Viruses and Acellular Microbes

Viruses and Acellular Microbes

• Viruses are exceptionally small and can only be seen using electron microscopes
• They are not considered living organisms
• They must invade a host cell to replicate
• Virions are complete virus particles
• The smallest known virus is about the size of a large hemoglobin molecule found in a red blood cell
• The negative staining procedure allows for the observation of unstained viruses against a dark background

Viral Infections

• Viral infections can affect any organism
• Oncogenic viruses lead to the development of specific cancers

Virus Structure

• Capsid: The protein coat of a virus
• Capsomeres: The protein subunits that make up the capsid
• Nucleocapsid: The nucleic acid and capsid together
• Enveloped viruses possess an outer envelope composed of lipids and polysaccharides

Viral Genomes

• Viral genomes can be in one of four forms:
  • Double-stranded DNA
  • Single-stranded RNA
  • Double-stranded RNA
  • Single-stranded DNA

Origin of Viruses Theories

• Coevolution Theory: Viruses emerged in the primordial soup and coevolved alongside bacteria and archaea (few supporters)
• Retrograde Evolution Theory: Viruses originated from free-living prokaryotes that invaded other organisms and lost functions provided by the host cell (little support)
• Escaped Gene Theory: Viruses consist of host cell RNA or DNA fragments that escaped from living cells and are no longer under cellular control (most widely accepted)

Multiplication of Animal Viruses

• Attachment: Virus binds to a protein or polysaccharide on the host cell surface
• Penetration: The entire virus enters the host cell, sometimes through phagocytosis
• Uncoating: Viral nucleic acid escapes the capsid
• Biosynthesis: Viral genes are expressed to produce viral components
• Assembly: Viral components are assembled to create complete virions
• Release: Complete virions exit the host cell via lysis or budding
  • Viruses escaping via budding become enveloped viruses

Viral Diagnostics and Latency

• Inclusion bodies, viral remnants in infected cells, are used to diagnose certain viral illnesses
• Negri bodies are cytoplasmic inclusion bodies in nerve cells

Latent Viral Infections

• Herpes viruses, like cold sores, exemplify latent viral infections
• Fever, stress, or excessive sunlight can trigger viral genes in latent infections
• Latent viral infections are usually suppressed by phagocytes and interferons
• Shingles is a painful nerve disease from a herpesvirus
• Chickenpox virus (varicella) can remain latent in the human body for many years

Oncogenic Viruses and Human Viruses

• Oncogenic viruses can cause cancer
• Epstein-Barr virus can cause infectious mononucleosis and cancers like nasopharyngeal carcinoma, Burkitt lymphoma, and B-cell lymphoma
• Kaposi sarcoma, common in AIDS patients, is caused by human herpesvirus 8
• Human papillomaviruses (warts viruses) cause cervical and genital cancers
• Human T-lymphotropic virus type 1 is a retrovirus related to HIV that causes adult T-cell leukemia

Human Immunodeficiency Virus (HIV)

• HIV causes AIDS
• It is an enveloped, single-stranded RNA virus
• A member of the lentivirus genus, part of the retrovirus family
• Retroviruses use reverse transcriptase to convert the viral RNA genome into provirus DNA, which integrates into the host cell genome
• CD4+ cells, especially T cells, possess the CD4 receptor
• Provirus is the viral genome, allowing latent infection and evasion of immune response

Global Viral Concerns

• Ebola virus: High mortality; thread-shaped virus suspected to transmit from bats to humans
• Zika virus: Causes serious birth defects, transmitted by mosquitoes

Antiviral Agents

• Antiviral drugs interfere with virus-specific enzymes

Bacteriophages

• Bacteriophages are viruses that infect bacteria
• Based on shape, bacteriophages are categorized as:
  • Icosahedron (spherical)
  • Filamentous (long tubes)
  • Complex (icosahedral heads with helical tails)

Bacteriophage Infection Styles

• Virulent bacteriophages cause the lytic cycle, destroying the bacterial cell
• Temperate bacteriophages do not immediately initiate the lytic cycle
• Lysis is caused by the enzyme endolysin
• Prophage refers to the bacteriophage genome

Multi-Drug Resistance

• Superbugs are multi-drug resistant bacteria

Multiplication of Bacteriophages (Lytic Cycle)

• Attachment: Phage attaches to host cell surface molecules
• Penetration: Phage injects DNA into the bacterial cell, leaving the capsid outside
• Biosynthesis: Phage genes are expressed, producing viral components
• Assembly: Viral components assemble into complete virions
• Release: Complete phages escape the host cell via lysis or budding

Giant Viruses of Amoebae

• Mimivirus: A very large, double-stranded DNA virus found in amoebas
• Megaviridae: A new viral order
• Pandoravirus: The largest virus discovered to date, twice the size of Mimivirus

Plant Viruses and Prions

• Over 1,000 viruses cause plant diseases in citrus, cocoa, rice, barley, and tobacco.
• Plant viruses transmit via insects, mites, nematodes, and contaminated tools
• Viroids: Infectious RNA molecules cause plant diseases
• No animal disease have been discovered that are caused by viroids
• Prions: Small infectious proteins that cause fatal neurologic diseases in animals and humans causing brain to become riddled with holes

Transmission and Degenerative Diseases

• Transmissible Spongiform Encephalopathies: Diseases transmitted by consuming contaminated agents that are untreatable and fatal
• Dementia: General mental deterioration involving disorientation, impaired memory, judgment, and intellect

Prokaryotic Domains

• Two domains of prokaryotic organisms: Bacteria and Archaea

Bacteria Key Traits

• Possess organisms that divide into three phenotypic categories:
  • Gram-negative: Have a cell wall
  • Gram-positive: Have a cell wall
  • Lacking a cell wall

Bacteria Shapes

• Cocci: Round or spherical bacteria in pairs (diplococci), clusters (staphylococci), chains (streptococci), groups of four (tetrads), or groups of eight (octads)
• Bacilli: Rectangular or rod-shaped bacteria in pairs (diplobacilli) or chains (streptobacilli) or elongate cocci (coccobacilli)
• Spirilla: Curved or spiral-shaped bacteria

Cell Wall Deficiencies

• Cell wall-deficient bacteria or L-forms lose characteristic shape due to adverse conditions preventing normal cell wall production
• Mycoplasma genus lack a cell wall
• Pleomorphic bacteria have variable shapes

Staining Procedures

• Bacteria are usually transparent and colorless, so staining is used to observe them
• Heat Fixation: Accomplished by placing the slide on a slide warmer
• Methanol Fixation: Accomplished by flooding the smear with absolute methanol, is a more satisfactory fixation technique
• Fixation general purposes:
  • Kills the organism
  • Preserves morphology
  • Anchors the smear to slides

Staining and Motility Analysis

• Simple stain determines bacterial shape and arrangement
• Structural staining identifies capsules, spores, and flagella
• Gram stain differentiates Gram-positive and Gram-negative bacteria
  • Gram-positive: End up blue to purple
  • Gram-negative: End up pink to red
• Acid-fast stain identifies Mycobacterium species
  • Carbol fuchsin (bright red dye) is used
  • Acid-fast bacteria appear red
• Differential staining differentiates bacteria groups
• Motile bacteria can "swim"
• Nonmotile bacteria cannot swim
• Motility is often associated with flagella or axial filaments
• Flagella stain demonstrates flagella presence, number, and location
• Hanging drop method is a bacterial suspension on a glass coverslip

Bacteria Classification

• Bacterial colony is a mound or pile of bacteria on a solid culture medium
• Bacteria are classified based on their relationship to oxygen and carbon dioxide:
  • Obligate aerobes require oxygen-rich atmosphere
  • Microaerophilic aerobes need lower oxygen concentrations
  • Facultative anaerobes survive in either the presence or absence of oxygen
  • Aerotolerant anaerobes don't need oxygen but can survive in it
  • Obligate anaerobes grow only without oxygen

Environmental Requirements

• Incubators are normally set at 35 °C to 37 °C in microbiology labs
• Some organisms prefer low or high temperatures but can't survive outside of 30-42°C

Bacteria Nutritional needs

• All elements required: carbon, hydrogen, oxygen, sulfur, phosphorus and nitrogen
• Special elements required: potassium, calcium, iron, manganese, magnesium, cobalt, copper, zinc, and uranium
• Fastidious organisms have special nutritional needs

Bacterial Virulence factors

• Many pathogens cause disease by capsules, fimbriae, and endotoxins (cell wall components of Gram-negative bacteria)
• Pathogenicity is tested by injecting organisms into mice or cell cultures

Genetic Composition

• Molecular diagnostic procedures identify bacteria using DNA or RNA tests
• A single-stranded DNA probe identifies an organism by hybridizing with a unique complementary DNA or RNA sequence
• Rickettsias, chlamydias, and mycoplasmas are often "unique" or "rudimentary" bacteria

Special types of Bacteria

• Rickettsias and chlamydias are bacteria with a Gram-negative-type cell wall
• They’re obligate intracellular pathogens that cause disease in humans and other animals
• Obligate intracellular pathogen needs to live within a host cell
• Rickettsia genus names after Howard T. Ricketts
• Diseases caused by Rickettsia species are arthropod borne
• "Chlamydias” are Chlamydia spp. and related organismsare
• Mycoplasmas are the smallest cellular microbes
• Formerly called pleuropneumonia-like organisms (PPLOs) initially from cattle with lung infections

Photosynthesis in Bacteria

• Pathogenic mycoplasmas cause primary atypical pneumonia and genitourinary infections
• Resistant to penicillin and other antibiotics
• Pleomorphic
• Photosynthetic bacteria include purple, green bacteria, and cyanobacteria
• Oxygenic photosynthesis produces oxygen
• Anoxygenic photosynthesis doesn't produceoxygen
• In photosynthetic eukaryotes, photosynthesis happens happens in plastids
• Photosynthesis by cyanobacteria occurs in thylakoids; complex protein pigment aggregates where light harvesting occurs
• Cyanobacteria can carry out oxygenic photosynthesis
• Cyanobacteria in pond or lake water can create blooms in water or pond scum

Nitrogen Fixation and Cyanotoxins

• Cyanobacteria convert nitrogen gas to ammonium ions via nitrogen fixation
• Cyanobacteria produce cyanotoxins that cause disease in humans and animals

Archaea Definition

• Once referred to as archaebacteria
• "Archaea" means ancient
• Assigned when thought that these prokaryotes were to have evolved earlier than bacteria
• Though closely related to prokaryotes related than to modern bacteria
• Extremeophiles for acidic, alkaline, cold, hot and high pressure environments
• Methanogens produce methane which is flammable gas
• Cell walls contain no peptidoglycan