This document provides an overview of plant viruses including their history, composition, structure, taxonomy, symptoms, and major types. It discusses how plant virus study has impacted virology and outlines some important discoveries such as Wendell Stanley's crystallization of TMV in 1935 and showing it contains RNA and protein. It also summarizes characteristics of plant pathogenic viruses and highlights plant viruses have simpler genomes than animal viruses, with RNA being the most common type of genome.
Biotechnology ammeriolation for viral diseaseswani amir
1. The document discusses molecular mechanisms of plant viral diseases and potential biotechnological interventions. It summarizes information on major viral diseases affecting important crops in India such as cassava, cotton, mungbean, potato, rice, maize, wheat, soybean, and vegetable crops.
2. Key points covered include the structure and composition of plant viruses, their genome organization and strategies for gene expression, the infection cycle involving entry into host cells, replication, cell-to-cell and long distance movement within the plant, and transmission between plants.
3. Major viral diseases reported for different crops in India are discussed along with the causal viruses and estimated yield losses. The current status of important viral diseases in different
This document provides an overview of plant pathology and the factors that influence plant disease development. It discusses the components of plant disease including pathogens, hosts, and the environment. Various types of pathogens are described such as fungi, bacteria, viruses, nematodes and their disease cycles. The document outlines environmental factors like moisture and temperature that affect disease buildup. It also discusses strategies for managing plant diseases, including cultural practices like sanitation, crop rotation and temperature management as well as chemical controls and host plant resistance.
1. Viruses are submicroscopic infectious agents that are composed of nucleic acid and proteins and require a host cell to replicate. They were first observed in 1886 to cause tobacco mosaic disease.
2. In 1892, Beijerinck discovered that the infectious agent causing tobacco mosaic disease was a "contagium vivum fluidum", or "living fluid contagion", which was later shown to be tobacco mosaic virus (TMV) in 1935.
3. Viruses have a variety of shapes including rod-shaped, spherical, filamentous, and bacilliform. They contain a protein capsid that protects the viral genome, which can be DNA or RNA but not both. Viruses use
- Viruses were first observed in the late 19th century through experiments showing that certain diseases could be transmitted through filters that removed bacteria. Early scientists disagreed on whether viruses were living or non-living.
- Viruses are microscopic particles that can only replicate inside host cells. They contain genetic material surrounded by a protein coat. Major advances in virus identification came in the 1930s-40s with the use of electron microscopy and X-ray crystallography to view viruses.
- The field of virology studies virus structure, classification, infection mechanisms, interaction with host immunity and physiology, diseases caused, and potential applications in research and medicine.
Lecture 1 - Introduction To Virology.pptxJonesChipinga
This lecture outlines why we study viruses, the virosphere,bacteriophage plaque assay, the nature of viruses, properties of viruese, viral genomics and comparison of viruses to other cells.
Viruses are obligate intracellular parasites that infect all types of cells. They consist of nucleic acid surrounded by a protein coat and in some cases an envelope. Viruses hijack the host cell's machinery to replicate themselves and are then released to infect new host cells. There are many variations in the viral life cycle depending on whether the virus has DNA or RNA as its genome and whether it is enveloped. Viruses are classified based on their structure, composition and genetics.
Viruses and bacteriophages are infectious pathogens that depend on host cells for replication. Viruses are too small to see with an electron microscope and contain nucleic acids surrounded by proteins. Bacteriophages infect bacteria and have either DNA or RNA genomes. Bacteriophages follow the lytic cycle of replicating within the host cell until it bursts, or the lysogenic cycle where the phage DNA integrates with the host and replicates with it without killing the cell.
Viruses are obligate intracellular parasites that infect all living organisms. They are much smaller than bacteria, ranging from 20-400nm in diameter. Viruses consist of nucleic acids surrounded by a protein capsid, and some have an outer envelope. They hijack host cell machinery to replicate, then are released to infect new cells. HIV is a retrovirus that causes AIDS by destroying CD4+ T cells. It is spherical with an RNA genome and envelope glycoproteins that bind host cells. Its life cycle involves reverse transcription of RNA to DNA, integration into host DNA, transcription/translation of new viral proteins, assembly of new virions, and cell lysis to spread infection. Management involves preventing transmission and using antire
Biotechnology ammeriolation for viral diseaseswani amir
1. The document discusses molecular mechanisms of plant viral diseases and potential biotechnological interventions. It summarizes information on major viral diseases affecting important crops in India such as cassava, cotton, mungbean, potato, rice, maize, wheat, soybean, and vegetable crops.
2. Key points covered include the structure and composition of plant viruses, their genome organization and strategies for gene expression, the infection cycle involving entry into host cells, replication, cell-to-cell and long distance movement within the plant, and transmission between plants.
3. Major viral diseases reported for different crops in India are discussed along with the causal viruses and estimated yield losses. The current status of important viral diseases in different
This document provides an overview of plant pathology and the factors that influence plant disease development. It discusses the components of plant disease including pathogens, hosts, and the environment. Various types of pathogens are described such as fungi, bacteria, viruses, nematodes and their disease cycles. The document outlines environmental factors like moisture and temperature that affect disease buildup. It also discusses strategies for managing plant diseases, including cultural practices like sanitation, crop rotation and temperature management as well as chemical controls and host plant resistance.
1. Viruses are submicroscopic infectious agents that are composed of nucleic acid and proteins and require a host cell to replicate. They were first observed in 1886 to cause tobacco mosaic disease.
2. In 1892, Beijerinck discovered that the infectious agent causing tobacco mosaic disease was a "contagium vivum fluidum", or "living fluid contagion", which was later shown to be tobacco mosaic virus (TMV) in 1935.
3. Viruses have a variety of shapes including rod-shaped, spherical, filamentous, and bacilliform. They contain a protein capsid that protects the viral genome, which can be DNA or RNA but not both. Viruses use
- Viruses were first observed in the late 19th century through experiments showing that certain diseases could be transmitted through filters that removed bacteria. Early scientists disagreed on whether viruses were living or non-living.
- Viruses are microscopic particles that can only replicate inside host cells. They contain genetic material surrounded by a protein coat. Major advances in virus identification came in the 1930s-40s with the use of electron microscopy and X-ray crystallography to view viruses.
- The field of virology studies virus structure, classification, infection mechanisms, interaction with host immunity and physiology, diseases caused, and potential applications in research and medicine.
Lecture 1 - Introduction To Virology.pptxJonesChipinga
This lecture outlines why we study viruses, the virosphere,bacteriophage plaque assay, the nature of viruses, properties of viruese, viral genomics and comparison of viruses to other cells.
Viruses are obligate intracellular parasites that infect all types of cells. They consist of nucleic acid surrounded by a protein coat and in some cases an envelope. Viruses hijack the host cell's machinery to replicate themselves and are then released to infect new host cells. There are many variations in the viral life cycle depending on whether the virus has DNA or RNA as its genome and whether it is enveloped. Viruses are classified based on their structure, composition and genetics.
Viruses and bacteriophages are infectious pathogens that depend on host cells for replication. Viruses are too small to see with an electron microscope and contain nucleic acids surrounded by proteins. Bacteriophages infect bacteria and have either DNA or RNA genomes. Bacteriophages follow the lytic cycle of replicating within the host cell until it bursts, or the lysogenic cycle where the phage DNA integrates with the host and replicates with it without killing the cell.
Viruses are obligate intracellular parasites that infect all living organisms. They are much smaller than bacteria, ranging from 20-400nm in diameter. Viruses consist of nucleic acids surrounded by a protein capsid, and some have an outer envelope. They hijack host cell machinery to replicate, then are released to infect new cells. HIV is a retrovirus that causes AIDS by destroying CD4+ T cells. It is spherical with an RNA genome and envelope glycoproteins that bind host cells. Its life cycle involves reverse transcription of RNA to DNA, integration into host DNA, transcription/translation of new viral proteins, assembly of new virions, and cell lysis to spread infection. Management involves preventing transmission and using antire
Viruses are obligate intracellular parasites that contain genetic material in the form of DNA or RNA. The tobacco mosaic virus was the first virus discovered and has a rod-like structure containing RNA surrounded by a protein coat. Yellow fever virus causes a mosquito-borne illness with symptoms of fever, muscle pain, and vomiting. Its transmission can be prevented through vaccination. Lumpy skin disease virus is a poxvirus that causes nodules on the skin and mucous membranes of cattle. Bacteriophages are viruses that infect bacteria and have been used therapeutically to treat bacterial infections.
This document discusses the classification of bacteria using taxonomy and Carl Woese's three domain system. It covers the main characteristics of different bacterial phyla including Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Spirochaetes, and Archaea. Key details are provided on pathogenic bacteria such as Staphylococcus aureus, Streptococcus pyogenes, Clostridium tetani, Salmonella typhi, and Mycobacterium tuberculosis. The principles of bacterial identification, nomenclature, and Bergey's Manual are also summarized.
Viruses are submicroscopic infectious agents that lack cellular organization and require a host cell to replicate. They contain either DNA or RNA surrounded by a protein coat called a capsid. Viruses have different structures depending on their symmetry - icosahedral, helical, or complex. They multiply through lytic or lysogenic cycles, depending on if they cause host cell lysis or integrate into the host genome. Important plant, animal, and bacterial viruses are described along with their structures and life cycles. Viruses, viroids, and prions are compared in terms of their genetic material and ability to infect hosts.
The document provides an introduction to plant viruses. It discusses that viruses are infectious pathogens too small to see that depend on host cells to reproduce. They can cause significant losses in crop yields. The history of plant virology began in the late 19th century with the discovery of Tobacco mosaic virus. Viruses have a variety of structures depending on their nucleic acid and presence of an envelope. Their genomes provide the information needed for reproduction. Plant viruses enter plants through wounds and have varying effects depending on the plant genotype.
This document provides information about the Virology/Parasitology course code 320 at semester 6. It discusses the lytic and lysogenic cycles of bacteriophages, including their adsorption, penetration, synthesis of phage components, maturation and assembly, and release stages. It also covers the significance of bacteriophages in phage typing, assays, conferring new properties to host bacteria, and applications in medicine, agriculture and wastewater treatment. Additionally, it introduces viroids as small circular RNA molecules that cause plant diseases, and prions as misfolded protein particles that cause transmissible spongiform encephalopathies in humans and animals.
This document discusses viroids, prions, and phytoplasmas. It defines them as follows: viroids are small circular RNA molecules that infect plants and disrupt protein synthesis; prions are misfolded infectious proteins that cause diseases like mad cow disease; and phytoplasmas are wall-less bacteria that infect plant phloem and are transmitted by insects. It provides details on their structures, modes of infection/multiplication, and diseases caused. Control measures mentioned include breeding resistance, insect control, cryotherapy, and antibiotics.
This document provides an overview of plant virology, including definitions and key discoveries. It discusses how viruses were shown to be infectious agents that depend on host cells for replication through experiments in the late 19th century. Major findings include identifying that the nucleic acid, not protein, is the infectious material, and that viruses can be reconstituted in vitro from isolated nucleic acid and protein. The structure and composition of viruses is also examined, including different symmetry types and the helical structure of Tobacco mosaic virus. The document traces important developments in the field from the late 1700s to present day, including the invention of techniques like PCR that advanced virus research.
Viruses can be cultivated through several methods, including inoculation in animals, embryonated eggs, and tissue/cell culture. Inoculation in animals allows study of viral replication and immune responses but is expensive. Embryonated eggs are widely used as they are inexpensive and viruses can replicate, though not all human viruses grow well. Tissue/cell culture is now preferred, using primary cultures, continuous cell lines, or explant cultures. Growth is detected through cytopathic effects, staining, or metabolic changes in infected cells.
Plant viruses can move from cell to cell through plasmodesmata with the help of viral movement proteins. Most plant viruses move as ribonucleoprotein complexes containing genomic RNA and viral movement proteins. Systemic spread within the plant occurs through the phloem. Plant viruses are transmitted to new hosts through mechanical means like contaminated tools, insect vectors, seed transmission, grafting, and nematodes. The type of transmission determines the epidemiology and spread of the virus.
Unit 8: Rare and Uncultured Microbes
LECTURE LEARNING GOALS
1. Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes.
2. Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life.
3. For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated.
6
This document provides an overview of plant pathology and the factors involved in plant disease development. It discusses the main types of plant pathogens including fungi, bacteria, viruses, nematodes and environmental factors. It describes how pathogens infect plants and cause disease symptoms. It also summarizes strategies for managing plant diseases, such as sanitation, fungicides, host plant resistance, crop rotation, cultural practices, temperature control, and biological control. The overall document provides a comprehensive introduction to the concepts of plant pathology.
Characteristics of pet/virus , plant disease , pest life cycle, regarding and repeating plant disease , selecting treatment methods, Control plant pest / virus .
This document contains information about a presentation on botany that a student named Morsheda Nur Tisha is preparing for a higher secondary class. It includes sections on microbiology, types of microorganisms, characteristics of living organisms, viruses, the structure and replication of viruses, bacteria, the structure of bacteria, and the economic and biological importance of viruses and bacteria.
Infection /certified fixed orthodontic courses by Indian dental academy Indian dental academy
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and offering a wide range of dental certified courses in different formats.
Indian dental academy provides dental crown & Bridge,rotary endodontics,fixed orthodontics,
Dental implants courses.for details pls visit www.indiandentalacademy.com ,or call
00919248678078
The earliest indications of the biological nature of viruses came from studies in 1892 by the Russian scientist Dmitry I. Ivanovsky and in 1898 by the Dutch scientist Martinus W. Beijerinck.
Beijerinck first surmised that the virus under study was a new kind of infectious agent, which he designated contagium vivum
fluidum, meaning that it was a live, reproducing organism that differed from other organisms.
Both of these investigators found that a disease of tobacco plants could be transmitted by an agent, later called tobacco mosaic virus, passing through a minute filter that would not allow the passage of bacteria.
Viruses are microscopic organisms that exist almost everywhere on earth. They can infect animals, plants, fungi, and even bacteria.Viruses vary in complexity. They consist of genetic material, RNA or DNA, surrounded by a coat of protein, lipid (fat), or glycoprotein. Viruses cannot replicate without a host, so they are classified as parasitic.They are considered the most abundant biological entity on the planet.
Here we discuss the general properties of viruses in detail.
- More than 2000 viruses are known to infect plants, with about 1/4 causing diseases. Some common plant viruses include tobacco mosaic virus, cucumber mosaic virus, and cauliflower mosaic virus.
- Viral diseases in plants show symptoms like mosaic patterns, leaf curling, vein clearing, and bunchy tops. Viruses are obligate parasites that replicate inside living cells and are composed of nucleic acids and proteins.
- Plant viruses are transmitted in several ways, including by insects, mechanical means, seed, vegetative propagation, fungi, nematodes, and soil. Effective management of plant viruses involves controlling vectors, using resistant varieties, and sterilizing agricultural tools.
This document provides information on plant viruses and plant parasitic nematodes. It defines plant viruses as nucleoproteins that can cause plant disease. It describes their size, morphology, genome, capsids, replication, and vectors. It also discusses the historical developments in plant virology, symptoms of virus-infected plants, modes of virus transmission, and methods of detection, identification, and control. The document then defines plant parasitic nematodes, describes their morphology, life cycle, reproduction terms, feeding groups, symptoms they cause, important diseases they cause in the Philippines, and sampling techniques.
Presentation comprises of introductory information on virus, related terminology, its composition and structure, classification, nomenclature and taxonomy for under graduate students.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Viruses are obligate intracellular parasites that contain genetic material in the form of DNA or RNA. The tobacco mosaic virus was the first virus discovered and has a rod-like structure containing RNA surrounded by a protein coat. Yellow fever virus causes a mosquito-borne illness with symptoms of fever, muscle pain, and vomiting. Its transmission can be prevented through vaccination. Lumpy skin disease virus is a poxvirus that causes nodules on the skin and mucous membranes of cattle. Bacteriophages are viruses that infect bacteria and have been used therapeutically to treat bacterial infections.
This document discusses the classification of bacteria using taxonomy and Carl Woese's three domain system. It covers the main characteristics of different bacterial phyla including Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Spirochaetes, and Archaea. Key details are provided on pathogenic bacteria such as Staphylococcus aureus, Streptococcus pyogenes, Clostridium tetani, Salmonella typhi, and Mycobacterium tuberculosis. The principles of bacterial identification, nomenclature, and Bergey's Manual are also summarized.
Viruses are submicroscopic infectious agents that lack cellular organization and require a host cell to replicate. They contain either DNA or RNA surrounded by a protein coat called a capsid. Viruses have different structures depending on their symmetry - icosahedral, helical, or complex. They multiply through lytic or lysogenic cycles, depending on if they cause host cell lysis or integrate into the host genome. Important plant, animal, and bacterial viruses are described along with their structures and life cycles. Viruses, viroids, and prions are compared in terms of their genetic material and ability to infect hosts.
The document provides an introduction to plant viruses. It discusses that viruses are infectious pathogens too small to see that depend on host cells to reproduce. They can cause significant losses in crop yields. The history of plant virology began in the late 19th century with the discovery of Tobacco mosaic virus. Viruses have a variety of structures depending on their nucleic acid and presence of an envelope. Their genomes provide the information needed for reproduction. Plant viruses enter plants through wounds and have varying effects depending on the plant genotype.
This document provides information about the Virology/Parasitology course code 320 at semester 6. It discusses the lytic and lysogenic cycles of bacteriophages, including their adsorption, penetration, synthesis of phage components, maturation and assembly, and release stages. It also covers the significance of bacteriophages in phage typing, assays, conferring new properties to host bacteria, and applications in medicine, agriculture and wastewater treatment. Additionally, it introduces viroids as small circular RNA molecules that cause plant diseases, and prions as misfolded protein particles that cause transmissible spongiform encephalopathies in humans and animals.
This document discusses viroids, prions, and phytoplasmas. It defines them as follows: viroids are small circular RNA molecules that infect plants and disrupt protein synthesis; prions are misfolded infectious proteins that cause diseases like mad cow disease; and phytoplasmas are wall-less bacteria that infect plant phloem and are transmitted by insects. It provides details on their structures, modes of infection/multiplication, and diseases caused. Control measures mentioned include breeding resistance, insect control, cryotherapy, and antibiotics.
This document provides an overview of plant virology, including definitions and key discoveries. It discusses how viruses were shown to be infectious agents that depend on host cells for replication through experiments in the late 19th century. Major findings include identifying that the nucleic acid, not protein, is the infectious material, and that viruses can be reconstituted in vitro from isolated nucleic acid and protein. The structure and composition of viruses is also examined, including different symmetry types and the helical structure of Tobacco mosaic virus. The document traces important developments in the field from the late 1700s to present day, including the invention of techniques like PCR that advanced virus research.
Viruses can be cultivated through several methods, including inoculation in animals, embryonated eggs, and tissue/cell culture. Inoculation in animals allows study of viral replication and immune responses but is expensive. Embryonated eggs are widely used as they are inexpensive and viruses can replicate, though not all human viruses grow well. Tissue/cell culture is now preferred, using primary cultures, continuous cell lines, or explant cultures. Growth is detected through cytopathic effects, staining, or metabolic changes in infected cells.
Plant viruses can move from cell to cell through plasmodesmata with the help of viral movement proteins. Most plant viruses move as ribonucleoprotein complexes containing genomic RNA and viral movement proteins. Systemic spread within the plant occurs through the phloem. Plant viruses are transmitted to new hosts through mechanical means like contaminated tools, insect vectors, seed transmission, grafting, and nematodes. The type of transmission determines the epidemiology and spread of the virus.
Unit 8: Rare and Uncultured Microbes
LECTURE LEARNING GOALS
1. Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes.
2. Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life.
3. For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated.
6
This document provides an overview of plant pathology and the factors involved in plant disease development. It discusses the main types of plant pathogens including fungi, bacteria, viruses, nematodes and environmental factors. It describes how pathogens infect plants and cause disease symptoms. It also summarizes strategies for managing plant diseases, such as sanitation, fungicides, host plant resistance, crop rotation, cultural practices, temperature control, and biological control. The overall document provides a comprehensive introduction to the concepts of plant pathology.
Characteristics of pet/virus , plant disease , pest life cycle, regarding and repeating plant disease , selecting treatment methods, Control plant pest / virus .
This document contains information about a presentation on botany that a student named Morsheda Nur Tisha is preparing for a higher secondary class. It includes sections on microbiology, types of microorganisms, characteristics of living organisms, viruses, the structure and replication of viruses, bacteria, the structure of bacteria, and the economic and biological importance of viruses and bacteria.
Infection /certified fixed orthodontic courses by Indian dental academy Indian dental academy
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and offering a wide range of dental certified courses in different formats.
Indian dental academy provides dental crown & Bridge,rotary endodontics,fixed orthodontics,
Dental implants courses.for details pls visit www.indiandentalacademy.com ,or call
00919248678078
The earliest indications of the biological nature of viruses came from studies in 1892 by the Russian scientist Dmitry I. Ivanovsky and in 1898 by the Dutch scientist Martinus W. Beijerinck.
Beijerinck first surmised that the virus under study was a new kind of infectious agent, which he designated contagium vivum
fluidum, meaning that it was a live, reproducing organism that differed from other organisms.
Both of these investigators found that a disease of tobacco plants could be transmitted by an agent, later called tobacco mosaic virus, passing through a minute filter that would not allow the passage of bacteria.
Viruses are microscopic organisms that exist almost everywhere on earth. They can infect animals, plants, fungi, and even bacteria.Viruses vary in complexity. They consist of genetic material, RNA or DNA, surrounded by a coat of protein, lipid (fat), or glycoprotein. Viruses cannot replicate without a host, so they are classified as parasitic.They are considered the most abundant biological entity on the planet.
Here we discuss the general properties of viruses in detail.
- More than 2000 viruses are known to infect plants, with about 1/4 causing diseases. Some common plant viruses include tobacco mosaic virus, cucumber mosaic virus, and cauliflower mosaic virus.
- Viral diseases in plants show symptoms like mosaic patterns, leaf curling, vein clearing, and bunchy tops. Viruses are obligate parasites that replicate inside living cells and are composed of nucleic acids and proteins.
- Plant viruses are transmitted in several ways, including by insects, mechanical means, seed, vegetative propagation, fungi, nematodes, and soil. Effective management of plant viruses involves controlling vectors, using resistant varieties, and sterilizing agricultural tools.
This document provides information on plant viruses and plant parasitic nematodes. It defines plant viruses as nucleoproteins that can cause plant disease. It describes their size, morphology, genome, capsids, replication, and vectors. It also discusses the historical developments in plant virology, symptoms of virus-infected plants, modes of virus transmission, and methods of detection, identification, and control. The document then defines plant parasitic nematodes, describes their morphology, life cycle, reproduction terms, feeding groups, symptoms they cause, important diseases they cause in the Philippines, and sampling techniques.
Presentation comprises of introductory information on virus, related terminology, its composition and structure, classification, nomenclature and taxonomy for under graduate students.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
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
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).
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.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
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)”
1. Plant Viruses
Bradley Hillman
Dept. of Plant Biology and Pathology
339 Foran Hall, Cook
932-9375 X 334
hillman@aesop.rutgers.edu
Comparative Virology course website:
http://www.rci.rutgers.edu/~bhillman/comparative_virology/Index.htm
2. Plant Viruses
• Introduction and history
– Why study plant viruses?
– How do they relate to animal viruses?
– How has their study impacted virology?
• Symptoms
• Composition and structure
• Taxonomy and nomenclature
– Four families contain both plant and animal viruses
– Seven families contain only plant viruses
– Many plant viruses belong to genera without family affiliation
4. Plant Viruses (cont’d)
• Survey of some major plant viruses (cont’d)
– Double-stranded RNA
• Wound tumor virus (Reoviridae)
– Single-stranded DNA
• Bean golden mosaic virus (Geminiviridae)
– Double-stranded DNA (pararetroviruses)
• Cauliflower mosaic virus (Caulimoviridae)
• Expression strategies of + strand RNA viruses
• Plant virus infection cycle
• Cell-to-cell movement and movement within plants
• Plant-to-plant transmission
• Brome mosaic virus, a well-studied plant virus
• Satellites, defective-interfering RNAs, viroids
• Plant defense response to virus infection
• Plant viruses and biotechnology
5. Host Systems: Plants 1
• Eukaryotic, but fundamentally different from
animals
• Plants don’t move, so vectors are very important
for moving viruses from one plant to another
• Plants are autotrophic and easy to grow in
quantity– great bioreactors
• Plants have rigid cell walls and very small cell-to-
cell connections (plasmodesmata)
• Synchronous infection of many cells can be
achieved using plant protoplasts (primary cell
cultures with cell walls removed)
6. Host Systems: Plants 2
• Developed plant cells are totipotent
• Virus in one part of a plant moves to another
slowly by cell-to-cell connections; more rapidly
through vascular system, mostly phloem
• Plant defense response system exists, but is
less specific than vertebrate or invertebrate
systems
• Plants are developmentally complex; viruses
may be excluded from some tissues
7. CHARACTERISTICS OF PLANT
PATHOGENIC VIRUSES
• Loss due to plant viruses is often difficult to quantify, but
they are often of great importance as plant pathogens
(fungi are most economically important )
• Viruses do not usually kill plants, and symptoms on
plants are often subtle
• Virus diseases of plants are not subject to chemical
control – no effective cure in individual plants
• Symptoms, serological, electron microscopic, or
molecular methods are used to identify plant viruses
• Plant virus disease cycles often are dependent on
vectors or alternate hosts
9. Tulipomania – late 16th century
Traded for 1 Viceroy
tulip bulb:
4 tons of wheat
8 tons of rye
4 fat oxen
8 fat pigs
12 fat sheep
2 hogsheads of wine
4 barrels of beer
2 barrels of butter
1000 lbs of cheese
1 bed with
accessories
1 full dress suit
1 silver goblet
Before it was known to be caused by a virus, tulips with color
breaking symptoms were prized and traded for large sums of
goods – this led to “tulipomania” in the late 1500’s
10. • Adolf Mayer –1886 – showed that Tobacco
mosaic virus was transmissible, could not
find bacteria or fungi associated with
disease
TMV
11. • Dmitri Ivanowski - 1892– showed that
Tobacco mosaic virus was not retained by
filters that retained all bacteria known at
that time
12. • Martinus Beijerinck - 1898– repeated
demonstration that Tobacco mosaic
virus was not retained by filters that
retained all bacteria known at that time
Believed results
Did extensive dilution experiments
Showed diffusion of infectious agent
through agar
Named “contagium vivum fluidum”, later
virus
13. Wendell Stanley – 1935
• At Rockefeller Foundation in Princeton
• Crystallized TMV, thought it was only
protein
Stanley Hall, U.C. Berkeley
TMV
14. Bawden and Pirie - 1936
• Crystallized Tomato
bushy stunt virus
(TBSV); find that it
and TMV contain
phosphorous –
conclude that it is
not a protein, but is
a nucleoprotein
TMV
TBSV
15. Markham and Smith - 1949
• Two classes of particles
in purified Turnip yellow
mosaic virus
preparations:
– light ones containing only
protein, which were not
infectious
– heavy ones containing
protein+nucleic acid,
which were infectious
empty full
16. Myron Brakke - 1951
• Development of density
gradient centrifugation
– Isopycnic: particles reach
position of equal density in
gradient
– Rate-zonal: Particles
sediment differentially
through medium as a
function of size, shape, and
density
– Equilibrium zonal:
Combination of the above
17. Fraenkel-Conrat
1955-56
• Complete, infectious TMV
particles can be
reconstituted in vitro from
the RNA and protein
components
• RNA alone is infectious
• RNA can be
“transcapsidated” in
protein from closely
related virus; resulting
virus has properties of
RNA strain
reconstitute
in vitro
Virus Aa:
RNA A
capsid a
RNA
protein
symptoms (A)
extract virus
virus Aa
inoculate plants
18. Fraenkel-Conrat – 1955-56 Transcapsidation
inoculate plants
Virus Aa:
RNA A
capsid a
RNA
protein
symptoms (A)
no
symptoms
extract virus
no virus
virus Aa
inoculate plants
Virus Bb:
RNA B
capsid b
RNA
protein
symptoms (B)
no
symptoms
extract virus
no virus
virus Bb
inoculate plants
Virus Ab:
RNA A
capsid a
RNA
protein
symptoms (A)
no
symptoms
extract virus
no virus
virus Aa
19. Crick and Watson – 1956
• TMV virions are
composed of one
nucleic acid and
many identical protein
subunits: RNA does
not have the coding
capacity to make
many different
subunits
20. Casper and Klug – 1962
• Structure of Tomato bushy stunt
virus solved by X-ray
crystallography, the first
icosahedral virus so determined
21. Heinz Sanger – 1978
• Complete sequence
of Potato spindle
tuber viroid
– First pathogen
sequence to be
determined
– Yielded relatively little
information that was
immediately useful
1 cggaactaaa ctcgtggttc ctgtggttca cacctgacct
cctgagcaaa aaagaaaaaa gataggcggc tcggaggagc
gcttcaggga tccccgggga aacctggagc gaactggcaa
aaaaggacgg tggggagtgc ccagcggccg acaggagtaa
ttcccgccga aacagggttt tcacccttcc tttcttcggg
tgtccttcct cgcgcccgca ggaccacccc tcgccccctt
tgcgctgtcg cttcggctac tacccggtgg aaacaactga
agctcccgag aaccgctttt tctctatctt cttgcttccg
gggcgagggt gtttagccct tggaaccgca gttggttcct 359
22. Paul Ahlquist – 1984
• Infectious viral RNA
transcribed in vitro from
cDNA clones
– Done with Brome mosaic
virus – with 3 RNAs
– Brought reverse genetics
to RNA viruses
RNA
cDNA
RNA Inoculate
plants
23. Roger Beachy – 1986
• Transgenic plants
expressing TMV coat
protein are resistant to
virus infection
• First example of
“pathogen-mediated
resistance”
24. Bill Dougherty – 1991
• RNA was critical component
in resistance in pathogen-
mediated resistance
• All of the hallmarks that later
came to be associated with
PTGS and RNAi were first
observed with Tobacco etch
virus (TEV) (1993 Lindbo et
al., Plant Cell 5:1749-1759)
26. Plant Virus Symptoms
• Viruses rarely kill plants
• Most severe disease usually in least well-adapted
host/pathogen systems
• Levels of tissue specificity differ among plant viruses
– Some infect all or most tissues
– Most cause symptoms only in aerial portions
– Some accumulate only in roots
– Symptoms in fruit or flowers may be most harmful
• Systemic symptoms only in developing tissue
• Local necrotic lesions undetectable in natural
infections
36. Necrotic lesions
Systemic
Local
“Local lesion” or “hypersensitive” response is an apoptotic response.
Cells within a short distance of the initially inoculated cell begin to
undergo programmed cell death in advance of virus invasion,
preventing further virus spread.
37. Hypersensitive response – an apoptotic
reaction to infection
May be viral coat
protein or another
viral gene product
39. Virus taxonomy and nomenclature
• Modified binomial is used
• Taxonomy depends on particle properties, nucleic
acid properties and especially sequence
• Family is the highest taxonomic level that is
commonly used; ends in viridae, e.g., Bromoviridae
• Genus ends in suffix virus, e.g., Bromomovirus
• Species is usually the commonly used virus name;
it is italicized in formal usage, e.g., Brome mosaic
virus
• Small genome sizes, gene shuffling make broad
taxonomic schemes difficult (above Family level)
41. Virus properties: Plant viruses are often
simpler than animal viruses
• Genome sizes 0.3 - 300 kb; plant viruses 0.3-30 kb
• May have single-stranded or double-stranded RNA
or DNA genome; most plant viruses ssRNA
• If RNA, may be + or – sense; most plant viruses +
sense ssRNA
• May have one or many proteins in particles; most
plant viruses have 1-2
• May or may not have lipid envelope; most plant
viruses do not
42. Types of plant virus genomes
• double-stranded (ds) DNA (rare)
• single-stranded (ss) DNA (rare)
• ssRNA, negative sense (rare)
• ssRNA, positive sense (common)
• dsRNA (rare)
45. Plant viruses are
diverse, but not as
diverse as animal
viruses – probably
because of size
constraints imposed by
requirement to move
cell-to-cell through
plasmodesmata of host
plants
Plant viruses often
contain divided
genomes spread
among several particles
47. Helical symmetry
• Tobacco mosaic virus is typical,
well-studied example
• Each particle contains only a single
molecule of RNA (6395 nucleotide
residues) and 2130 copies of the
coat protein subunit (158 amino
acid residues; 17.3 kilodaltons)
– 3 nt/subunit
– 16.33 subunits/turn
– 49 subunits/3 turns
• TMV protein subunits + nucleic
acid will self-assemble in vitro in an
energy-independent fashion
• Self-assembly also occurs in the
absence of RNA
TMV rod is 18 nanometers
(nm) X 300 nm
48. Cubic (icosahedral) symmetry
• Tomato bushy stunt
virus is typical, well-
studied example
• Each particle contains
only a single molecule
of RNA (4800 nt) and
180 copies of the coat
protein subunit (387 aa;
41 kd)
• Viruses similar to TBSV
will self-assemble in
vitro from protein
subunits + nucleic acid
in an energy-
independent fashion
TBSV icosahedron is 35.4
nm in diameter
Protein Subunits Capsomeres
T= 3 Lattice
C
N
50. Plant virus genome organizations
• Very compact
• Most are +sense RNA viruses, so translation
regulation very important
• Use various strategies for genome expression
• Only a few genes absolutely required:
– Replicase
– Coat protein
– Cell-to-cell movement protein
• Other genes present in some viruses
51. Plant viruses have members in all 3 supergroups of + strand RNA viruses
From Principles of Virology,
Academic Press 1999
52. Genome expression of + strand RNA viruses
• Most use more than one strategy
– Polyprotein processing
– Subgenomic RNA
– Segmented genome
– Translational readthrough
– Frameshift
– Internal initiation of translation (without scanning)
– Scanning to alternative start site (truncated product)
– Alternative reading frame (gene-within-a-gene)
53. Polyprotein processing
• Post-translational cleavage of viral proteins
may occur in cis or in trans
• Some viruses use polyprotein processing
exclusively to regulate gene expression
• Many viruses use polyprotein processing as
one of several regulation mechanisms
• Examples:
– Potyviruses*
– Comoviruses*
– Closteroviruses
– Carlaviruses
54. Subgenomic RNA
• Similar to traditional mRNA, but synthesized
from an RNA template
• Many viruses use polyprotein processing as
one of several regulation mechanisms
• Examples:
– Tobamoviruses (TMV)*
– Bromoviruses (BMV)*
– Tombusviruses (TBSV)
– Potexviruses (PVX)
55. Segmented genome
• Positive sense RNA genomes are usually
encapsidated in separate particles
• Segmented genomes lend themselves to
recombination
• Examples:
– Bromoviruses (Brome mosaic virus, BMV)*
– Dianthoviruses (Red clover necrotic mosaic virus,
RCNMV)*
– Hordeiviruses (Barley stripe mosaic virus, BSMV)
56. Translational readthrough
• Usually UAG codon is read through using
suppressor tyrosine tRNA
• Common mechanism in plant viruses
• Examples:
– Tobamoviruses (Tobacco mosaic virus, TMV)*
– Dianthoviruses (Red clover necrotic mosaic virus,
RCNMV)*
– Hordeiviruses (Barley stripe mosaic virus, BSMV)
57. Translational frameshift
• Typically +1 or -1
• Common mechanism in plant viruses
• Examples:
– Luteoviruses (Barley yellow dwarf virus, BYBV)*
– Dianthoviruses (Red clover necrotic mosaic virus,
RCNMV)*
– Closteroviruses (Beet yellow vein virus, BYVV)
58. Internal initiation
• Cap-free translation
• Less complex in plant viruses than in
animal viruses
• Examples:
– Potyviruses (Tobacco etch virus, TEV)*
– Sobemoviruses (Southern bean mosaic
virus, (SBMV)*
59. Tobacco mosaic virus is a typical positive-sense RNA
plant virus with a 6.4 kilobase genome
61. Plant Virus Life Cycle
• Virus entry into host
– no attachment step with plant viruses
– by vector, mechanical, etc. – must be forced
– requires healable wound – delivery into cell
• Uncoating of viral nucleic acid
– may be co-translational for + sense RNA viruses
– poorly understood for many
• Replication
– replication is a complex, multistep process
– viruses encode their own replication enzymes
62. Plant Virus Life Cycle 2
• Cell-to-cell movement
– cell-to-cell movement through plasmodesmata
– move as whole particles or as protein/nucleic
acid complex (no coat protein required)
• Long distance movement in plant
– through phloem
– as particles or protein/nucleic acid complex (coat
protein required)
• Transmission from plant to plant
– requires whole particles
63. Typical RNA-containing plant virus replication cycle
From Shaw, 1996 Ch. 12 in Fundamental Virology (Academic Press)
2. RNA is released;
translates using
host machinery
3. Replication in
cytoplasm
4b. New virus particles
are assembled
1. Virus particle enters
first cell through
healable wound
4a. Infectious TMV
RNA is shuttled to
adjacent cell through
plasmodesmata, by
virus-coded
movement protein
64. Cell-to-Cell Movement of Plant Viruses
• Plant viruses move cell-to-cell slowly through
plasmodesmata
• Most plant viruses move cell-to-cell as
complexes of non-structural protein and
genomic RNA
• The viral protein that facilitates movement is
called the “movement protein” (MP)
• Coat protein is often dispensable for cell-to-cell
movement
65. Cell-to-Cell Movement of Plant Viruses
• Several unrelated lineages of MP proteins have
been described
• MPs act as host range determinants
• MP alone causes expansion of normally
constricted plasmodesmata pores; MPs then
traffic through rapidly
• MPs are homologs of proteins that naturally
traffic mRNAs between cells
• MPs may act as suppressors of gene silencing
66. Plant cells are bound by rigid cell walls and are interconnected
by plasmodesmata, which are too small to allow passage of
whole virus particles.
Plasmodesma
67.
68.
69. Understanding
virus infection
and movement
through plants
requires
understanding
architecture of
dicotyledonous
plants and the
connections
between
different cell
types.
This has been
studied
extensively with
GFP-labeled
virus
70. Some plant viruses radically modify plasmodesmata,
allowing for cell-to-cell movement as whole particles
72. Plant Virus Transmission
• Generally, viruses must enter plant through
healable wounds - they do not enter through
natural openings (no receptors)
• Insect vectors are most important means of
natural spread
• Type of transmission or vector relationship
determines epidemiology
• Seed transmission is relatively common, but
specific for virus and plant
73. Plant Virus Transmission
• Mechanical transmission
– Deliberate – rub-inoculation
– Field – farm tools, etc.
– Greenhouse – cutting tools, plant handling
– Some viruses transmitted only by
mechanical means, others cannot be
transmitted mechanically
74. • Transmission by vectors: general
– Arthropods most important
– Most by insects with sucking mouthparts
• Aphids most important, and most studied
• Leafhoppers next most important
– Some by insects with biting mouthparts
– Nematodes are important vectors
– “Fungi” (protists) may transmit soilborne viruses
– Life cycle of vector and virus/vector relationships
determine virus epidemiology
– A given virus species generally has only a single
type of vector
Plant Virus Transmission by Vectors
75. • Insect transmission (vectors)
– Aphids most important
– Leafhoppers
– Whiteflies
– Thrips
– Mealybugs
– Beetles
– Mites (Arachnidae)
– Ants, grasshoppers, etc. – mechanical
– Bees, other pollinators – pollen transmission
76. Types of vector relationships
Terms apply mainly, but not exclusively, to
aphid transmission
• Non-persistent transmission
– virus acquired quickly, retained short
period (hours), transmitted quickly
– “stylet-borne” transmission
– virus acquired and transmitted during
exploratory probes to epidermis
77. Types of vector relationships
• Persistent transmission
– virus acquired slowly, retained long period
(weeks), transmitted slowly
– circulative or propagative transmission
– virus acquired and transmitted during
feeding probes to phloem
78. Types of vector relationships
• Semi-persistent transmission
– virus acquired fairly quickly, retained
moderate period (days), transmitted fairly
quickly
– virus acquired and transmitted during
exploratory probes
79. Brome mosaic virus
• Relatively little studied prior to 1980
• Relatively narrow host range
• Causes no important disease
• Mechanically transmitted, probably not
vectored
• Similar to Alfalfa mosaic virus and
Cucumber mosaic virus, two important plant
pathogens
• Now most thoroughly understood plant virus
at RNA level
80. BMV structure
• Rigid isometric particles 27 nm
• RNA1 (3.2 kb) and RNA2 (2.9 kb)
packaged alone; RNA3 (2.1 kb) and
RNA4 (1.2 kb) packaged together
• Particle is held together primarily by
protein/RNA interactions
• With RNA, 180-subunit, T=3
particles predominate; without RNA,
120-subunit, T=1, particles
81. Brome mosaic virus genome organization
• 3 genomic RNAs, one
subgenomic RNA
• Only RNAs 1 and 2
required for replication in
protoplasts
• 3’-terminal 200 bases of
segments nearly identical
• All three genomic and
subgenomic RNA are
capped
• Non-templated C and A at
3’-ends
Capping Helicase
Polymerase
Movement Capsid
82. Why is BMV such a powerful system
• 3 RNAs
– only 1 and 2 required for replication
– RNAs can be studied independently
• All three promoter types (+, -, sg) found on RNA
3, which is not required for infection
• Replication is fast in plant protoplasts
• Infects monocot and dicot host plants
• Replicates in yeast, best eukaryotic genetic
system
• Efficient transcriptase/replicase complex has
been isolated for in vitro studies
• Structurally stable particles allow for
encapsidation studies
83. Brome mosaic virus contributions
• 1980
– studies of 3’-terminal pseudoknot (Ahlquist/Kaesburg)
• 1984
– complete BMV sequence (Ahlquist/Kaesburg)
– 3’-terminal replicase recognition site (- strand
promoter) identified (Ahlquist/Hall)
– Nonstructural proteins of BMV, TMV, and alfaviruses
are similar (Haseloff; also Ahlquist)
– First infectious transcripts from a cloned RNA virus
genome (Ahlquist)
• 1985
– Continued dissection of 3’-end functions
84. Brome mosaic virus contributions
• 1986
– CAT gene substituted for CP (French/Ahlquist)
• 1987
– Requirement of intercistronic region of RNA 3 for
replication (French/Ahlquist)
• 1988
– Identification of subgenomic RNA promoter
(French/Ahlquist)
• 1990
– Rescue of CCMV deletion mutants by recombination
(Allison/Ahlquist)
85. Brome mosaic virus contributions
• 1992
– Determination of 5’-terminal sequences involved in transcription
and replication (+ strand promoter (Pogue/Hall)
– TMV movement protein can substitute for BMV MP
(DeJong/Ahlquist)
• 1993
– BMV replication in yeast (Janda/Ahlquist)
– BMV transcription and replication requires compatibility between
polymerase and helicase proteins (Dinant/Ahlquist)
• 1994
– Recombination between viral RNA and transgenic plant transcripts
(Green/Allison)
• 1995
– Formation of RdRp in yeast requires coexpression of RNA 1 and 2
proteins (Quadt/Ahlquist)
86. Brome mosaic virus contributions
• 1997
– Inducible expression of active RNA 3 replicons in yeast from DNA
plasmids (Ishjkawa/Ahlquist)
– Yeast mutations in multiple complementation groups inhibit BMV
RNA replication and transcription (Ishjkawa/Ahlquist)
• 1998
– Specific residues critical for recognition of the 33 nt subgenomic
RNA promoter by the BMV RdRp identified, demonstrating
functional homology of RNA and DNA promoters (Siegel/Kao)
• 1999
– BMV 1a protein functions in in vitro, in yeast, and in plants in
methylation of GTP and cap analogs (Ahola/Ahlquist; Kong/Kao)
– BMV RdRp can use RNA, DNA, or hybrid to initiate RNA
synthesis, suggesting that transition from RNA to DNA world may
have been relatively easy (Siegel/Kao)
87. Brome mosaic virus contributions
• 2000
– Host protein associated with efficient RNA template
selection identified (Diez/Ahlquist)
– BMV protein 2a (RdRp) is directed to ER by
capping/helicase-like 1a protein (Chen/Ahlquist)
• 2001
– Factors regulating template switching during RNA
synthesis by viral RdRps identified using in vitro
assays (Kiml/Kao)
• 2002
– 3’-terminal tRNA-like structure of BMV RNAs mediate
particle assembly (Choi/Dreher/Rao)
– Crystallographic structure of BMV solved
(Lucas/McPherson)
88. Brome mosaic virus contributions
• 2003
– The BMV 3’-terminal core promoter element, stem-loop
C (SLC), functions at different positions on the
template, can initiate RNA synthesis internally, and can
potentiate RNA synthesis from a cellular tRNA
template (Ranjith-Kumarl/Kao)
– Systematic, genome-wide identification of host genes
affecting replication of BMV (Kushner/Ahlquist)
• 2004
– Two distinct types of homologous RNA recombination
in BMV replication (Bujarski)
• 2005
– Gold nanoparticles encapsidated in BMV coat protein
form normal, solid particles (Rao)
89. Some major BMV contributors
• Ahlquist – most prolific, many aspects
• Hall – Cis-acting RNA elements
• Dreher – 3’-terminal structure
• Kao – recent dissection of cis-acting RNA
elements
• Bujarski – Intra-strand and inter-strand RNA
recombination
• Rao – RNA packaging
90. BMV promoters for + strand RNA synthesis
• Promoter sequence for
genome-length plus strand
synthesis is on 3’-end of
minus strand; corresponding
sequences on plus strand are
important for efficient
transcription
• 5’-terminal regions are less
highly conserved than 3’-
terminal regions
• Internal poly(A) tract of
variable length precedes
subgenomic promoter and is
required for efficient sgRNA
transcription
• Core promoter elements
91. Three classes of 3’ termini among + sense RNA viruses
TLS = tRNA-like structure
Het = Heteropolymeric, non-tRNA-
like sequence
An = poly(A) tail
A. Full phylogeny, Supergroups 1-3
B. Supergroup 3
From Dreher 1999, Annu. Rev. Phytopathol. 37: 151-174
Type of 3’-terminal structure
cannot be predicted based on
polymerase phylogeny alone,
supporting the role of interviral
recombination in selection of 3’-
end.
92. Brome mosaic virus 3’-terminal tRNA-like
structure is a multifunctional domain
• Promoter for – strand RNA
synthesis
• RNA protection against
nuclease
• Can be charged with
tyrosine in vitro and in vivo
• (ATP, CTP) tRNA
nucleotidyl transferase
adds terminal C and A
residues
• Involved in RNA packaging
into virions – intact tRNA-
like fold is required
• Relatively little involvement
of 3-end of BMV RNA in
translation regulation
94. Brome mosaic virus replication
• 1a protein (capping &
helicase) localizes to ER
• 1a protein recruits 2a
protein (RdRp) during
active translation of 2a
• Viral RNA templates are
recruited to nascent
replication complex by
1a protein
• RNA replication occurs
in membrane-bound,
capsid-like spherules
95. Identification of host genes involved in BMV
replication (Kushner/Ahlquist 2003, PNAS 100:15764)
• Used yeast – genetics
easy, many mutants
available
• Provides information
about replication, not
systemic infection
• Transform with
inducible two plasmid
system requiring
replication for reporter
gene expression
• Screen for replication-
associated genes by
monitoring luciferase
expression
• 4500 yeast mutants examined
(~80% or yeast genes)
• ~100 yeast genes whose deletion
altered BMV-directed expression
of luciferase by > 3 fold
96. Identification of host genes involved in BMV
replication (Kushner/Ahlquist 2003, PNAS 100:15764)
• Mutants that were positive in the luciferase screen were
examined further by northern and western blot
98. Comparative properties of BMV and TBSV
• TBSV
– A T=3 icosahedral virus with a 40
kDa capsid subunit and monopartite
RNA genome of 5 kb
– RdRp supergroup 2
– No known helicase domain
– 5’ end of RNA uncapped; 3’ end has
no poly(A) or tRNA-like structure
– Expression of 5 gene products via
cap-independent translation (1)
readthrough (1), subgenomic RNAs
(2), and internal initiation (1)
– Defective-interfering (DI) RNAs
replicate to high levels in permissive
plant host; equally high in yeast
• BMV
– A T=3 icosahedral virus with a 20
kDa capsid protein subunit and
tripartite RNA genome of 8 kb
– RdRp supergroup 3
– No known helicase domain
– 5’ end of RNA capped; 3’ end has
tRNA-like structure aminoacylated
with tyrosine
– Expression of 4 gene products via
normal cap-dependent translation
(3) and subgenomic RNA (1)
– Defective-interfering (DI) RNAs
present, not prevalent
100. Yeast genome-wide screen reveals dissimilar sets of
host genes affecting replication of RNA viruses
Tadas Panavas, Elena Serviene, Jeremy Brasher, and Peter D. Nagy*
2005 PNAS 102:7326-7331
• Replication of both BMV and TBSV is suppressed in about 100
out of 4,800 yeast knock-out mutants (YKOs)
• Of those 100 mutants, only 4 were common between the two
viruses: three genes involved in protein metabolism (ubiquitin
pathway), and the fourth a transcription regulator
• Another 10 mutants affecting replication of one or the other
viruses represented genes with known functions in common.
These were involved in: i) protein biosynthesis; ii) protein
metabolism; iii) transcription/DNA remodeling
• Genes involved in protein targeting, membrane association,
vesicle transport, and lipid metabolism affect TBSV, but none in
BMV
102. Viroids
• Very small, covalently closed, circular RNA molecules
capable of autonomous replication and induction of
disease
• Sizes range from 250-450 nucleotides
• No coding capacity - do not program their own
polymerase
• Use host-encoded polymerase for replication
• Mechanically transmitted; often seed transmitted
• More than 40 viroid species and many variants have
been characterized
• “Classical” viroids have been found only in plants
103. Viroids are divided into two groups, based on site and
details of replication
104. Viroid Diseases
• Potato spindle tuber
viroid (PSTVd)
– May be limiting to potato
growers
– First viroid characterized
– Many variants described
– Control with detection in
mother stock, clean seed
PSTVd in tomato
PSTVd in potato
105. Viroid Diseases
• Citrus exocortis viroid (CEVd)
– Causes stunting of plants,
shelling of bark
– May result in little yield loss
– May be useful to promote
dwarfing for agronomic
advantage
– Transmitted though stock, graft
– Control by removal of infected
plants, detection, clean stock
Citrus exocortis viroid
106. Apple crinkle fruit viroid Avocado sun blotch viroid
Citrus exocortis viroid
Healthy Infected
107. Potato spindle tuber viroid (PSTVd) is the most
thoroughly characterized viroid disease
(From R. Owens, USDA, Beltsville)
108. Viroid structures
-All are covalently closed circular RNAs fold to tightly base-paired structures
-Two main groups of viroids: self-cleaving and non-self-cleaving
-Non-self cleaving viroids replicate in nucleus and fold into “dog bone” or rod-like
structure
-Five domains identifiable in non-self-cleaving
-Left hand (LH) and right hand (RH) domains are non-base-paired loops
-Single mutations to pathogenic domain often alter virulence
-Mutations to conserved central domain are often lethal
-Mutations to variable domain are often permitted
109. Minor variations in viroid sequence, and presumably attendant
RNA structure changes, are associated with virulence differences
(From R. Owens, USDA, Beltsville)
110. Viroid replication
• In nucleus or chloroplasts, depending on class of viroid
• Chloroplast-associated viroids process into monomers by
ribozyme-mediated cleavage; nucleus-associated viroids
process into monomers by using host-derived enzyme
• In both classes, host DNA-dependent RNA polymerase is
the performs RNA polymerization on + and – strand RNA
templates
Ribozyme-mediated Cleavage by host-factor
RZ RZ
RZ RZ HF HF
111. Viroid movement
• Traffic within cell
through nuclear
pores using VirP1, a
nuclear localization
protein that binds
viroid RNA
• Traffic cell-to-cell
through
plasmodesmata
• Traffic long distance
through phloem
• All of these
processes are
associated with host
proteins
112. + and – viroid strands are differentially localized
within the nucleus
• Viroid strands of + polarity localized to nucleolus, as well
as nucleoplasm
• Viroid strands of - polarity localized to only to nucleoplasm
Qi and Bing, 2003, Plant Cell 15:2566
113. Hepatitis delta
• Hepatitis delta virus has many viroid-like properties, but
the RNA is larger (1.7 kb), is encapsidated, and encodes a
virion-associated protein (hepatitis delta antigen)
• Intensifies HBV infection
• HDV requires HBV as helper virus for encapsidation, so it
has satellite-like properties (like a “virusoid”)
• Replicates in nucleus via cellular DNA-dependent RNA
polymerase II