scholarly journals The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2424
Author(s):  
Aleksandr V. Ivanov ◽  
Irina V. Safenkova ◽  
Anatoly V. Zherdev ◽  
Boris B. Dzantiev
Keyword(s):  
Molecular Diagnostics ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Isothermal Amplification ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Advantages And Disadvantages ◽  
Fungal Phytopathogens ◽  
Highly Sensitive Detection ◽  
And Control

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.

scholarly journals Assessment of the Diagnostic Ability of Four Detection Methods Using Three Sample Types of COVID-19 Patients

2021 ◽  
Vol 11 ◽  
Author(s):  
Fei Yu ◽  
Guoliang Xie ◽  
Shufa Zheng ◽  
Dongsheng Han ◽  
Jiaqi Bao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Reverse Transcription ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Sample Type ◽  
Rt Pcr ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Oropharyngeal Swab ◽  
And Control

BackgroundViral nucleic acid detection is considered the gold standard for the diagnosis of coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2 infection. However, unsuitable sample types and laboratory detection kits/methods lead to misdiagnosis, which delays the prevention and control of the pandemic.MethodsWe compared four nucleic acid detection methods [two kinds of reverse transcription polymerase chain reactions (RT-PCR A: ORF1ab and N testing; RT-PCRB: only ORF1ab testing), reverse transcription recombinase aided amplification (RT-RAA) and droplet digital RT-PCR (dd-RT-PCR)] using 404 samples of 72 hospitalized COVID-19 patients, including oropharyngeal swab (OPS), nasopharyngeal swabs (NPS) and saliva after deep cough, to evaluate the best sample type and method for SARS-CoV-2 detection.ResultsAmong the four methods, dd-RT-PCR exhibited the highest positivity rate (93.0%), followed by RT-PCR B (91.2%) and RT-RAA (91.2%), while the positivity rate of RT-PCR A was only 71.9%. The viral load in OPS [24.90 copies/test (IQR 15.58-129.85)] was significantly lower than that in saliva [292.30 copies/test (IQR 20.20-8628.55)] and NPS [274.40 copies/test (IQR 33.10-2836.45)]. In addition, if OPS samples were tested alone by RT-PCR A, only 21.4% of the COVID-19 patients would be considered positive. The accuracy of all methods reached nearly 100% when saliva and NPS samples from the same patient were tested simultaneously.ConclusionsSARS-CoV-2 nucleic acid detection methods should be fully evaluated before use. High-positivity rate methods such as RT-RAA and dd-RT-PCR should be considered when possible. Furthermore, saliva after deep cough and NPS can greatly improve the accuracy of the diagnosis, and testing OPS alone is not recommended.

scholarly journals Food Sensing: Detection of Bacillus cereus Spores in Dairy Products

Biosensors ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 15 ◽  
Author(s):  
Jasmina Vidic ◽  
Carole Chaix ◽  
Marisa Manzano ◽  
Marc Heyndrickx
Keyword(s):  
Bacillus Cereus ◽  
Dairy Products ◽  
Food Samples ◽  
Detection Methods ◽  
Economic Losses ◽  
Processing Plant ◽  
Advantages And Disadvantages ◽  
Microbiological Methods ◽  
Highly Sensitive ◽  
Highly Sensitive Detection

Milk is a source of essential nutrients for infants and adults, and its production has increased worldwide over the past years. Despite developments in the dairy industry, premature spoilage of milk due to the contamination by Bacillus cereus continues to be a problem and causes considerable economic losses. B. cereus is ubiquitously present in nature and can contaminate milk through a variety of means from the farm to the processing plant, during transport or distribution. There is a need to detect and quantify spores directly in food samples, because B. cereus might be present in food only in the sporulated form. Traditional microbiological detection methods used in dairy industries to detect spores show limits of time (they are time consuming), efficiency and sensitivity. The low level of B. cereus spores in milk implies that highly sensitive detection methods should be applied for dairy products screening for spore contamination. This review describes the advantages and disadvantages of classical microbiological methods used to detect B. cereus spores in milk and milk products, related to novel methods based on molecular biology, biosensors and nanotechnology.

scholarly journals ANTIFUNGAL ACTIVITY OF TRICHODERMA VIRIDAE, CALOTROPIS GIGANTEA EXTRACT AGAINST FUNGAL PATHOGENS OF JUTE PLANT.

2020 ◽  
pp. 343-348
Author(s):  
Kabiraj Khadka ◽  
Jenish Shakya ◽  
Bidhya Dhungana ◽  
Hemanta Khana ◽  
Bijay Kumar Shrestha
Keyword(s):  
Antifungal Activity ◽  
Fusarium Solani ◽  
Fungal Pathogens ◽  
Methanolic Extract ◽  
Phytopathogenic Fungi ◽  
Biological Control Agents ◽  
Calotropis Gigantea ◽  
Fusarium Rot ◽  
Fungal Phytopathogens ◽  
And Control

Jute is infected by more than 12 types of phytopathogenic fungi. Charcoal rot, anthracnose and Fusarium rot are major jute diseases of eastern Nepal. Hence, the objective of this study was to control three fungal pathogens viz; Macrophominia phaseolinia, Fusarium solani and Colletotrichum species using Trichoderma viridae and Calotropis gigantea extract. All fungal pathogens were isolated from jute field. Occurrence of each disease was checked. Calotropis gigantea extract as well as Trichoderma showed good antifungal activity. In this study, 7% methanolic extract solution of Calotropis showed 43.6% inhibition of Colletotrichum, 38.91% inhibition on Fusarium solani and 37.81% inhibition on Macrophominia phaseolinia. Similarly, Trichoderma viridae inhibited the Fusarium solani growth by 51.33%, Macrophominia phaseolinia growth by 39.50% and Colletotrichum growth by 36.12%. The antifungal activity of Calotropis extract against test and control was statistically significant (p<0.001). It is concluded that biological control agents like Trichoderma viridae, Calotropis gigantea can effectively reduce the fungal phytopathogens of jute and can be used as good alternatives to fungicides in farming

Peculiarities of improving interbudgetary relations in conditions of authorities’ decentralization

2020 ◽  
pp. 46-54
Author(s):  
Zenoviy Siryk
Keyword(s):  
Economic Development ◽  
Social Development ◽  
Social Services ◽  
The State ◽  
Major Objective ◽  
Formal Approach ◽  
Advantages And Disadvantages ◽  
Local Areas ◽  
And Control ◽  
Different Levels

Ukraine is a unitary state, yet historically various regions, oblasts, districts, and local areas have different levels of economic development. To secure sustainable economic and social development and provide social services guaranteed by the state for each citizen according to the Constitution, the mechanism of redistribution between revenues and expenditures of oblasts, regions, and territories through the budgets of a higher level is used. The paper aims to research the peculiarities of improving interbudgetary relations in conditions of authorities’ decentralization. The paper defines the nature of interbudgetary relations. The basic and reverse subsidies to Ukraine and Lvivska oblast are analyzed. The advantages and disadvantages the communities face at changing approaches to balancing local budgets are determined. Regulative documents that cover the interbudgetary relations in Ukraine are analyzed. Special attention is paid to the problem of local finances reforming, including the development of interbudgetary relations. The scheme of the economic interbudgetary relations system in Ukraine is developed. The ways to improve the system of interbudgetary relations in Ukraine are suggested. The negative and positive aspects, advantages, and disadvantages of the system of interbudgetary relations in Ukraine require the following improvements. 1. It is necessary to avoid the complete budget alignment in the process of budgets balancing by interbudgetary transfers as the major objective. 2. The interbudgetary transfers should be distributed based on a formal approach. 3. The changes have to be introduced to the calculation of medical and educational subsidies in terms of financial standard of budget provision to avoid the money deficit for coverage of necessary expenditures. 4. There is a need to improve interbudgetary relations at the levels of districts, villages, towns, and cities of district subordination. 5. Improvement of the mechanism of targeted benefits provision, their real evaluation, and control for the use of funds.

scholarly journals The Potential of Rhizoctonia-Like Fungi for the Biological Protection of Cereals against Fungal Pathogens

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 349
Author(s):  
Dominik Bleša ◽  
Pavel Matušinský ◽  
Romana Sedmíková ◽  
Milan Baláž
Keyword(s):  
Biological Control ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Higher Plants ◽  
Fusarium Culmorum ◽  
Suppressive Effect ◽  
Plant Production ◽  
Shoot Biomass ◽  
Organic Substrates

The use of biological control is becoming a common practice in plant production. One overlooked group of organisms potentially suitable for biological control are Rhizoctonia-like (Rh-like) fungi. Some of them are capable of forming endophytic associations with a large group of higher plants as well as mycorrhizal symbioses. Various benefits of endophytic associations were proved, including amelioration of devastating effects of pathogens such as Fusarium culmorum. The advantage of Rh-like endophytes over strictly biotrophic mycorrhizal organisms is the possibility of their cultivation on organic substrates, which makes their use more suitable for production. We focused on abilities of five Rh-like fungi isolated from orchid mycorrhizas, endophytic fungi Serendipita indica, Microdochium bolleyi and pathogenic Ceratobasidium cereale to inhibit the growth of pathogenic F. culmorum or Pyrenophora teres in vitro. We also analysed their suppressive effect on wheat infection by F. culmorum in a growth chamber, as well as an effect on barley under field conditions. Some of the Rh-like fungi affected the growth of plant pathogens in vitro, then the interaction with plants was tested. Beneficial effect was especially noted in the pot experiments, where wheat plants were negatively influenced by F. culmorum. Inoculation with S. indica caused higher dry shoot biomass in comparison to plants treated with fungicide. Prospective for future work are the effects of these endophytes on plant signalling pathways, factors affecting the level of colonization and surviving of infectious particles.

scholarly journals The Ustilago hordei–Barley Interaction is a Versatile System for Characterization of Fungal Effectors

2021 ◽  
Vol 7 (2) ◽  
pp. 86
Author(s):  
Bilal Ökmen ◽  
Daniela Schwammbach ◽  
Guus Bakkeren ◽  
Ulla Neumann ◽  
Gunther Doehlemann
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Expression System ◽  
Pathogenic Fungi ◽  
Effector Proteins ◽  
Mating Partner ◽  
Fungal Virulence ◽  
Functional Studies ◽  
Infection Structures ◽  
Ustilago Hordei

Obligate biotrophic fungal pathogens, such as Blumeria graminis and Puccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence or pathogenicity. In this study, we present the Ustilago hordei–barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We generate U. hordei solopathogenic strains, which form infectious filaments without the presence of a compatible mating partner. Solopathogenic strains are suitable for heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available for U. hordei. In addition, U. hordei infection structures during barley colonization are analyzed using transmission electron microscopy, showing that U. hordei forms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus, U. hordei has high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.

scholarly journals Isolation and Characterization of Root-Associated Bacterial Endophytes and Their Biocontrol Potential against Major Fungal Phytopathogens of Rice (Oryza sativa L.)

Pathogens ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 172
Author(s):  
Maqsood Ahmed Khaskheli ◽  
Lijuan Wu ◽  
Guoqing Chen ◽  
Long Chen ◽  
Sajid Hussain ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Fungal Pathogens ◽  
Oryza Sativa L ◽  
Defense Responses ◽  
Growth And Yield ◽  
Bacterial Endophytes ◽  
16S Rrna Sequence ◽  
Resistance Response ◽  
Isolation And Characterization ◽  
Fungal Phytopathogens

Rice (Oryza sativa L.) is a major cereal food crop worldwide, and its growth and yield are affected by several fungal phytopathogens, including Magnaporthe oryzae, Fusarium graminearum, F. moniliforme, and Rhizoctonia solani. In the present study, we have isolated and characterized root-associated bacterial endophytes that have antifungal activities against rice fungal phytopathogens. A total of 122 root-associated bacterial endophytes, belonging to six genera (Bacillus, Fictibacillus, Lysinibacillus, Paenibacillus, Cupriavidus, and Microbacterium) and 22 species were isolated from three rice cultivars. Furthermore, the 16S rRNA sequence-based phylogeny results revealed that Bacillus was the most dominant bacterial genera, and that there were 15 different species among the isolates. Moreover, 71 root-associated endophytes showed antagonistic effects against four major fungal phytopathogens, including M. oryzae, F. graminearum, F. moniliforme, and R. solani. Additionally, the biochemical, physiological, and PCR amplification results of the antibiotic-related genes further supported the endophytes as potential biocontrolling agents against the rice fungal pathogens. Consequently, the findings in this study suggested that the isolated bacterial endophytes might have beneficial roles in rice defense responses, including several bioactive compound syntheses. The outcomes of this study advocate the use of natural endophytes as an alternative strategy towards the rice resistance response.

scholarly journals Genetic and Pathogenic Characterization of QX(GI-19)-Recombinant Infectious Bronchitis Viruses in South Korea

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1163
Author(s):  
So-Youn Youn ◽  
Ji-Youn Lee ◽  
You-Chan Bae ◽  
Yong-Kuk Kwon ◽  
Hye-Ryoung Kim
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Prevention ◽  
South Korea ◽  
Prevention And Control ◽  
Genetic Recombination ◽  
Detection Methods ◽  
Infectious Bronchitis ◽  
Reference Sequences ◽  
And Control

Infectious bronchitis viruses (IBVs) are evolving continuously via genetic drift and genetic recombination, making disease prevention and control difficult. In this study, we undertook genetic and pathogenic characterization of recombinant IBVs isolated from chickens in South Korea between 2003 and 2019. Phylogenetic analysis showed that 46 IBV isolates belonged to GI-19, which includes nephropathogenic IBVs. Ten isolates formed a new cluster, the genomic sequences of which were different from those of reference sequences. Recombination events in the S1 gene were identified, with putative parental strains identified as QX-like, KM91-like, and GI-15. Recombination detection methods identified three patterns (rGI-19-I, rGI-19-II, and rGI-19-III). To better understand the pathogenicity of recombinant IBVs, we compared the pathogenicity of GI-19 with that of the rGI-19s. The results suggest that rGI-19s may be more likely to cause trachea infections than GI-19, whereas rGI-19s were less pathogenic in the kidney. Additionally, the pathogenicity of rGI-19s varied according to the genotype of the major parent. These results indicate that genetic recombination between heterologous strains belonging to different genotypes has occurred, resulting in the emergence of new recombinant IBVs in South Korea.

Plant MicroRNAs Responsive to Fungal Infection

2014 ◽  
Vol 941-944 ◽  
pp. 1141-1145 ◽  
Author(s):  
Hui Li Zhang ◽  
Lin Chen ◽  
Wen Na Li ◽  
Li Li Wang ◽  
Hong Yu Xie
Keyword(s):  
Fungal Pathogens ◽  
High Throughput Sequencing ◽  
Adaptive Immune System ◽  
Messenger Rnas ◽  
Disease Mechanism ◽  
Adaptive Immune ◽  
Alternative Approach ◽  
Crop Disease ◽  
Transcriptional Gene Regulation ◽  
And Control

MicroRNAs (miRNAs) are endogenous small RNAs transcribed from non-coding DNA, which have the capacity to base pair with the target mRNAs (messenger RNAs) to repress their translation or resulted in cleavage. We have paid much attention on the DNA and its coded proteins, the discovery of miRNAs as gene negatively regulators has led to a fundamental change in understanding of post-transcriptional gene regulation in plants. Fungal pathogens infection is the main cause of most economic crops diseases. Unlike humans, plants don’t evolved to have a adaptive immune system, they protect themselves with a mechanism consists of activation and response. Recently, high throughput sequencing validated that miRNA play a crucial role in plant-fungus interaction. A better understanding of miRNA-mediated disease mechanism in fungi should clarify the strategy of crop disease control. MiRNA-based manipulations as gene suppressors, such as artificial miRNAs, may emerge as a new alternative approach for the improvement of crops and control of crop disease.

Potential New Herbicides – Phytotoxins from Plant Pathogens

1988 ◽  
Vol 2 (4) ◽  
pp. 519-524 ◽  
Author(s):  
Doug Kenfield ◽  
Greg Bunkers ◽  
Gary A. Strobel ◽  
Fumio Sugawara
Keyword(s):  
Organic Synthesis ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Biological Activities ◽  
Biological Data

A rationale for the study of phytotoxins from fungal pathogens of plants is presented. Structural chemistries and biological data are given for numerous, recently discovered phytotoxins in such diverse chemical classes as polyketides, terpenoids, diketopiperazines, and isocoumarins. The biological activities of these compounds range from broadly toxic (curvulin) to host specific (maculosin-1). Phytotoxicology offers a viable supplement to organic synthesis as a means of developing and implementing new, biorational, and economical herbicides.

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