Insights about isothermal Polymerase Chain Reaction (PCR) assays and how they can be used to diagnose the presence of latent diseases in the field, including those which are especially difficult to identify. They will show how assays are developed, and how they may be used to improve disease management choices.
The target audience are researchers, agri-business and forestry experts, farmers and foresters and any other interested in plant health.
Do not hesitate to contact EMPHASIS project through Facebook, Twitter, email (emphasisproject@gmail.com) or through their website (http://www.emphasisproject.eu/) if you want to be updated on webinars dates and content and book a ticket.
To watch on Youtube: https://youtu.be/yFEG9uTEhdc
Current methods for plant disease diagnosisSHIVANI PATHAK
Shivani presents an overview of current and prospective methods for plant disease detection. Several techniques are discussed including serological based methods like ELISA and lateral flow devices, nucleic acid based methods like PCR and real-time PCR, optical sensor based methods like fluorescence imaging and hyperspectral imaging, and digital imaging based methods. Examples of each technique being used to detect various plant viruses, bacteria, fungi, and nematodes are provided. The techniques allow for rapid, sensitive, and accurate detection of pathogens before symptom development.
This document discusses advance portable tools for on-site detection of plant pathogens. It covers various disease detection tools including visual observation, cultural techniques, and the Foldscope microscope. It also discusses indirect detection methods like thermography, fluorescence imaging, hyperspectral techniques, and gas chromatography. Biosensor approaches for plant pathogen detection are also presented, including antibody-based biosensors, optical immunosensors, fluorescent approaches using quantum dots, and surface plasmon resonance systems. Loop mediated isothermal amplification is also discussed as a rapid detection method. The document emphasizes the importance of early detection in plant disease management and hopes that more portable detection devices will be developed to support efficient on-site diagnosis.
Detection of plant pathogens using non pcr based techniquesPuja41124
This document discusses various molecular techniques for detecting and identifying plant pathogens, beginning with conventional techniques like visual observation, culture-based methods, and microscopy. It then covers several antibody-based techniques like serological methods, ELISA, immunofluorescence, and immunoelectron microscopy. Hybridization methods like Southern blotting, Northern blotting, and DNA microarrays are also introduced. Biochemical approaches involving fatty acid analysis, Biolog identification systems, and volatile compound analysis are briefly covered. The document concludes by discussing the surface plasmon resonance technique for pathogen detection. In summary, it provides an overview of conventional, antibody-based, hybridization-based, and biochemical molecular techniques for plant pathogen detection and identification.
Different techniques for detection of plant pathogens.Zohaib Hassan
Plant pathology is the study of plant diseases. Major plant pathogens include fungi, bacteria, nematodes, and viruses. Techniques used to detect pathogens include histopathological examination of infected tissues, culture growth on media, staining, microscopy, and analysis of biochemical properties. Symptoms caused by pathogens can provide clues to identification. Isolation and purification of the pathogen allows for reinoculation to fulfill Koch's postulates.
This document discusses methods for identifying plant pathogens. Traditional visual examination can only identify damage after it has already occurred. More sensitive early diagnosis methods are needed to treat pathogens before irreparable damage. Modern methods like polymerase chain reaction (PCR) and serological techniques can identify pathogens before visible symptoms appear, allowing treatment before significant yield losses. These methods help identify the causal agent through DNA analysis and other laboratory techniques.
Seed certification and type of losses caused by seed borne diseases in true a...Summer
Seed certification is a regulatory process to ensure the availability of high quality seed varieties. It encourages the production of improved and hybrid seeds through certifying departments that inspect seed production based on variety requirements. Seed certification procedures verify genetic and physical purity, as well as freedom from diseases and weeds. Certification is conducted by state or national agencies and involves application review, field inspections, processing oversight, testing, and certification granting. Seedborne diseases can impact seed quality by causing rots, decay, discolouration and reduced germination, affecting market and nutritional value.
This Presentation includes various tactics of IDM like Cultural control, Physical control, Chemical control, Biological control of plant disease. Useful for UG, PG Botany and Agriculture students
Current methods for plant disease diagnosisSHIVANI PATHAK
Shivani presents an overview of current and prospective methods for plant disease detection. Several techniques are discussed including serological based methods like ELISA and lateral flow devices, nucleic acid based methods like PCR and real-time PCR, optical sensor based methods like fluorescence imaging and hyperspectral imaging, and digital imaging based methods. Examples of each technique being used to detect various plant viruses, bacteria, fungi, and nematodes are provided. The techniques allow for rapid, sensitive, and accurate detection of pathogens before symptom development.
This document discusses advance portable tools for on-site detection of plant pathogens. It covers various disease detection tools including visual observation, cultural techniques, and the Foldscope microscope. It also discusses indirect detection methods like thermography, fluorescence imaging, hyperspectral techniques, and gas chromatography. Biosensor approaches for plant pathogen detection are also presented, including antibody-based biosensors, optical immunosensors, fluorescent approaches using quantum dots, and surface plasmon resonance systems. Loop mediated isothermal amplification is also discussed as a rapid detection method. The document emphasizes the importance of early detection in plant disease management and hopes that more portable detection devices will be developed to support efficient on-site diagnosis.
Detection of plant pathogens using non pcr based techniquesPuja41124
This document discusses various molecular techniques for detecting and identifying plant pathogens, beginning with conventional techniques like visual observation, culture-based methods, and microscopy. It then covers several antibody-based techniques like serological methods, ELISA, immunofluorescence, and immunoelectron microscopy. Hybridization methods like Southern blotting, Northern blotting, and DNA microarrays are also introduced. Biochemical approaches involving fatty acid analysis, Biolog identification systems, and volatile compound analysis are briefly covered. The document concludes by discussing the surface plasmon resonance technique for pathogen detection. In summary, it provides an overview of conventional, antibody-based, hybridization-based, and biochemical molecular techniques for plant pathogen detection and identification.
Different techniques for detection of plant pathogens.Zohaib Hassan
Plant pathology is the study of plant diseases. Major plant pathogens include fungi, bacteria, nematodes, and viruses. Techniques used to detect pathogens include histopathological examination of infected tissues, culture growth on media, staining, microscopy, and analysis of biochemical properties. Symptoms caused by pathogens can provide clues to identification. Isolation and purification of the pathogen allows for reinoculation to fulfill Koch's postulates.
This document discusses methods for identifying plant pathogens. Traditional visual examination can only identify damage after it has already occurred. More sensitive early diagnosis methods are needed to treat pathogens before irreparable damage. Modern methods like polymerase chain reaction (PCR) and serological techniques can identify pathogens before visible symptoms appear, allowing treatment before significant yield losses. These methods help identify the causal agent through DNA analysis and other laboratory techniques.
Seed certification and type of losses caused by seed borne diseases in true a...Summer
Seed certification is a regulatory process to ensure the availability of high quality seed varieties. It encourages the production of improved and hybrid seeds through certifying departments that inspect seed production based on variety requirements. Seed certification procedures verify genetic and physical purity, as well as freedom from diseases and weeds. Certification is conducted by state or national agencies and involves application review, field inspections, processing oversight, testing, and certification granting. Seedborne diseases can impact seed quality by causing rots, decay, discolouration and reduced germination, affecting market and nutritional value.
This Presentation includes various tactics of IDM like Cultural control, Physical control, Chemical control, Biological control of plant disease. Useful for UG, PG Botany and Agriculture students
This document summarizes conventional and biotechnological approaches for managing viral plant diseases. Conventional approaches include using virus-free planting materials, cultural practices, vector management, heat therapy, meristem tip culture, and barrier crops. Biotechnological approaches involve pathogen-derived resistance through expression of viral coat proteins or RNA interference mechanisms to inhibit viral genes. The document provides examples and details of various conventional and biotechnological techniques for eliminating viruses from infected plants.
The concept of gene for gene hypothesis was first developed by Flor in 1956 based on his studies of host pathogen interaction in flax, for rust caused by Melampsora lini. The gene for gene hypothesis states that for each gene controlling resistance in the host, there is corresponding gene controlling pathogenicity in the pathogen. The resistance of host is governed by dominant genes and virulence of pathogen by recessive genes. The genotype of host and pathogen determine the disease reaction. When genes in host and pathogen match for all loci, then only the host will show susceptible reaction. If some gene loci remain unmatched, the host will show resistant reaction. Now gene – for –gene relationship has been reported in several other crops like potato, sorghum, wheat, etc. The gene for gene hypothesis is also known as “Flor Hypothesis.”
This document discusses different types of plant resistance to pathogens. It describes true resistance, which includes partial/quantitative/polygenic resistance controlled by multiple genes (horizontal resistance) and R-gene/monogenic resistance controlled by single genes (vertical resistance). It also discusses the genetics of virulence in pathogens and resistance in host plants using the gene-for-gene concept. Specifically, it explains how avirulence genes in pathogens interact with resistance genes in plants to determine compatibility.
The document discusses the development of Phytophthora and Pythium databases to support the identification and monitoring of these major plant pathogen groups. It describes the objectives of building a cyberinfrastructure to archive genotype, phenotype and distribution data on Phytophthora species/isolates. The Phytophthora Database provides tools for sequence analysis, phylogenetic analysis and molecular identification. Future directions include expanding to other plant pathogen databases and integrating genomic and geospatial data.
The document discusses plant disease resistance genes (R-genes) and their importance in crop breeding for disease resistance. It contains the following key points:
1. R-genes encode receptors that recognize pathogen effector proteins and trigger plant immune responses. Most R-genes contain nucleotide binding and leucine-rich repeat domains.
2. Dozens of R-genes have been cloned from various plants using map-based cloning, transposon tagging, or a new method called MutRenSeq that enriches for R-gene sequences.
3. Introducing R-genes from wild crop relatives into domestic crops can provide natural and sustainable resistance to diseases while avoiding pesticide use and potential environmental damage.
This document discusses plant disease outbreaks and epidemics. It defines an outbreak as a sudden increase in disease occurrences in a particular place and time, while an epidemic is a change in disease over time and space that can affect regions or countries. Epidemics develop from a combination of susceptible hosts, virulent pathogens, and favorable environmental conditions over a long period. Factors like host genetics, crop type, and moisture levels can influence epidemic development. The document also outlines management strategies like computer modeling, forecasting, and warning systems to help control epidemics.
This document discusses genes in plants that provide disease resistance. It begins by outlining the plant immune system and the zig-zag model involving PAMP-triggered immunity and effector-triggered immunity. It then describes different classes of plant resistance genes based on their structural features and domains. The document also discusses the functions of resistance genes in signaling plant defenses, and provides examples of resistance genes that have been cloned and provide resistance against various pathogens like fungi, viruses, nematodes, and more.
Plant defense strategies which act against the plant pathogen attack are explained in short. The major plant defense strategies are 1) Oxidative burst 2) Phenolics 3) Hypersensitive response (HR) 4) Phytoalexins.
This document discusses techniques for serologically detecting plant viruses. It begins by defining serology and its use in agriculture for detecting pathogens with variable or latent symptoms. It then describes the basics of antigen-antibody reactions and the types of antigens, antibodies, and reactions. The rest of the document focuses on specific serological tests used in plant virology, including liquid phase tests like precipitation, agglutination, and immunodiffusion assays as well as solid phase tests like ELISA, SDS-PAGE, ISEM, western blotting, and dot/tissue immunobinding assays. These tests allow detection of plant viruses through the reaction of viral coat proteins or antigens with specific antibodies.
1. Dolichos lablab is a multipurpose crop native to India or Southeast Asia. It is cultivated for its young pods, dry seeds, as fodder, green manure, cover crop, and ornamental uses.
2. The flowers are hermaphroditic and self-pollinating, with 6-10% natural cross-pollination occurring depending on environmental conditions. The flowers open in the morning from 6-11 AM and remain open from 11 AM to 5 PM.
3. For artificial crossing, emasculation is done by removing the male parts from young flower buds followed by artificial pollination of the emasculated flower and bagging to
INTRODUCTION
Trichoderma -A Bio-Control Agent
General characteristics, PREPARATION OF MOTHER CULTURE, Materials required, Method of application, Precautions.
SEROLOGICAL METHODS FOR DETECTION OF PLANT PATHOGENSHARISH J
This document discusses serological methods for detecting plant pathogens. It explains that serodiagnosis involves inducing an immune response in an animal to produce antibodies against a pathogen's antigens. These antibodies can then be used to detect the presence of the pathogen. The document describes several serological testing methods including ring interface tests, microprecipitin tests, double diffusion tests, ELISA, immunosorbent electron microscopy, and immunofluorescent staining. It concludes that serodiagnosis is a sensitive tool for identifying pathogens, detecting infections, and quantifying crop diseases.
This document discusses biological control of plant diseases. Biological control involves using living organisms to control pests. It has received more attention recently. Some advantages are that it is specific to pests and cheaper after initial costs. Disadvantages include narrow effectiveness and high start-up expenses. Biological control agents include parasitoids, pathogens, and predators. Parasitoids lay eggs on or in a host insect and kill it. Pathogens infect insects and kill them or affect future generations. Predators are larger than prey and eat several. The document also discusses antagonists that compete with or produce toxins against plant pathogens. Common release methods are inoculative, where small numbers are released to spread, and augmentation, where organisms are mass
Mechanism of disease control by endophytesPooja Bhatt
The document discusses alternative methods for pest management to address problems with chemical pesticides such as development of resistance and environmental contamination. It suggests that biological control using endophytic microorganisms is a promising alternative as endophytes have antagonistic properties against plant pathogens. Endophytes can inhibit pathogens through direct mechanisms such as hyperparasitism, competition, antibiosis, and lytic enzyme production or indirect induction of host plant resistance. Case studies provide examples of endophytes inhibiting fungal plant pathogens through siderophore production, parasitic growth, and antibiotic compounds.
This document discusses the use of biocontrol agents, specifically Trichoderma species, for managing plant pathogens and diseases. Some key points:
- Pathogens threaten global crop production and excessive fungicide use pollutes the environment and leads to resistance, so alternative biological control methods are needed.
- Trichoderma is an effective biocontrol agent that controls pathogens through mycoparasitism, antibiosis, competition, and other mechanisms without environmental pollution.
- Mass production of Trichoderma uses liquid fermentation or solid substrates like wheat bran to grow the fungus, which is then mixed with carriers like talc or vermiculite before application to seeds, soil, or plants.
This document discusses disease forecasting models that use weather data to predict outbreaks. It provides examples of models for rice blast, potato late blight, wheat yellow rust, and more. The potato late blight model for India, JHULSACAST, is specifically discussed. Disease forecasting is useful for giving advance warning to apply protective chemicals before infection starts and help control economically important crop diseases. Both empirical and fundamental forecasting systems are covered, along with their components and requirements for developing useful forecasting.
Avs molecular diagnostic techniques for detection of plant pathogensAMOL SHITOLE
PCR is a technique used to detect plant pathogens through amplification of DNA. It involves denaturing DNA, annealing primers, and polymerizing new strands of DNA. This process is repeated to exponentially increase the amount of target DNA. Nested PCR improves sensitivity by adding a second round of amplification. Other techniques like RT-PCR, IC-PCR, bio-PCR, and co-operational PCR have also been used to detect pathogens through nucleic acid amplification and analysis. PCR provides an efficient way to diagnose and study plant pathogens.
Bio303 laboratory diagnosis of infectionMark Pallen
In this Bio303 module talk, I provide an overview of how infections are diagnosed in the clinical microbiology lab, focusing on technologies, old and new, and also on practical issues and workflows crucial to optimal use of the lab.
The document discusses general principles for diagnosing infectious diseases, including:
1. Physical examination, clinical diagnosis, and epidemiological assessment help identify possible pathogens.
2. Laboratory tests are needed to confirm the causative agent, including microscopic examination, culture-based methods, and immunological or molecular detection techniques.
3. Proper specimen collection, transport, and timing are important for accurate diagnostic results.
This document summarizes conventional and biotechnological approaches for managing viral plant diseases. Conventional approaches include using virus-free planting materials, cultural practices, vector management, heat therapy, meristem tip culture, and barrier crops. Biotechnological approaches involve pathogen-derived resistance through expression of viral coat proteins or RNA interference mechanisms to inhibit viral genes. The document provides examples and details of various conventional and biotechnological techniques for eliminating viruses from infected plants.
The concept of gene for gene hypothesis was first developed by Flor in 1956 based on his studies of host pathogen interaction in flax, for rust caused by Melampsora lini. The gene for gene hypothesis states that for each gene controlling resistance in the host, there is corresponding gene controlling pathogenicity in the pathogen. The resistance of host is governed by dominant genes and virulence of pathogen by recessive genes. The genotype of host and pathogen determine the disease reaction. When genes in host and pathogen match for all loci, then only the host will show susceptible reaction. If some gene loci remain unmatched, the host will show resistant reaction. Now gene – for –gene relationship has been reported in several other crops like potato, sorghum, wheat, etc. The gene for gene hypothesis is also known as “Flor Hypothesis.”
This document discusses different types of plant resistance to pathogens. It describes true resistance, which includes partial/quantitative/polygenic resistance controlled by multiple genes (horizontal resistance) and R-gene/monogenic resistance controlled by single genes (vertical resistance). It also discusses the genetics of virulence in pathogens and resistance in host plants using the gene-for-gene concept. Specifically, it explains how avirulence genes in pathogens interact with resistance genes in plants to determine compatibility.
The document discusses the development of Phytophthora and Pythium databases to support the identification and monitoring of these major plant pathogen groups. It describes the objectives of building a cyberinfrastructure to archive genotype, phenotype and distribution data on Phytophthora species/isolates. The Phytophthora Database provides tools for sequence analysis, phylogenetic analysis and molecular identification. Future directions include expanding to other plant pathogen databases and integrating genomic and geospatial data.
The document discusses plant disease resistance genes (R-genes) and their importance in crop breeding for disease resistance. It contains the following key points:
1. R-genes encode receptors that recognize pathogen effector proteins and trigger plant immune responses. Most R-genes contain nucleotide binding and leucine-rich repeat domains.
2. Dozens of R-genes have been cloned from various plants using map-based cloning, transposon tagging, or a new method called MutRenSeq that enriches for R-gene sequences.
3. Introducing R-genes from wild crop relatives into domestic crops can provide natural and sustainable resistance to diseases while avoiding pesticide use and potential environmental damage.
This document discusses plant disease outbreaks and epidemics. It defines an outbreak as a sudden increase in disease occurrences in a particular place and time, while an epidemic is a change in disease over time and space that can affect regions or countries. Epidemics develop from a combination of susceptible hosts, virulent pathogens, and favorable environmental conditions over a long period. Factors like host genetics, crop type, and moisture levels can influence epidemic development. The document also outlines management strategies like computer modeling, forecasting, and warning systems to help control epidemics.
This document discusses genes in plants that provide disease resistance. It begins by outlining the plant immune system and the zig-zag model involving PAMP-triggered immunity and effector-triggered immunity. It then describes different classes of plant resistance genes based on their structural features and domains. The document also discusses the functions of resistance genes in signaling plant defenses, and provides examples of resistance genes that have been cloned and provide resistance against various pathogens like fungi, viruses, nematodes, and more.
Plant defense strategies which act against the plant pathogen attack are explained in short. The major plant defense strategies are 1) Oxidative burst 2) Phenolics 3) Hypersensitive response (HR) 4) Phytoalexins.
This document discusses techniques for serologically detecting plant viruses. It begins by defining serology and its use in agriculture for detecting pathogens with variable or latent symptoms. It then describes the basics of antigen-antibody reactions and the types of antigens, antibodies, and reactions. The rest of the document focuses on specific serological tests used in plant virology, including liquid phase tests like precipitation, agglutination, and immunodiffusion assays as well as solid phase tests like ELISA, SDS-PAGE, ISEM, western blotting, and dot/tissue immunobinding assays. These tests allow detection of plant viruses through the reaction of viral coat proteins or antigens with specific antibodies.
1. Dolichos lablab is a multipurpose crop native to India or Southeast Asia. It is cultivated for its young pods, dry seeds, as fodder, green manure, cover crop, and ornamental uses.
2. The flowers are hermaphroditic and self-pollinating, with 6-10% natural cross-pollination occurring depending on environmental conditions. The flowers open in the morning from 6-11 AM and remain open from 11 AM to 5 PM.
3. For artificial crossing, emasculation is done by removing the male parts from young flower buds followed by artificial pollination of the emasculated flower and bagging to
INTRODUCTION
Trichoderma -A Bio-Control Agent
General characteristics, PREPARATION OF MOTHER CULTURE, Materials required, Method of application, Precautions.
SEROLOGICAL METHODS FOR DETECTION OF PLANT PATHOGENSHARISH J
This document discusses serological methods for detecting plant pathogens. It explains that serodiagnosis involves inducing an immune response in an animal to produce antibodies against a pathogen's antigens. These antibodies can then be used to detect the presence of the pathogen. The document describes several serological testing methods including ring interface tests, microprecipitin tests, double diffusion tests, ELISA, immunosorbent electron microscopy, and immunofluorescent staining. It concludes that serodiagnosis is a sensitive tool for identifying pathogens, detecting infections, and quantifying crop diseases.
This document discusses biological control of plant diseases. Biological control involves using living organisms to control pests. It has received more attention recently. Some advantages are that it is specific to pests and cheaper after initial costs. Disadvantages include narrow effectiveness and high start-up expenses. Biological control agents include parasitoids, pathogens, and predators. Parasitoids lay eggs on or in a host insect and kill it. Pathogens infect insects and kill them or affect future generations. Predators are larger than prey and eat several. The document also discusses antagonists that compete with or produce toxins against plant pathogens. Common release methods are inoculative, where small numbers are released to spread, and augmentation, where organisms are mass
Mechanism of disease control by endophytesPooja Bhatt
The document discusses alternative methods for pest management to address problems with chemical pesticides such as development of resistance and environmental contamination. It suggests that biological control using endophytic microorganisms is a promising alternative as endophytes have antagonistic properties against plant pathogens. Endophytes can inhibit pathogens through direct mechanisms such as hyperparasitism, competition, antibiosis, and lytic enzyme production or indirect induction of host plant resistance. Case studies provide examples of endophytes inhibiting fungal plant pathogens through siderophore production, parasitic growth, and antibiotic compounds.
This document discusses the use of biocontrol agents, specifically Trichoderma species, for managing plant pathogens and diseases. Some key points:
- Pathogens threaten global crop production and excessive fungicide use pollutes the environment and leads to resistance, so alternative biological control methods are needed.
- Trichoderma is an effective biocontrol agent that controls pathogens through mycoparasitism, antibiosis, competition, and other mechanisms without environmental pollution.
- Mass production of Trichoderma uses liquid fermentation or solid substrates like wheat bran to grow the fungus, which is then mixed with carriers like talc or vermiculite before application to seeds, soil, or plants.
This document discusses disease forecasting models that use weather data to predict outbreaks. It provides examples of models for rice blast, potato late blight, wheat yellow rust, and more. The potato late blight model for India, JHULSACAST, is specifically discussed. Disease forecasting is useful for giving advance warning to apply protective chemicals before infection starts and help control economically important crop diseases. Both empirical and fundamental forecasting systems are covered, along with their components and requirements for developing useful forecasting.
Avs molecular diagnostic techniques for detection of plant pathogensAMOL SHITOLE
PCR is a technique used to detect plant pathogens through amplification of DNA. It involves denaturing DNA, annealing primers, and polymerizing new strands of DNA. This process is repeated to exponentially increase the amount of target DNA. Nested PCR improves sensitivity by adding a second round of amplification. Other techniques like RT-PCR, IC-PCR, bio-PCR, and co-operational PCR have also been used to detect pathogens through nucleic acid amplification and analysis. PCR provides an efficient way to diagnose and study plant pathogens.
Bio303 laboratory diagnosis of infectionMark Pallen
In this Bio303 module talk, I provide an overview of how infections are diagnosed in the clinical microbiology lab, focusing on technologies, old and new, and also on practical issues and workflows crucial to optimal use of the lab.
The document discusses general principles for diagnosing infectious diseases, including:
1. Physical examination, clinical diagnosis, and epidemiological assessment help identify possible pathogens.
2. Laboratory tests are needed to confirm the causative agent, including microscopic examination, culture-based methods, and immunological or molecular detection techniques.
3. Proper specimen collection, transport, and timing are important for accurate diagnostic results.
This document discusses the process of diagnosing bacterial plant diseases. It outlines the key steps: assessing symptoms, isolating pathogenic bacteria, obtaining a pure culture, identifying the pure culture, conducting a pathogenicity test, re-isolating from inoculated plants, re-identifying the re-isolate, and producing a diagnosis report. These steps follow Koch's postulates to prove a bacterium causes a disease. The document then discusses each step in more detail, including how to isolate and identify bacteria using conventional methods, and explains the stages of pathogenesis and functions of bacterial virulence factors.
Bacterial Canker of Mango Diagnostic Methods.pptxAVKaaviya
Bacterial canker of mango, caused by the bacterium Xanthomonas citri subsp. mangiferae, poses a significant threat to mango cultivation worldwide. Diagnosing this disease accurately is a pivotal step in effectively managing its impact on orchards. A range of diagnostic methods is employed to identify the presence of the pathogen and confirm the disease's occurrence. These methods encompass both visual observations and sophisticated laboratory techniques, collectively providing a comprehensive understanding of the disease's prevalence and severity. Through these diagnostic measures, farmers and agricultural experts can make informed decisions to mitigate the disease's effects and safeguard mango production.
Chapter_ 3 Plant pathogenic Bacteria _identification and classification.pptDawitGetahun6
Identification and classification of plant pathogenic bacteria involves observation of symptoms, isolation of the pathogen, characterization through tests, and fulfilling Koch's postulates. A diagnosis requires field observation, examination of diseased tissues, isolation, characterization, and pathogenicity testing. Bacteria are identified using their visible characteristics, physiological properties, serological reactions, and ability to cause disease in plants. Classification is based on Gram staining, biochemical tests, host specificity, and comparison to known genera. The concept of bacterial species and pathovars helps classify plant pathogenic bacteria.
1. The document discusses breeding objectives in chili pepper such as higher yield, resistance to biotic and abiotic stresses, and improved quality.
2. Case studies on breeding for resistance to diseases like anthracnose and viruses are presented. Sources of resistance to bacterial spot, Phytophthora root rot, and other stresses were identified.
3. Breeding methods discussed include pure line selection, pedigree breeding, backcrossing, and marker-assisted breeding. Achievements include new varieties with resistance to multiple stresses.
The document discusses various methods for diagnosing important bacterial diseases through laboratory examination. Effective diagnosis allows for timely treatment and control measures. Key methods discussed include microscopy, culture techniques, biochemical reactions, serological identification, and molecular diagnosis. Microscopy can identify bacterial morphology and staining properties. Culture techniques isolate bacteria on selective media and examine colony characteristics. Biochemical tests identify metabolic properties. Serology detects bacterial antigens and antibodies. Molecular methods like PCR and sequencing provide sensitive, specific identification and can detect non-culturable bacteria. Together, these diagnostic methods allow clinicians to initiate appropriate treatment and control of bacterial outbreaks.
The document provides information on the diagnosis of important bacterial diseases. It discusses the importance of quick diagnostic results for effective treatment during disease outbreaks. It covers the types and activities of various antimicrobial classes against different bacteria and microorganisms. It also describes the scope of bacterial infections, types of bacteria, why diagnosis is needed, recommended diagnostics for various diseases, steps in diagnosis, prerequisites for laboratory examination including appropriate sample collection and transport, and various microbiological diagnostic techniques like microscopy, culture, and biochemical identification.
Optical sensors, especially RGB imaging sensors, show potential for plant disease detection. RGB sensors utilize visible light to detect color changes caused by biotic stresses like diseases. Digital images from RGB sensors can be analyzed using software to identify disease symptoms and quantify severity. Early detection of diseases using optical sensors allows targeted treatment and reduces economic and environmental impacts of agriculture.
Microbiological tests of periodontal significanceMehul Shinde
This document discusses diagnostic microbiology techniques for periodontal infections. It covers specimen collection, transport, and various laboratory analysis methods including bacterial culturing, microscopic analysis, and molecular biology techniques. Specifically, it provides details on collecting a subgingival plaque sample for periodontal infections, transporting it anaerobically with minimal time, and analyzing it using methods like culturing, Gram stain, and molecular analysis to identify putative periodontal pathogens.
disease diagnosis, types of diagnostic kits, nucleic acid based that include pcr, rt pcr, microarray, protein based which include ELISA, types of elisa, comparision among all types of diagnostic kits
1. Soil borne pathogens have significantly impacted human health over centuries by causing infections that contributed to population declines and societal changes.
2. These pathogens reside in soil communities and include bacteria, viruses, parasites, and protozoa that are important to public and animal health. Many are potential bioterrorism agents.
3. Real-time PCR is an effective technique for detecting soil borne pathogens due to its ability to quantify pathogens during each reaction cycle without needing gel electrophoresis. This allows for safer and earlier detection compared to culturing and conventional PCR.
1. The document discusses various laboratory diagnostic techniques for infectious diseases including microscopy, staining, culture-based, and molecular methods.
2. Key techniques covered include wet mount microscopy, Gram staining, acid-fast staining, immunofluorescence staining, and molecular methods like nucleic acid hybridization and PCR.
3. The document emphasizes the importance of proper specimen collection for maximizing recovery of pathogens and minimizing contamination. Adequate specimen quantity and avoidance of antimicrobial treatment prior to collection are important.
1) Microbial identification determines the broad or narrow group to which a microorganism belongs. It is important for characterizing microorganisms detected in pharmaceutical products and facilities.
2) The U.S. Pharmacopeia outlines requirements for microbial identification in various chapters related to nonsterile products, sterility testing, and environmental monitoring. Identification to the species or strain level can provide insights for assessing and mitigating risks.
3) Identification methods include phenotypic methods based on biochemical reactions and genotypic methods based on nucleic acid sequences. Phenotypic methods are commonly used while genotypic methods are more reliable but require more specialized equipment and are typically used for critical investigations. The "polyphasic taxonomy" approach uses multiple
Analytical techniques in plant pathology Iram Wains
Agricultural crops are threatened by a wide variety of plant diseases and pests that can damage crops and lower yields. Correct diagnosis of plant diseases is important so that treatments can be tailored to specific pathogens. There are indirect and direct methods used for diagnosis. Indirect methods include environmental reviews and microscopic examination, while direct methods use molecular techniques like antibody-based methods (e.g. ELISA, polyclonal antibodies) and nucleic acid-based methods (e.g. PCR, DNA microarrays) to identify causal agents. DNA microarrays allow screening for multiple pathogens simultaneously. Correct diagnosis is key to minimizing crop losses from diseases and pests.
This document discusses clinical microbiology and the processes used to diagnose and treat infections. It describes how microbiologists isolate, identify, and test bacteria to determine the most effective treatment and prevent the spread of infection. Key steps include collecting specimens, examining them under the microscope, growing bacterial cultures, conducting tests to identify bacteria and determine antibiotic susceptibility, and using these results to inform patient care and public health efforts.
This document provides an introduction and overview of artificial intelligence applications in plant disease detection. It discusses how machine learning and deep learning are being used to identify plant diseases through image recognition. Examples of algorithms commonly used include convolutional neural networks, recurrent neural networks, and support vector machines. The scope of AI in agriculture is also summarized, including how IoT sensor data, drone images, and automation can be used for tasks like crop monitoring, irrigation, and recommending optimal agricultural practices. Machine learning is also being applied to disease predictions and molecular-level interactions between plants and pathogens.
This document discusses microbiological control in biopharmaceutical manufacturing. It is important to prevent microbial contamination as most biopharmaceuticals are injectable and large protein molecules susceptible to degradation. Contamination can occur at any stage from cell culture to purification to filling. Strict controls are needed to maintain sterile conditions and prevent bacteria, fungi, viruses and other microbes such as mycoplasma from entering and compromising production. Regular monitoring and testing helps ensure the safety of biopharmaceutical products.
pathogens in periodontal microbiology. the red complex bacteria described in detail. recent updates regarding proteases and virulence factors of all pathogens.
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An analytical framework for consistent evaluation of pest and disease managem...EMPHASIS PROJECT
Presentation at the ICPP 2018.
• The Analytical Framework evaluates technologies against 27 indicators across 4 dimensions
• This allows to:
• Integrate a multi-actor approaching to technology development
• Identify the strengths and weaknesses of individual technologies
• Compare novel technologies with each other and conventional measures
• Identify market opportunities and support business plans
The strategic role of dissemination and communication in raising awareness on...EMPHASIS PROJECT
Role of dissemination and communication in raising awareness on IPM practical solutions
The dissemination and communication of scientific messages isn’t an easy task, as the figures generated in labs are difficult to translate into popular formats. We know that the first communication tool for researchers are scientific papers, but research projects have to facilitate the transfer of scientific results to enterprises, policy makers, farmers, associations, and to a wide public at large.
“Key messages for policy makers” presented at the "H2020 projects for evidence-based agricultural related policies" roundtable at the European Parliament on the 25th April 2018.
Do not hesitate to contact EMPHASIS project through:
Facebook https://www.facebook.com/emphasisproject/
Twitter https://twitter.com/EmphasisProject
Email emphasisproject@gmail.com
Website http://www.emphasisproject.eu
Slideshare https://www.slideshare.net/EMPHASISPROJECT/
“SURVEY ADDRESSED TO END-USERS” presented at the "H2020 projects for evidence-based agricultural related policies" roundtable at the European Parliament on the 25th April 2018.
Do not hesitate to contact EMPHASIS project through:
Facebook https://www.facebook.com/emphasisproject/
Twitter https://twitter.com/EmphasisProject
Email emphasisproject@gmail.com
Website http://www.emphasisproject.eu
Slideshare https://www.slideshare.net/EMPHASISPROJECT/
Novel solutions for the management of plant diseasesEMPHASIS PROJECT
“Novel solutions for the management of plant diseases” presented at the "H2020 projects for evidence-based agricultural related policies" roundtable at the European Parliament on the 25th April 2018.
Do not hesitate to contact EMPHASIS project through:
Facebook https://www.facebook.com/emphasisproject/
Twitter https://twitter.com/EmphasisProject
Email emphasisproject@gmail.com
Website http://www.emphasisproject.eu
Slideshare https://www.slideshare.net/EMPHASISPROJECT/
Introduction to EMPHASIS project: aims and objectives EMPHASIS PROJECT
This document summarizes information about the EMPHASIS project, which received over 6.5 million euros in funding from the European Union's Horizon 2020 research program. The project involves 10 countries and over 1000 person-months of effort from 11 enterprises and universities. The overall goal is to ensure European food security and protect biodiversity from pest threats by developing integrated solutions to predict, prevent, and protect against native and alien pests in agriculture and forestry. Results already achieved include detection tools for pest identification and management strategies. Ongoing work involves guidelines for integrated pest management and testing biological control agents. The project aims to disseminate results to policymakers and host workshops to engage with stakeholders.
The invasion of the North American Heterobasidion irregulare in central ItalyEMPHASIS PROJECT
The session was delivered by Italy's University of Torino (UNITO) - one of EMPHASIS partners. The talk dealt with the invasion of the North American fungal forest pathogen Heterobasidion irregulare in Europe. In addition to the introduction pathways, the talk presented the factors that are likely to play role in the invasiveness of the pathogen and strategies and tactics for the containment of the disease, some of which tested in the frame of EU Emphasis project.
Overview on Heterobasidion root and butt rots of conifersEMPHASIS PROJECT
The session was delivered by Italy's University of Torino (UNITO) - one of EMPHASIS partners. The talk gave an overview on symptoms and impact of diseases caused by the fungal pathogens included in the Heterobasidion annosum species complex. The biology and epidemiology of these pathogens were presented as well as the main strategies of disease control, with emphasis on integrated forest disease management.
Speaker was UNITO researcher Dr Luana Giordano.
"New approaches to managing cabbage stem flea beetle in oilseed rape"EMPHASIS PROJECT
Cabbage stem flea beetle (CSFB) was an insignificant pest of oilseed rape years ago, but loss of neonicotenoid seed treatments has meant that it poses a serious threat to crop establishment. NIAB described a new approach using companion crops which may help to manage the pest in the future.
Speaker was NIAB researcher Simon Kightley.
The target audience are researchers, agri-business and forestry experts, farmers and foresters and any other interested in plant health.
Do not hesitate to contact EMPHASIS project through Facebook, Twitter, email or through their website if you want to be updated on webinars dates and content and book a ticket.
LAMP is a DNA amplification technology which enables rapid and sensitive detection and when run on the Genie III platform enables detection of pests and diseases outside of the laboratory at any point in the agri-food chain where decisions are being made.
The target audience are researchers, agri-business and forestry experts, farmers and foresters and any other interested in being introduced to this portable molecular diagnostic tools on plant diseases.
Do not hesitate to contact EMPHASIS project through Facebook, Twitter, email (emphasisproject@gmail.com), Youtube or through our website (http://www.emphasisproject.eu/) if you want to be updated on webinars dates and content and book a ticket.
To watch on Youtube: https://youtu.be/Dg-lAjuCYuQ
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
"In field molecular diagnostics as an aid to disease management"
1. This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 634179.
EMPHASIS
Effective Management of Pests and Harmful Alien Species - Integrated Solutions
Dr. Jane Thomas
Dr.Rosa Caiazzo
NIAB
“In field molecular diagnostics as an aid to disease management”
2. EMPHASIS’ WORK PACKAGES
PLANT HEALTH CHALLENGES AND EVALUATION
PRACTICAL SOLUTIONS FOR SURVEILLANCE
AND MONITORING
PRACTICAL SOLUTIONS FOR PROTECTION,
MANAGEMENT AND ERADICATION
OPEN-ENDED MULTI-ACTOR ACTIVITIES: ON-FARM
VALIDATION AND PRODUCT DEVELOPMENT
DISSEMINATION AND TRAINING
WP1
WP2
WP3
WP4
WP5
3. Why Is Diagnosis Important?
Correct and fast diagnosis is important to prevent or
reduce the amount of damage or economic loss
Plant disease management practices rely on anticipating occurrence
of disease and a correct diagnosis of a disease is necessary to
identify the pathogen
4. Why Is Diagnosis Important?
In field diagnosis – why is it needed?
- Early infections are symptomless
- Some diseases have long latent periods
- Disease complexes are difficult to diagnose
- Improve product choice
- Select better curative products
- Change programme depending on disease identification
- Potential to switch products if resistant populations detected
5. Phoma stem canker
Leptosphaeria maculans/L. biglobosa
•Airborne ascospores released from infected stem debris
•€60 M losses in UK
•Susceptible varieties
•Warm temperatures and available moisture
• Early symptoms similar for L. biglobosa/L. maculans
6. Light leaf spot
•Favours cool, wet conditions
•€30 M losses in UK
•Loss of field resistance in North of UK
•Reduced Triazole efficacy?
Pyrenopeziza brassicae
Effective chemical control of this disease
depends on the timing of fungicide sprays
7. Forecasting airborne inoculum
•to control both diseases there is a need for effective methods of
forecasting the availability of airborne inoculum in the autumn,
when newly emerged crops are susceptible to infection
•PCR-based assays or LAMP used in conjunction with conventional
spore traps have potential as a method for detecting airborne
fungal spores
Conventional methods of monitoring airborne fungal spores
use either microscopy or cultural methods
Both pathogens can be dispersed by airborne ascospores
8. Soilborne pathogens
Some diseases caused by soilborne pathogens may be difficult to
diagnose due to the absence of characteristic symptoms.
They survive for long periods on host plant debris, soil organic
matter, or as free-living organisms.
Each vegetable crop may be susceptible to several pathogens.
Many soil factors including soil type, texture, pH, moisture,
temperature, nutrient levels, and ecology affect the activity of
soilborne pathogens
9. Diagnosis in plant pathology
Proper plant identification
Identify characteristic symptoms and signs
Understand the biology of the microorganisms
Identification of the pathogen
Disease management
Accurate diagnosis is important, but not necessarily an easy task...
10. Symptoms
wilting temporary or permanent drooping of leaves, shoots, or entire plants from lack of water
necrotic localized or general death of cells or disintegration of tissues
blast sudden blighting or death of young buds, flowers, or young fruit; failure to produce fruit
or seeds
blight sudden or total discoloration and killing of large numbers of blossoms, leaves, shoots,
or limbs or the entire plant; usually young tissues are attacked;
canker a definite, dead, often sunken or swollen and cracked area on a stem, limb, trunk,
tuber, or root surrounded by living tissues
damping-off rapid death of germinating seedlings before emergence, or emerged seedlings suddenly
wilting, toppling over, and dying from rot at or near the soil line
spot a definite, localized, round to regular lesion, often with a border of a different colour
(brown spot, black spot), characterized as to location (leaf spot, fruit spot)
stripe narrow, elongated, parallel, necrotic lesions especially in leaf diseases of cereals and
grasses
chlorosis yellowing or whitening of normal green tissue
stunting or
dwarfing
the underdevelopment of the plant or some of its organs
callus overgrowth of tissues, often at margins of a canker or wound
scab roughened to crust like, more or less circular, slightly raised or sunken lesions on the
surface of leaves, stems, fruit, or tubers
11. Signs
To properly identify a fungal or bacterial disease, one must look
for the signs of the pathogen:
• Physiological symptoms (lesions etc.)
• mycelium
• spore masses (moulds or rusts)
• Sclerotia
Verticillium stem stripingPeronospora
12. Identification of the pathogen
Direct agar plating technique
Isolation and growth of the pathogen on artificial medium
Morphological identification of the pathogen
Macroscopic observation of the mycelium
Microscopic observation of multiplicative structure
Morphological identification in the plant diagnostic laboratory is
typically only made to the genus level, due to time and difficulty in
differentiating species within a genus with very close
morphologies
13. Early Blight
Alternaria spp.
• A. solani, A. alternata (syn. A. tenuissima), other Alternaria spp.
• Global threat - Major foliar pathogen in the USA, Asia and Africa
• Favours warm, wet, humid conditions
• Affects older leaves, lesions coalesce leading to defoliation
It is not always easy to distinguish the Alternaria species visually, and even with a
microscope unless spores are present
Selection of products to control disease depends on which organism is present
14. Koch's Postulates
To identify the causative agent of a particular disease
1.the microorganism or other pathogen must be present in all cases
of the disease
2.the pathogen can be isolated from the diseased host and grown in
pure culture
3.the pathogen from the pure culture must cause the disease when
inoculated into a healthy, susceptible plant
4.the pathogen must be re-isolated from the new host and shown to
be the same as the originally inoculated pathogen
15. Molecular Technologies for diagnosis
Technological advances in the identification of pathogenic
agents can allow
the identification of morphologically similar species or strains
the detection of infection prior to symptom formation
to detect an organism without prior culturing
increasing the efficacy, accuracy and speed of diagnosis
16. Molecular Technologies for diagnosis
Serology or immunoassay based techniques such as enzyme linked
immunosorbent assay (ELISA) particularly used for the identification
of plant viruses.
Nucleic acid based techniques such as conventional PCR, nucleic
acid hybridization, quantitative real-time PCR (qPCR) and
isothermal loop mediated amplification (LAMP)
17. Ribosomal RNA (rRNA/rDNA)
26S28S
FungiETS = External Transcribed Spacer
ITS = Internal Transcribed Spacer
IGS = InterGenic Spacer
PLANTS
ITS1 ITS2 IGS
ETS 18S 5.8S 25S ETS
• is an essential gene that
is present in all organisms
• is a common target for
sequencing studies; large
database for comparisons
• contains sites that are
relatively conserved
(stems) and sites that are
more free to vary (loops)
•ITS more variable than
ribosomal sub-units
20. Primers Enzyme Sensitivity Equipment Detection Time
PCR 2 Taq 10-100ng thermal cycler Agarose gel 2-3 hrs
qPCR 2 Taq 10-100pg thermal cycler fluorescence 2 hrs
LAMP 4-6 Bst <10pg Heat block/bath visible or UV
light
30-60 min
Loop-mediated isothermal Amplification
•High specificity and sensitivity
•No high-tech equipment required ( it can be used in the field)
•Faster
•Cheaper
Molecular diagnostics
21. LAMP detection
Identification of a specific gene and primers design
Optimization of LAMP reaction conditions
Validation of the specificity and sensitivity of the assay
Design of an internal control assay (i.e. COX )
Test on field samples
25. Important UK Crop diseases
oilseed rape
Disease pathogen
Phoma leafspot/stemcanker L. maculans and L.biglobosa
Light leaf spot Pyrenopeziza brassicae
Sclerotinia stem rot Sclerotinia sclerotiorum
Clubroot Plasmodiophora brassicae
Verticillium wilt Verticillium longisporum
Alternaria pod spot Alternaria sp.
potato
Disease pathogen
Late blight Phythopthora infestans
Black scurf/stem canker Rhizoctonia solani
PCN Globodera spp.
Early blight Alternaria solani mainly
wheat/barley
Disease pathogen
Tan spot Pyrenophora tritici-repentis
Septoria leaf blotch Zymoseptoria tritici
Black point Alternaria spp
Brown (leaf) rust Puccinia triticina
Yellow (stripe) rust P. striiformis f.sp.tritici
Ear blights (fusarium) F. culmorum and F. graminearum
Potato (Solanum tuberosum)
Oilseed Rape (Brassica napus)
26. In-field testing
Asymptomatic detection in LLS
Discerning between pathotypes for determining fungicide insensitivity
Optimise chemical controls through improving spray timings and monitoring for resistance
29. Sensitivity of LAMP
Sensitivity of the LAMP using 10 fold serial dilution of purified target DNA from Verticillium longisporum: A)
electrophoresis of the products which were run on 1.5% agarose gel lane 1-5ng, lane 2-0.5ng, lane 3-0.05ng, lane
4-0.005ng , lane 5-0.5pg,lane 6 negative control, lane L-ladder 100bp. B) Amplification plot and melting curve of
the specific target .
1 2 3 4 5 6 L
A B
5pg
30. Pathogen Target Assay
designed
Tested on
DNA
Tested on
infected sample
Assay validated
A. alternata Alt a 1 allergene P P P P
L. biglobosa beta-tubulin P P
L. maculans nitrate reductase P P P P
Pyrenophora tritici
repensis GPDH P P P
V. longisporum elongation factor P P P P
Pyrenopeziza
brassicacea beta-tubulin P P P
A. solani cytb P P P P
Peronspora belbahrii ITS P P P
Peronospora vicae
f.sp. Pisi ATPase P
Pathogens targeted
31. Conclusion
Molecular technology increases understanding of the
biology and population structure of plant pathogens,
provides quick and accurate answers to epidemiological
questions about plant diseases
support disease-management decisions
that rely on anticipating occurrence of disease
32. Plant Disease Control
Avoidance—prevent disease by selecting a time of the year or a site
where there is no inoculum or where the environment is not favourable
for infection.
Exclusion—prevent the introduction of inoculum.
Eradication—eliminate, destroy, or inactivate the inoculum.
Protection—prevent infection by means of a toxicant or some other
barrier to infection.
Resistance—utilize cultivars that are resistant to or tolerant of infection.
Therapy—cure plants that are already infected.
33. Integrated pest management
uses all suitable techniques that complement each other in order to:
keep pest populations below the threshold at which economic
damage occurs
avoid the problem of pests developing resistance to widely used
insecticides
Using resistant crop varieties in conjunction with chemical treatment,
crop rotation and manipulation of the environment