Microscopy-Panopto

a. Definition of Microbes

  • Microbe: Any organism too small to be seen with the naked eye (includes bacteria, archaea, viruses, and some eukaryotic organisms like protists and algae).

b. Properties of Microbes

  • All microbes contain nucleic acid (DNA or RNA), can replicate, and evolve.

c. Habitats of Microbes

  • Microbes inhabit various environments including soil, water, within organisms, and in the air.

7. Evolution of Microbes
a. Historical Context

  • Example of E. coli and Salmonella as closely related species despite significant differences in pathogenicity.

  • Discussion on the species definition in prokaryotes versus eukaryotes (prokaryotes defined via genetic similarity—98.7% identity of the 16S rRNA gene).

8. Microbial Functions and Ecosystem Contribution
a. Photosynthesis and Nitrogen Fixation

  • Microbes are responsible for 50% of Earth's photosynthesis and nitrogen fixation.

b. Decomposition Role

  • Importance of microbes—particularly bacteria and fungi—in decomposition processes to maintain ecosystem health.

Review of Microbial Definitions and Types

  • The definition of a microbe revisited: organisms too small to be seen by the naked eye.

  • Key comparison points between bacteria and eukaryotes highlighted during review:

    • Membrane-bound organelles (present in eukaryotes, absent in bacteria).

    • Differences in cell wall structures (peptidoglycan present in bacteria, absent in archaea).

    • Modes of reproduction (e.g., binary fission in bacteria).

    • Size distinctions (eukaryotic cells are generally larger than bacterial cells).

Differences between Bacteria and Archaea

  • Archaea's unique ability to thrive in high-temperature environments (extremophiles).

  • Discussions on the ribosome composition differences between bacteria and archaea.

  • Notable mention: No known pathogenic archaea.

  • Common misperception clarifications: not all archaea are extremophiles; many exist in moderate environments.

Common Light Microscopy Applications

  • Use of wet mounts for observing living microorganisms.

  • Staining techniques (e.g., Gram stain) for examining dead samples.

  • Dark field and phase contrast microscopy explained with focus on visualization of internal structures.

  • Differential interference contrast (DIC) microscopy characterized by its ability to show shadows on specimens.

  • Confocal microscopy utilizing focused pinpoint lights to explore three-dimensional structures.

  • Fluorescent microscopy's role in real-time observation of live specimens, with emphasis on proteins like GFP.

Super-Resolution Microscopy

  • Advancements in light microscopy post-2014 with super-resolution methodologies:

    • PALM, STORM, STED, and SIM techniques that break diffraction limits.

    • Key understanding: super-resolution microscopy allows scientists to see fine details (as small as 10-40 nanometers)

Scanning Probe Microscopy (AFM)

  • Definition and application of atomic force microscopy (AFM):

    • Uses a cantilever to map surfaces at high resolutions (0.1 nm). Both alive and dead specimens can be imaged but only dead specimens are used in AFM.

Electron Microscopy Techniques

  • Electron Microscopy (EM) principles:

    • Types of EM include scanning EM (SEM) and transmission EM (TEM).

    • Samples must be prepared in a vacuum; staining with heavy metals is necessary for visibility.

    • High resolutions attainable (as low as 0.2 nm in TEM).

Furthermore, EM allows for the visualization of cellular structures and intricate details that are often not visible with light microscopy, making it an invaluable tool in research and diagnostic applications.

9. Microscopy Techniques
a. Light Microscopy

  • Characteristics: Light as the medium for viewing small objects.

  • Key historical figure: Antony van Leeuwenhoek pioneered microscope use.

  • Magnification and resolution discussed, with light microscopy limit at point two microns.

Key Factors

What microscope can view interior structures?

  • Transmission Electron Microscope (TEM): This microscope allows for viewing the interior structures of cells and materials at high resolutions, often down to the atomic level.

  • Confocal microscope

  • Phase contrast microscope

  • Differential microscope

What microscope types can view surfaces?

  • Scanning Electron Microscope (SEM) - Provides high-resolution images of surfaces by scanning with focused beams of electrons

  • Atomic Force Microscope (AFM) - Measures surface topography at the nanoscale using a cantilever to probe surfaces

What microscope types are high resolution and expensive?

  • Transmission Electron Microscope (TEM) - Offers incredibly high-resolution imaging capabilities by transmitting electrons through a specimen, but comes at a significantly higher cost due to its complex technology.

  • Super resolution microscope

What microscope types only work with dead samples?

  • Scanning Electron Microscope (SEM) - Utilizes focused beams of electrons to create detailed images of samples, which must be fixed and dried before imaging, making it unsuitable for live specimens.

  • TEM -

  • AFM

What microscope types work with live samples?

    Dark field microscope - views unstained, transparent, and live specimens with high contrast. white halo around

Bright field microscope - dark sample on bright background, transmitted light, low contrast for unstained cell

  1. Bright field microscopy

    • Dark, often stained specimen against a bright background

  2. Dark field microscopy

    • brigthly illuminatedspecimens are observed against a dark background, enhancing contrast and revealing fine details that are typically obscured in bright field microscopy.

  3. Differential Interference contrast (DIC)

    • provides pseudo-3D, shadow cast or relief-like image of unstained living specimen

  4. Transmission Electron Microscopy (TEM)

    • high-resolution, often black and white, 2D cross-section showing incredible detail of internal cellular ultrastructure

  5. Scanning Electron Microscopy (SEM)

    • high resolution, often black and white, 3D like image of the surface topography of a specimen

  6. Confocal Microscopy

    • vibrant, a typo of fluorescent microscopy and 3D. You will see specific structures withing cells or tissues

  7. Fluorescent microscopy

    • shows specific cellular components or molecules glowing brigthly against a dark background