ◽

Geological Surveys ◽

Depth Analysis ◽

Numerical Simulation Methods ◽

Complex Geological Structure ◽

Stress And Deformation

This article is based on geological surveys combined with finite element and discrete element numerical simulation methods. In-depth analysis of the complex geological structure, deformation characteristics and stress - deformation problems of dumping rock, we clarify different deformation characteristics of deformable landslide inside, at the bottom and the deep part of trailing edge, and demonstrate the deformation will gradually shift from dumping to shear slip. Potential deformation failure mode will be dumped into the whole sliding - tension, which is controlled by the bottom broken belt, and potential deformation is mainly subject to the bottom fault F207-3 of deformed rock and the dumping broken belt at the deep part of trailing edge.

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Reduced Dosage of Methyl Bromide for Controlling Verticillium Wilt of Potato in Experimental and Commercial Plots

Plant Disease ◽

10.1094/pdis.1997.81.5.469 ◽

1997 ◽

Vol 81 (5) ◽

pp. 469-474 ◽

Cited By ~ 27

Author(s):

A. Gamliel ◽

A. Grinstein ◽

Y. Peretz ◽

L. Klein ◽

A. Nachmias ◽

...

Keyword(s):

Verticillium Wilt ◽

Methyl Bromide ◽

Large Scale ◽

Field Experiments ◽

Tuber Yield ◽

Total Yield ◽

Effective Control ◽

Large Scale Field ◽

Commercial Applications

The use of gas-impermeable films to reduce the dosage of methyl bromide (MB) required to control Verticillium wilt in potatoes was examined in field experiments, conducted in soils naturally infested with Verticillium dahliae. The incidence and severity of Verticillium wilt were significantly reduced (by 74 to 94%) by fumigation with MB at 50 g/m2 under standard low density polyethylene (LDPE) or at 25 g/m2 under gas-impermeable films. Fumigation at 25 g/m2 under LDPE was less effective. Disease severity was inversely correlated (r2 = 0.89 to 0.91) with chlorophyll content in the leaves. Fumigation also reduced (by 89 to 100%) stem colonization by the pathogen. Potato yield in the fumigated plots was significantly higher (26 to 69%), than in their nonfumigated counterparts, and was inversely correlated with disease index (r2 = 0.69 to 0.9). The percentage of high-value tubers (above 45 g) was 52 to 56% of total yield in the fumigated plots as compared with 32 to 40% in the nonfumigated controls. Thus, fumigation also improved the commercial quality of tuber yield. Effective control of V. dahliae and yield increases following MB fumigation at the recommended dosage or at a reduced dosage with gas-impermeable films was also observed in a consecutive crop. These results were verified in a large-scale field experiment using commercial applications, further demonstrating the feasibility of reducing MB dosages under farm conditions, without reducing its effectiveness in terms of disease control and yield improvement.

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A Synthesis of Knowns, Unknowns, and Policy Recommendations from the Sea Lamprey International Symposium

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f80-263 ◽

1980 ◽

Vol 37 (11) ◽

pp. 2202-2208 ◽

Cited By ~ 16

Author(s):

Carl J. Walters ◽

George Spangler ◽

W. J. Christie ◽

Patrick J. Manion ◽

James F. Kitchell

Keyword(s):

International Symposium ◽

Large Scale ◽

Fishery Management ◽

Field Experiments ◽

Lake Trout ◽

Sea Lamprey ◽

Future Research ◽

Fish Stock ◽

Total Production ◽

Pilot Studies

The Sea Lamprey International Symposium (SLIS) has provided a broad spectrum of facts and speculations for consideration in future research and management programs. Many aspects of the laboratory biology and field life history of the sea lamprey (Petromyzon marinus) are now well understood. There is little question that it can now be controlled by chemical larvicides, and perhaps in the future by more efficient integrated control programs. There is correlative evidence (wounds, scars, catch curves) that lamprey caused major mortalities in some fish species, and that control in conjunction with stocking has lead to remarkable recoveries of salmonid stocks in the Great Lakes. However, there are great gaps in understanding about just what the lamprey does under field conditions, and it is not yet possible to reject several hypotheses that assign lamprey a minimum or transient role in fish stock changes. Further studies on details of lamprey biology are, in themselves, unlikely to fill the gaps; one alternative is to conduct a large-scale field experiment involving cessation of lamprey control while holding other factors (fishing, stocking) as steady as possible. If it is decided to proceed with management on the assumption that lamprey are important, without the major field experiments to confirm it, then at least the following steps should be taken: (1) the chemical treatment program should be reviewed in detail, with a view to finding treatment schedules that will minimize frequency and dose rates for lampricide applications; (2) pilot studies on alternative control schemes (sterile male, attractants, barriers) should only be funded if they are statistically well designed (several replicate and control streams), and involve quantitative monitoring of lamprey spawning success and subsequent total production of transforming larvae; (3) the lake trout (Salvelinus namaycush) stocking program should be maintained at its present level, and should involve diverse genotypes rather than a few hatchery strains; (4) growth in the sport fisheries for lake trout should be curtailed, and commercial fisheries should not yet be permitted; (5) a multispecies harvesting policy should be designed that takes into account the buffering effect of each species on lamprey mortality suffered by others (i.e. should some species not be harvested at all, and viewed instead as buffers for more valuable species?); and (6) a program should be developed for restoring, by culture if necessary, native forage species in case the introduced smelt and alewife should collapse under pressure from fishing and prédation by the growing salmonid community.Key words: sea lamprey, proposed research, fishery management, mathematical models, population dynamics

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Effects of irrigation regimes on powdery scab disease and yield of potatoes

Australian Journal of Experimental Agriculture ◽

10.1071/ea9860745 ◽

1986 ◽

Vol 26 (6) ◽

pp. 745 ◽

Cited By ~ 10

Author(s):

PA Taylor ◽

SP Flett ◽

RFde Boer ◽

D Marshall

Keyword(s):

Large Scale ◽

Field Experiments ◽

Field Trials ◽

Powdery Scab ◽

Infested Soil ◽

Spongospora Subterranea ◽

Potato Tubers ◽

Potato Plants ◽

Tuber Set ◽

Large Scale Field

The period of susceptibility of potato tubers to powdery scab (Spongospora subterranea) was studied by inoculating potato plants with spores, or by watering plants in infested soil, at different stages of plant development in greenhouse conditions. Maximum susceptibility began about 1 week before the stage when 50% of stolons had swollen to at least 5-mm diameter (tuber set), and ended 3-4 weeks later. With holding irrigation water during this period reduced the severity of powdery scab by 65-75% in field experiments in 1981-82 and 1982-83, but had no apparent effect on disease severity in 3 out of 6 large-scale field trials during 1984-85.

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