Microscopy and Microbiology

Posted on Oct 15, 2024 in Biology

Types of Microscopes

Optical Microscopes

Compound Microscope: Uses two lenses (ocular and objective) for a maximum magnification of 1000x. Ideal for detailed cell studies.

Stereo Microscope: Offers a 3D view with low magnification (up to 100x). Useful for viewing larger, opaque samples.

Other Microscopes

Confocal Laser Scanning Microscope: Uses lasers for in-depth scanning, creating high-resolution 3D images. Primarily used in research applications.

Electron Microscope: Employs electron beams for high-resolution imaging (up to 2 million x) due to shorter wavelengths. Ideal for studying cells and particles.

X-ray Microscope: Uses X-rays for high-resolution 3D imaging, particularly suitable for living cells. Magnification falls between optical and electron microscopes.

Scanning Helium Ion Microscope (SHIM): Uses helium ions for high resolution with less sample damage. Introduced in 2007.

Scanning Acoustic Microscope (SAM): Uses sound waves for imaging, detecting physical properties like tension and stress in biological structures.

Neutron Microscope: An experimental microscope using neutrons with potential for high-contrast imaging.

Scanning Probe Microscope: Visualizes atoms using a fine tip, generating computer-based 3D images.

Microscope Components

  • Ocular (Eyepiece): Magnifies the initial image.
  • Objectives: Lens set forming the initial image.
  • Nosepiece: Holds and rotates the objectives.
  • Coarse/Fine Adjustment: Coarse for low power, fine for high power focus.
  • Stage/Stage Clips: Holds the slide.
  • Illuminator/Diaphragm: Light source; controls light amount.
  • Body Tube: Connects the ocular to the objectives.
  • Arm/Base: Provides structural support.

Principles of Microscopy

  • Orientation: Objects appear upside-down and reversed.
  • Magnification: Total magnification = Ocular x Objective. Higher magnification results in a smaller field of view, increased resolution, and a darker image.
  • Refraction: Bending of light; the index of refraction determines the angle change. Biconvex lenses converge light.
  • Electron Microscopes: Use electromagnetic coils for beam focusing.

Viral Life Cycles

Lytic Cycle

The virus injects its genome into the host cell, using host machinery to produce viral mRNA and proteins. Host DNA is destroyed, new viruses are assembled, and the cell lyses, releasing hundreds or thousands of viruses, rapidly spreading the infection.

Lysogenic Cycle

Viral DNA integrates into the host genome as a prophage, remaining dormant and replicating with host DNA. Reactivation leads to the lytic cycle. Dormancy allows spread through cell divisions. Example: HIV.

Subviral Agents

Satellite Viruses/Nucleic Acids

These subviral agents require a helper virus for replication. Genome types include ssRNA, ssDNA, and dsDNA. They have smaller genomes (<1.5 kb) compared to viruses.

  • Satellite Virus: Encodes capsid proteins (e.g., Hepatitis D with Hepatitis B).
  • Satellite Nucleic Acids: Rely on helper virus capsids.
  • Virophages: Depend on co-infecting giant viruses, parasitizing viral replication factories in the cytoplasm. Genome: circular/linear dsDNA, ~16-18 kb. Examples: Sputnik, Zamilon with Mimivirus.
  • Virusoids: Viroids enclosed in helper virus capsids. Circular ssRNA genome. Depend on helper virus and RNA polymerase II for replication.

Bacterial Characteristics

Gram Staining

Differentiates bacteria by cell wall structure.

  1. Primary Stain (crystal violet): Stains all cells.
  2. Mordant (Gram’s iodine): Forms a complex with the stain in Gram-positive cells.
  3. Decolorizer (ethanol/acetone): Removes stain from Gram-negative cells.
  4. Counterstain (safranin): Colors Gram-negative cells pink; Gram-positive cells remain purple.

Gram-positive: Thick peptidoglycan layer, stains purple, no outer membrane.

Gram-negative: Thin peptidoglycan layer, outer membrane, stains pink after counterstain.

Oxygen Dependence

  • Obligate Aerobes: Require oxygen for ATP production.
  • Obligate Anaerobes: Die in the presence of oxygen, rely on anaerobic respiration or fermentation.
  • Microaerophiles: Require low oxygen levels.
  • Facultative Anaerobes: Can switch between aerobic and anaerobic respiration.
  • Aerotolerant Anaerobes: Do not use oxygen but tolerate its presence.

Nutritional Classifications

Defined by energy source (chemical = chemo-, light = photo-), electron source (organic = organo-, inorganic = litho-), and carbon source (organic = hetero-, CO₂ = auto-). Examples include chemoorganoheterotrophs (most bacteria, fungi) and photoautotrophs (plants, algae).

Extremophiles

Microbes thriving in extreme environments.

Protists

Protozoa

Unicellular, motile via flagella, cilia, or pseudopodia. Complex life cycles with trophozoite (active) and cyst (dormant) forms. Examples: Plasmodium (malaria), Giardia.

Algae

Photosynthetic organisms with chloroplasts, playing a key role in oxygen production. Types: green algae (Chlorophyta), red algae (Rhodophyta), diatoms, dinoflagellates. Found in aquatic and terrestrial habitats.

Parasitic Worms (Helminths)

Flatworms (Platyhelminthes)

  • Cestodes (tapeworms): Segmented, attach via scolex. Diseases: Taeniasis, cysticercosis.
  • Trematodes (flukes): Diseases: Schistosomiasis, clonorchiasis.

Roundworms (Nematodes)

Complete digestive tract, pseudocoelom. Diseases: Ascariasis, hookworm.

Thorny-headed Worms

Rarely infect humans, rigid proboscis for attachment.