Microbial Genetics and Biotechnology

Chapter 8 - Microbial Genetics Terminology

• Genetics: Study of genes and the method by which traits are passed on.
• Gene: A piece of DNA that provides instructions for making a protein.
• Chromosomes: Long strands of DNA containing many genes.
• Genome: The complete set of DNA in an organism.
• Genomics: The study of whole genomes.
• Genotype: The genetic composition of an organism (the specific genes an individual has).
• Phenotype: The observable physical traits of an organism.

History of Microbial Genetics

1. Johannes Miescher (1869)
   • First to discover DNA.
2. Rosalind Franklin
   • Conducted X-ray diffraction studies to reveal the shape of DNA.
3. James Watson and Francis Crick (1953)
   • Utilized Franklin’s findings to elucidate the double helix structure of DNA.
4. Human Genome Project (1990 to 2003)
   • Mapped over 3 billion DNA bases in the human genome.

Sequencing a Fragment of DNA

• Method used to determine the order of nucleotides (A, T, C, G) within a segment of DNA.
• Base pairing rules:
  • Adenine (A) pairs with Thymine (T).
  • Cytosine (C) pairs with Guanine (G).
• In RNA, the rules change slightly:
  • A pairs with Uracil (U) instead of Thymine.
  • C still pairs with G,
  • T pairs with A.

DNA Replication Components

1. Topoisomerase or DNA Gyrase: Unwinds the DNA to alleviate twisting.
2. DNA Helicase: Unzips DNA strands to allow replication.
3. Replication Fork: The Y-shaped region indicating where DNA replication is occurring.
4. Primase: Synthesizes the RNA primer necessary for DNA replication.
5. RNA Primer: The starting point for DNA polymerase to begin DNA synthesis.
6. DNA Polymerase: Enzyme responsible for building the new DNA strand.
7. DNA Ligase: Enzyme that joins DNA fragments together.
8. 5' and 3' Ends: Indicates the directionality; new strands grow from 5' to 3'.
9. Leading Strand: The DNA strand that is synthesized continuously.
10. Lagging Strand: Synthesized in pieces (Okazaki fragments).
11. Okazaki Fragments: Short sections of DNA formed on the lagging strand during replication.
12. New Strand: The strand of DNA being synthesized during replication.
13. Template Strand: The original DNA strand being copied.

The DNA Replication Process

• Steps involved in DNA Replication:
  1. DNA unwinds with the help of helicase.
  2. Primase adds an RNA primer to initiate replication.
  3. DNA Polymerase synthesizes the new strand:
     • On the leading strand, DNA is made as a continuous piece.
     • On the lagging strand, it is made in short pieces (Okazaki fragments).
  4. DNA ligase seals the gaps between the Okazaki fragments.
  5. The process results in two identical DNA molecules.

Transcription (DNA to mRNA)

• mRNA: A messenger RNA that is a copy of the DNA.
• RNA Polymerase: The enzyme that synthesizes mRNA from the DNA template.
• Promoter: A sequence of DNA that indicates where transcription should start.
• Terminator: A sequence that signals where transcription ends.

Transcription Steps

1. RNA polymerase binds to the promoter.
2. The enzyme unwinds the DNA and synthesizes mRNA using one strand of the DNA as a template.
3. Transcription continues until terminating at the terminator.
4. The newly formed mRNA exits the nucleus (in eukaryotic cells).

RNA Processing (Eukaryotes Only)

• RNA Transcript: The initial raw mRNA strand.
• Exons: Portions of the mRNA that are retained and used to code for proteins.
• Introns: Non-coding segments that are removed during RNA processing.
• snRNPs (small nuclear ribonucleoproteins): Complexes of proteins and RNA that cut and splice exons together.

RNA Processing Steps

1. Introns are cut out from the RNA transcript.
2. Exons are glued together to form the final mRNA.
3. A protective cap and tail are added to the mRNA.
4. The processed mRNA leaves the nucleus to participate in translation.

Degeneracy of the Genetic Code

• Some amino acids are encoded by more than one codon.
• Example: AUG is a start codon that encodes Methionine in eukaryotes and Formylmethionine in bacteria.

Translation Process (mRNA to Protein)

• The process through which ribosomes synthesize proteins based on mRNA sequences:
• The ribosome reads the mRNA sequence.
• Transfer RNA (tRNA) molecules transport amino acids to the ribosome.
• Codons on the mRNA match with anticodons on the tRNA.
• Amino acids are joined together to form a polypeptide chain, resulting in a protein.

Gene Regulation in Bacteria

1. Jacob and Monod - Lac Operon (1961): Founding description of the operon system in genetic regulation in bacteria.
2. Operon Structure:
   • Promoter (P): Location where RNA polymerase begins transcription.
   • Operator (O): Regulatory switch that can turn transcription on or off.
   • Structural Genes: Genes that encode proteins involved in a common metabolic pathway.
   • Regulatory Gene (I): Gene that codes for a repressor protein.
3. Repressor Protein:
   • When inactive, allows transcription (induction).
   • When active, halts transcription.
4. Constitutive Genes: 60 to 80% of genes expressed continuously regardless of the environmental conditions.
5. Control of mRNA Production: Determines the synthesis of proteins, such as enzymes for lactose metabolism.

Regulation of Gene Expression

1. Bacteria prioritize glucose over lactose for energy use.
2. The lac operon is turned off when glucose is present; it turns on in the presence of lactose when glucose is scarce.
3. cAMP (cyclic AMP): Levels rise when glucose levels are low, aiding in the activation of the lac operon.
4. CAP (Catabolite Activator Protein): Works alongside cAMP to facilitate transcription by promoting RNA polymerase action.

Cyclic AMP and Gene Expression Regulation

1. Conditions: Lactose present, glucose scarce:
   • High cAMP activates CAP, which enhances the lac operon leading to mRNA production necessary for lactose digestion.
2. Conditions: Lactose and glucose both present:
   • Low cAMP means CAP cannot stimulate transcription; thus, lactose metabolism is inhibited.

Epigenetic Control of Gene Expression

1. DNA Methylation: Mechanism occurring in both prokaryotes and eukaryotes that silences specific genes.
2. This process can be transferred to progeny and may exhibit flexibility, allowing genes to be turned back on, but is not permanent.

Mutations

1. Spontaneous Mutations: Random errors that occur at a frequency of approximately 1 in 10 billion bases.
2. Mutagen: Any factor that can induce mutations, including chemicals and radiation.
3. Base Substitution: A mutation that changes one DNA nucleotide for another.
4. Frame Shift Mutation: Involves the insertion or deletion of nucleotides, resulting in a shift in the reading frame.
5. Typical Chain of Events (Central Dogma):
   • DNA → mRNA → Protein → Function.

Mutation Examples

1. Base Substitution:
   • Sickle Cell Anemia: A genetic disorder caused by a single nucleotide substitution that leads to abnormal hemoglobin.
   • Thalassemia: A condition leading to the inadequate production of hemoglobin due to mutations.
2. Consequences of Sickle Cell Disease:
   • Clumping of Blood Cells: Results in various circulatory issues and damage to organs such as the brain and lungs.
   • Symptoms: Heart failure, paralysis, pneumonia, and other serious health issues.
3. Spleen Interactions:
   • Concentrates sickle cells in the spleen, leading to splenomegaly and immunocompromised status.
   • Rapid destruction of sickle cells leads to anemia (weakness, fatigue, development issues).
4. Frame Shift Mutation Examples:
   • Huntington’s Disease: An inherited condition that leads to brain nerve cell degeneration.
   • Cystic Fibrosis: Causes thick mucus in various organs, leading to function impairment.

Mutagens

1. Nucleoside Analogs: Molecules resembling DNA bases but pairing incorrectly during replication.
2. Nitrous Acid: A chemical that modifies base pairings, altering their interactions:
   • Normal adenine becomes altered and pairs with cytosine instead of thymine.
   • Results in the transmission of mutations through generations.

Radiation as a Mutagen

1. Types of Radiation:
   • Ionizing Radiation: X-rays and gamma rays cause breakage of DNA and formation of free radicals.
   • Non-ionizing Radiation: UV light induces the formation of thymine dimers.
2. Repair Mechanisms:
   • Light Repair Mechanism: Involves photolyase, which repairs thymine dimers caused by UV exposure.
   • Excision Repair Mechanism:
     • Endonuclease: Cuts out damaged portions of DNA;
     • Exonuclease: Removes damaged DNA;
     • DNA Polymerase: Synthesizes new DNA to fill in gaps;
     • DNA Ligase: Seals the repaired strand.

Ames Test for Identifying Carcinogens

• Utilizes mutant bacteria that require histidine for growth. If a chemical agent causes mutations, the bacteria will grow in its absence, indicating the chemical is likely a carcinogen.

Identifying Mutants (Auxotrophs)

1. Positive Selection (Direct): Only mutants grow (e.g., antibiotic resistance).
2. Negative Selection (Indirect): Mutants identified by inability to grow under certain conditions; utilizes replica plating techniques.

Horizontal Genetic Transfer in Bacteria

1. Frederick Griffith (1928): Pioneered studies on genetic transformation in bacteria.
2. Methods of Genetic Transfer:
   • Transformation: Uptake of free DNA from dead cell remains.
   • Conjugation: DNA is transferred from one bacterium to another through a pilus.
   • Transduction: Viruses (bacteriophages) mediate DNA transfer between bacteria.
3. Transposons: Segments of DNA that can move within the genome, transferring traits such as antibiotic resistance.
   • Ranging in size from approximately 700 to 40,000 base pairs.
   • Example: Vancomycin resistance gene transferred from Enterococcus faecalis to Staphylococcus aureus.

Chapter 9 - Biotechnology

Biotechnology and Recombinant DNA

1. Biotechnology: The use of living organisms to create useful products.
2. Recombinant DNA: DNA that has been artificially created by combining DNA from different organisms.

Agrobacterium tumefaciens (Crown Gall Disease)

1. Infects plants using the Ti plasmid (tumor-inducing plasmid) which is instrumental in the genetic engineering of plants.
2. Restriction Enzymes: Bacterial enzymes that act as molecular scissors, cutting DNA at specific sequences:
   • Examples include BamHI, EcoRI, HaeIII, HindIII.

Genetic Modification in Plants (Using Ti Plasmid)

1. The Ti plasmid is used to insert new genes into plant cells, providing traits such as pest resistance.

Methods of DNA Insertion into Cells

1. Protoplast Fusion: Two plant cells without cell walls fuse to combine DNA.
2. Gene Gun: Shoots DNA-coated particles into plant cells for insertion.
3. Microinjection: Injects DNA molecules directly into animal cells using a fine needle.
4. Transformation: Soaking cells in calcium chloride and exposing them to heat-shock facilitates DNA entry.
5. Electroporation: Applying an electric pulse opens the pores in the cell membrane, allowing DNA entry.

Vectors in Genetic Engineering

1. Function: Vectors are designed to deliver foreign DNA into host cells.
2. Types:
   • Plasmids: Small circular DNA molecules.
   • Viruses: Infectious agents that can integrate DNA into host cells.

Cloning and Genomic Libraries

1. Clone: A genetically identical copy of DNA, a cell, or an organism.
2. Genomic Libraries: Collections of DNA from an organism:
   • Created by cutting DNA into pieces with restriction enzymes and inserting them into vectors that enter host cells.
   • Types include plasmid libraries and phage libraries.

Applications of Genetic Engineering

1. Inserting genes that code for pest resistance into plant cells.
2. Inserting genes encoding degradative enzymes into bacterial cells for environmental use (e.g., cleaning up toxic waste).
3. Producing enzymes such as amylase and cellulase for industrial applications (e.g., fabric preparation).
4. Synthesis of human growth hormone to treat growth disorders.

Producing Gene Products

1. E. coli:
   • Model organism for production: rapidly grown, well-characterized but poorly folds proteins.
2. Saccharomyces cerevisiae (Yeast):
   • Easily cultured, larger genome than bacteria, efficiently expresses eukaryotic genes.
3. **Plant Cells & Whole Plants: **
   • Efficiently express eukaryotic genes and can be produced on a large scale economically.
4. Mammalian Cells:
   • Best for producing human proteins; however, they are more challenging and costly to culture.

Subunit Vaccines

• Clinical details to be rewritten.

Genetically Modified Humans

1. Over 15,000 serious genetic disorders exist.
2. Gene Therapy: Method of treating genetic defects or disorders through transfer of normal or modified genes into individuals.
3. **Steps: **
   1. Incorporate the healthy gene into a viral vector.
   2. Remove bone marrow stem cells from the patient.
   3. Infect the stem cells with the viral vector.
   4. Return the modified stem cells back to the patient.
   5. The gene is expressed, producing the necessary protein.

Case Study: David Vetter

• A boy with a severe immune disorder who lived in a sterile environment (bubble boy) showcasing the potential of gene therapy.

Unpredictable Outcomes (Risks)

1. Inserting a gene into the wrong genomic location could disrupt normal functions and potentially induce cancer.
2. Severe allergic reactions to viral vectors may result in fatal consequences.

CRISPR-Cas9 Gene Editing Tool

1. Acts as DNA scissors targeting and cutting specific genes.
2. Applications include:
   • Repairing defective genes such as those causing muscular dystrophy in mice.
   • Approved clinical trials in 2016 for modifying T-cells against cancer.
3. Mechanism of CRISPR:
   • Cas9 protein forms a complex with guide RNA in the cell.
   • The complex binds to a matching sequence of DNA and cuts it.
   • This cutting process allows for programmed DNA insertion at the targeted location.

RNA Interference Technology - Gene Silencing

1. siRNA (Small Interfering RNAs):
   • Play a role in silencing specific genes, naturally found in eukaryotes as a response to transposon activity and viral attacks.
2. Steps for silencing:
   • Dicer enzyme cuts double-stranded RNA into siRNA.
   • siRNA binds to mRNA for degradation.
3. Applications:
   • Gene therapy employing siRNA insert linked to a gene of interest in a plasmid leading to gene silencing.

DNA Fingerprinting

1. Approximately 99% of a person's DNA is shared among all humans.
2. Unique patterns arise from the distribution of Short Tandem Repeats (STRs) present in the DNA among individuals.
3. RFLP (Restriction Fragment Length Polymorphism): Technique using restriction enzymes to compare genetic differences by analyzing the lengths of DNA fragments.
4. Applications of RFLP:
   • Identification of pathogens.
   • Tracing sources of foodborne disease outbreaks.

Forensic Microbiology

1. Genetic fingerprinting techniques assist in the identification of pathogens related to STDs in legal evidence cases.
2. Individual microbiome patterns can serve as unique identifiers.

Nanotechnology in Microbiology

1. Deployment of nanoscale technologies for detecting:
   • Food contamination.
   • Plant disease.
   • Biological threats.
2. Certain bacteria synthesize nanoparticles from various elements including gold, silver, selenium, and cadmium.
3. Medical applications arise from utilizing bacteria-produced nanospheres for targeted drug delivery.
4. Acetobacter xylinium: Used to produce cellulose nanofibers applicable in artificial blood vessel manufacturing.

Chapter 12 - Protozoa, Algae, Fungi, Helminths, and Disease

Mycology (Study of Fungi)

1. Kingdom: Fungi
2. Domain: Eukarya
3. Characteristics of Fungi:
   • Saprophytic organisms acting as decomposers that break down organic matter.
   • Fungi can withstand osmotic pressure.
   • Thrive in low moisture environments.

Comparison: Fungi vs. Bacteria

• Fungi:

  • Cell Type: Eukaryotic
  • Cell Membrane: Contains sterols.
  • Cell Wall Composition: Composed of glucans, mannas, and chitin.
  • Types of Spores: Both sexual and asexual spores are formed.
  • Metabolism: Heterotrophic, limited to decomposing organic materials, and facultative anaerobic.

• Bacteria:

  • Cell Type: Prokaryotic.
  • Cell Membrane: No sterols (exceptions in Mycoplasma).
  • Cell Wall Composition: Mainly made of peptidoglycan.
  • Types of Spores: Include endospores and some asexual reproductive spores.
  • Metabolism: Heterotrophic and autotrophic, capable of aerobic, anaerobic, and facultative anaerobic processes.

Structures of Fungi

1. Hyphae: Thread-like structures that compose molds.
   • Two types:
     • Septate Hyphae: Contain dividing cross walls.
     • Coenocytic Hyphae: No cross walls present, allowing for a continuous cytoplasm.
2. Dimorphism in Fungi: Some fungi exhibit two forms depending on temperature conditions:
   • Yeast-like form at 37°C.
   • Mold-like form at 25°C.

Fungal Groups

Economic Effects of Fungi

Types of Fungal Diseases (Mycoses)

1. Systemic Mycoses: Occurs deep within the body (lungs, bloodstream).
2. Subcutaneous Mycoses: Affects tissues beneath the skin.
3. Cutaneous Mycoses: Involves skin, hair, and nails (e.g., dermatophytes).
4. Superficial Mycoses: Limited to the surface of the skin or hair.
5. Opportunistic Mycoses: Typically precipitated in individuals with weakened immune systems.

Algae

1. Kingdom: Protista
2. Domain: Eukarya
3. Characteristics of Algae:
   • Can be unicellular, filamentous, or multicellular.
   • Mostly photoautotrophic, utilizing sunlight for energy.
4. Reproductive Methods:
   • Sexual reproduction via conjugation and gamete formation.
   • Asexual reproduction through spores, fragmentation, and binary fission.

Algal Groups

Algal Blooms

1. Definition: Overgrowth of algae in aquatic environments.
2. Consequences: Can deplete available oxygen and release harmful toxins into the environment.

Protozoa

1. Kingdom: Protista.
2. Domain: Eukarya.
3. Characteristics of Protozoa:
   • Unicellular organisms.
   • Feature a flexible outer membrane called the pellicle.
   • Exhibit two forms: Trophozoite (active feeding form) and Cyst (dormant form).
   • Habitat predominantly in water and soil.
4. Reproductive Methods:
   • Sexual reproduction through conjugation and gamete formation.
   • Asexual reproduction through fission, budding, and multiple fission (schizogony).

Helminths

1. Kingdom: Animalia.
2. Domain: Eukarya.
3. Phylum 1: Platyhelminthes (Flatworms): a. Flat structural form with no internal body cavity. b. Two classes:
   • Trematodes (Flukes): Leaf-shaped, absorb nutrients through a cuticle.
   • Cestodes (Tapeworms): Long and ribbon-like, inhabiting the intestines, lacking a digestive system.
4. Phylum 2: Nematodes (Roundworms):
   a. Cylindrical body form.
   b. Possessing a complete digestive system.

Vectors

1. Biological Vectors: Organisms in which pathogens reproduce.
2. Mechanical Vectors: Organisms that merely carry pathogens without reproduction.

Chapter 13 - Viruses and Viral Infection

Viruses

1. Defined as obligatory intracellular parasites requiring a host cell for reproduction.
2. Composed of single or double-stranded DNA or RNA (never both).
3. Enclosed by a capsid, which is a protein coat made of capsomeres.
4. May possess an envelope, a membrane-like layer that contains spikes for attachment to host cells.
5. Size Range: 20 to 1000 nm in length.

Comparison: Viruses vs. Bacteria

Size Comparison of Various Viruses

1. Bacteriophage f2, MS2: 24 nm
2. Poliovirus: 30 nm
3. Rhinovirus: 30 nm
4. Adenovirus: 90 nm
5. Rabies Virus: 170 x 70 nm
6. Prion: 200 x 20 nm
7. Bacteriophage T4: 225 nm
8. Tobacco Mosaic Virus: 250 x 18 nm
9. Viroid: 300 to 10 nm
10. Vaccinia Virus: 300 x 200 x 100 nm
11. Bacteriophage M13: 800 x 10 nm
12. Ebola Virus: 970 nm
13. Chlamydia Bacteria: 300 nm
14. E. coli: 3000 x 1000 nm
15. Human Red Blood Cell: 10,000 nm in diameter, with a plasma membrane thickness of 10 nm.

Historical Context

1. Adolf Mayer (1886): Discovered a plant disease caused by an infectious agent.
2. Dimitri Ivanowski (1892): Demonstrated that this agent could pass through a filter.
3. Martinus Willem Beijerinck (1898): Coined the term “contagious living fluid.”
4. Wendell Stanley: Isolated the tobacco mosaic virus; a landmark revelation highlighting the dual nature of viruses (living and non-living characteristics).

Viral Taxonomy

1. Genus Names: Typically end with -virus.
2. Family Names: End with -viridae.
3. Order Names: End with -ales.
4. Viral Species: Defined groups sharing genetic information and hosts, often described with common names and numbered subspecies.
   • Example: Family: Herpesviridae; Genus: Simplexvirus; Species: Human Herpesvirus 1.
   • Example: Family: Retroviridae; Genus: Lentivirus; Species: Human Immunodeficiency Virus 1.

Viral Morphology

1. Helical: Spiral-shaped viruses.
2. Polyhedral: Many-sided viruses reminiscent of a soccer ball.
3. Complex Viruses:
   • Examples include:
     • T Even Bacteriophage: Exhibits a head and tail structure.
     • Orthopoxvirus: Shaped like a brick.

Propagating Viruses

• Steps Involved:
  1. Tissue treated with enzymes to separate cells.
  2. Cells are suspended in culture medium.
  3. Normal (primary) cells grow in monolayers; transformed (continuous) cells can grow in multiple layers.

Cystopathic Effects of Viruses

• Characterization:
  1. Altered morphology: Viruses may change cell shape.
  2. Virus-specific antigens appear within the host cell.
  3. Loss of contact inhibition: Infected cells may pile up.
  4. Chromosomal abnormalities may occur.

Viral Terminology

1. Virion: Complete virus particle outside a host cell ready for infection.
2. Prophage: Form of viral DNA integrated into a bacterial genome, remaining dormant until conditions trigger its activation.

Lytic Cycle of T Even Bacteriophage

1. Attachment: The phage binds to a host bacterial cell.
2. Penetration: The phage injects its DNA into the bacterium.
3. Biosynthesis: The bacterial cellular machinery assembles new viral components as directed by phage DNA.
4. Maturation: New virions are assembled within the host cell.
5. Release: The host cell lyses, releasing new virions to infect additional cells.

Lysogenic Cycle of Bacteriophage Lambda

1. Can alternate between lytic and lysogenic cycles, only killing the bacterial cell during the lytic phase.
2. Phage Conversion: Virus DNA integration can bestow new traits, such as toxin production, to the bacterial cell.
3. Steps:
   • Phage binds to cell and injects DNA, which circularizes.
   • Path A (Lytic Cycle): Viral components assemble and trigger cell lysis.
   • Path B (Lysogenic Cycle): Phage DNA integrates into the host chromosome, becoming a prophage, which replicates with the host genomic DNA.
   • Stress-Induced Excision: Triggers the prophage to exit the chromosome and shift back to the lytic cycle.

Specialized Transduction (Horizontal Gene Transfer)

1. Occurs when a prophage carries a gal gene from its host into a new bacterial cell.
2. When the new host lacks the gal gene, it can integrate the gene along with the prophage’s genetic material, thus gaining the ability to metabolize galactose.

Animal Virus Multiplication (General)

1. Stages:
   1. Attachment to the host cell.
   2. Entry via endocytosis or fusion.
   3. Uncoating occurs, whereby the viral nucleic acids are released.
   4. Biosynthesis: Production of viral proteins and nucleic acids.
   5. Maturation: Newly formed virions are assembled.
   6. Release: Depends on type:
      • Budding (enveloped viruses): Virus acquires membrane components from the host.
      • Cell Rupture (naked viruses): Leads to cell death.

DNA-Containing Virus Multiplication

1. Phases:
   1. Attachment to the host cell.
   2. Entry and uncoating.
   3. Initial transcription creates early mRNA for viral proteins.
   4. Biosynthesis: Complete replication of viral DNA.
      • Late translation occurs to produce capsid proteins.
   5. Maturation of virions.
   6. Release of mature virions.

RNA Viruses: Types and Processes

1. ssRNA (+ sense strand): Viral RNA acts directly as mRNA for protein synthesis.
2. ssRNA (- antisense strand): Must convert its RNA into a (+ strand) to serve as mRNA for protein synthesis.
3. dsRNA: Contains both - and + strands of RNA.

Retrovirus Multiplication: HIV Example

1. Retroviruses utilize reverse transcriptase for DNA synthesis:
   1. Retrovirus attaches to host cell and enters through fusion.
   2. Virus uncoats, releasing two RNA strands and enzymes (reverse transcriptase, integrase, protease).
   3. Reverse transcriptase synthesizes DNA from the viral RNA.
   4. New viral DNA integrates into the host's chromosome as a provirus by integrase.
   5. Provirus replication occurs when host cell undergoes division.
   6. Provirus can be transcribed and ultimately lead to the production of new RNA genomes and viral proteins.
   7. Proteins are processed by viral protease, culminating in the assembly of a mature virus.

Latent Viral Infection

1. Certain viruses can remain dormant in the host body:
   • Examples include simplexvirus (causing cold sores) and varicellovirus (causing shingles).

Persistent Infections

• Characterized by gradual worsening over time; details to be included in summary charts.

Oncogenic Viruses (Associated with Cancer)

1. Oncogenic DNA Viruses: include various families such as Adenoviridae, Papovaviridae, Herpesviridae (e.g., Epstein-Barr virus), and more.
2. RNA Viruses: Certain retroviruses such as HTLV types 1 and 2 are known to cause leukemias and lymphomas.

Virus-Cancer Connections

Prions (Infectious Proteins)

1. Associated with spongiform encephalopathies, diseases caused by misfolded proteins.
2. Normal (PrP^C) and misfolded (PrP^Sc) proteins interact through ingestion, transplants, and surgical means.
3. Diseases include Kuru, Creutzfeldt-Jakob disease, and Mad Cow disease.

Viroids

1. Infectious agents consisting solely of RNA, lacking capsids or envelopes.
2. Replication occurs within plant cells using the host's enzymes.
3. Example: Potato spindle tuber disease caused by viroids.

Major Plant Virus Classification

• Formatting for a classification table is yet to be completed.