Microscopy and Bacterial Physiology

General Topics

• The lecture focuses on readings from the week.
• A quiz will be administered, covering the first reading, which is "How Microscopes Made Microbiology Possible" by Sung Lee.
• The microscopy chapter from the microbiology book will not be covered due to time constraints.
• The professor acknowledges that the material is still dense, despite efforts to simplify it.
• Important aspects of microscopy in microbiology will be discussed, even though the dedicated microscopy chapter is omitted.

Microscopy Techniques

• For viewing proteins, samples need to be crystallized.
• GFP (Green Fluorescent Protein) is a key microscopy technique discussed.
  • GFP was originally found in bacteria.
  • It is now engineered to bind to specific targets like DNA or other proteins.
  • GFP can be used to track movement within a cell.
  • The process involves taking samples over time and observing them.
  • This involves cutting cells and observing them internally.
  • Samples are taken at different times to observe changes.
• Electron microscopes use electrons, not photons, to illuminate samples.
  • Therefore, the statement that electron microscopes use photons is false.

Discussion of News Articles

• Three news articles will be discussed:
  • "Treasure Hunt for Microbes in the Atacama Desert"
  • "How Bacteria Swim" (focusing on the flagellum).
  • "How Penicillin Eliminated Bacterial Physiology".
• The discussion format will be similar to the previous session, but with more time for in-depth analysis.
• The goal is to link the articles to concepts learned in Chapter 3, particularly concerning bacteria.

Group Discussion Questions

• Students are divided into breakout rooms to answer specific questions related to the articles.
• Room assignments:
  • Rooms 1 & 2: Question 1
  • Rooms 3 & 4: Question 2
  • Rooms 5 & 6: Question 3
  • Rooms 7 & 8: Question 4
  • Rooms 9 & 10: Question 5
  • Rooms 11 & 12: Question 6
• Each group has approximately 20 minutes to discuss and answer their assigned question.

Question 3 Discussion: Cryo-EM

• Question 3 involves designing a hypothetical experiment using cryo-EM to explore a new protein involved in bacterial motility.
• The discussion references an article from Yale about using cryo-EM to visualize the structure of proteins involved in how bacteria swim.
• Cryo-electron tomography is mentioned as a method for obtaining close-up images.
• Not all bacteria use flagella for movement; some use other motor structures.
• The hypothetical experiment should start by observing a bacterium's motility.
• Cryo-EM would then be used to examine a new protein and how it interacts with the bacterium's structures related to movement.
• The goal is to observe conformational changes in the protein and how these changes affect the bacteria's functions.
• The experiment aims to understand the protein's role in the bacteria's mobility by analyzing its structure under cryo-EM.
• It's noted that the protein's functions may not be well understood initially, as was the case in the Yale article.