Mid Term Review (HEROES)

Week 1 Review

• Expectations for Pre-lab, Lab, Post-lab: Confirm understanding of weekly responsibilities.

• Team Collaboration:

  • Know team members' names and contact information.

  • Participate in the Collegiality Check each week, contributing to all members' success.

• LockDown Browser: Ensure it’s installed or make arrangements for a computer for the mid-term.

• BIO-HEROES Definition:

  • Stands for Biological Hands-on Explorations with Research Organisms for Experiential Science.

• Course Model Organisms: Introduced to four "heroes" in the course:

  1. Saccharomyces cerevisiae: Yeast

  2. Caenorhabditis elegans: Nematode worm

  3. Rattus norvegicus: Norway rat

  4. Tetrahymena thermophila: Ciliate protozoa

• Knowledge Transfer:

  • Definition: Applying learned knowledge in different contexts.

  • Emphasizes hands-on research and the development/application of biological knowledge.

• Important Characteristics for Model Organisms:

  1. Genetic Similarity: E.g. Mus musculus (mice) for human disease research.

  2. Short Life Cycle & Rapid Reproduction: E.g. Drosophila melanogaster (fruit flies), C. elegans.

  3. Ease of Maintenance & Cost-Effectiveness: E.g. Saccharomyces cerevisiae is simple and inexpensive to grow.

  4. Well-Mapped Genome & Genetic Tools: Essential for studying gene function; e.g. E. coli and Zebrafish.

  5. Ethical Considerations: Avoid higher organisms due to ethical guidelines.

  6. Relevance to Research Question: Select organisms appropriate for specific studies.

Week 2/3 Review

• Lab Safety Guidelines: Confirm knowledge and adherence to BIO 1106 guidelines.

• Teamwork in Lab Cleanup: Know proper disposal of biological waste and cleaning protocols.

• JoVE Videos:

  • Description: High-quality peer-reviewed videos demonstrating lab techniques.

  • Importance: Enhances reproducibility of experiments with visual guidance.

• Sterilization Methods:

  1. Autoclaving: High-pressure steam, best for heat-stable solutions.

  2. Filtration: Removes microbes through small pores; best for heat-sensitive liquids.

  3. Chemical Sterilization: Uses agents like ethylene oxide; best for sensitive solutions.

  4. Radiation Sterilization: Damages DNA; used in large-scale sterilization but not practical daily.

  5. Boiling: Simple heat method; effective but less reliable than autoclaving.

• Aseptic Zone Setup:

  1. Prepare Work Area: Clear, disinfect, and minimize airflow.

  2. Establish Aseptic Zone: Use Bunsen burners or laminar flow hoods.

  3. Practice Aseptic Techniques: Flame sterilize tools and minimize sterile material exposure.

  4. Exit Zone: Proper disposal and clean surfaces after use; wash hands.

• Volume Calculations: Use C1V1=C2V2 for stock solution calculations.

Week 4 Review

• Scientific Name of Baker’s Yeast: Saccharomyces cerevisiae.

• Reasons Yeast is a Good Model:

  1. Eukaryotic structure for studying cellular processes.

  2. Rapid growth and reproduction.

  3. Well-characterized genome aids in research.

  4. Genetic manipulation is straightforward.

• Cell Structure:

  • Yeast cells are eukaryotic, unicellular but can form multicellular structures.

  • Have a tough outer cell wall made of polysaccharides.

• Yeast vs. Human Genome:

  • Human genome is larger, complex with specialized functions; yeast has a simpler and efficient genome.

• Nobel Prize Winners:

  • Hartwell: Gene control in the cell cycle.

  • Nurse: Cyclin-dependent kinase identification.

  • Horvitz: Genes controlling apoptosis.

Week 5 Review

• Reasons to Use C. elegans:

  1. Transparent body for observing cellular processes.

  2. Well-characterized genetics with various genetic tools.

  3. Short life cycle for rapid experimentation.

  4. Ease of maintenance and high reproductive rates.

  5. Conserved biological pathways relevant to humans.

• Life Cycle of C. elegans:

  • Egg stage, larval stages (L1-L4), and adulthood.

  • Dauer stage can occur under harsh conditions.

• Hermaphrodites vs. Males:

  • Hermaphrodites (XX) possess both reproductive structures; generally larger than males (XO).

• Microscope Use:

  • Setup and adjust based on specimen type; focus on proper lighting and magnification.

• Gene Similarity: C. elegans has a significant number of human disease-related genes, aiding genetic research and modeling human diseases.

Spot Assays and BLAST Analysis

• Spot Assays: Utilize NGM plates, introduce worms, observe behavioral changes in response to test substances.

• BLAST Analysis: Identifies sequence similarity, helps in finding homologous genes, and predicting functions.