Environmental Influence on Gene Networks Module – Unit Plan
In this module, students complete the steps scientists take when using systems biology to investigate how organisms induce phenotypic changes in response to the environment. Student teams apply their background knowledge of genetics and networks to experiment with a model organism. They then exchange and interpret information in order to build a possible network, and in the laboratory, test this network by altering environmental conditions. This leads to further experimentation to verify and draw conclusions about network interactions using experimental data and a computer simulation. Students act as scientists while planning, implementing, and evaluating an investigation in the context of a real regulatory network.
These lessons allow students to investigate the interplay between the environment and organisms authentically, instead of through extrapolating from artifically transformed E. coli bacteria. Through experimentation and integration of different data types, students build a comprehensive model of how genetic, cellular, and molecular components (genes, proteins, metabolites) work together in organisms and how cells function as collections of networks while being impacted by their environment.
See Standards Addressed for all NGSS and WA State (Science, Math and Literacy) Standards Connections. In addition to the aligned objectives linked above, for this lesson, here is a breakdown of:
- Cellular networks allow cells to respond dynamically to stimuli.
- A response to a stimulus occurs by changing the relative amount or function of individual nodes in a cellular network.
- A stimulus affecting one node can cause a change in many other nodes because they are all interconnected in the network.
- Scientists use computer programs and simulations to analyze networks because networks are often very complex.
- Some nodes have bigger system-wide affect than others.
- Understanding relative importance of nodes allows greater understanding of how to perturb and use the system.
- Multiple data sets from various experimental techniques are needed to show network relationships.
- Observations lead to hypotheses and experimental design.
- One change in the environment could affect an entire cellular network due to the interdependent nature of networks.
- Halobacterium (Halo) respond to the amount of light in their environment
- Halo change color from pink to purple in the presence of light and from pink to tan/white in the absence of light.
- Halo grow better in the presence of light.
- Using a centrifuge separates a culture into a supernatant and pellet, which allows the phenotype of cells to be more easily viewed.
- Qualitative measurement is a way of describing data with words, whereas quantitative measurement is a way of describing data with numbers.
- The reliability of data increases with an increase in the size of the data pool/set.
- To draw reliable conclusions, multiple trials/replicates should be performed.
- Mutant strains, with known genotypes, are a useful tool when studying organisms.
- Students use scientific thinking to consider how the environment impacts gene expression and cellular networks.
- Students conduct a controlled investigation and analyze lab results to determine how the amount of light affects Halobacterium.
- Students use wild type and mutant strains of Halobacterium to investigate quantitatively and qualitatively.
- Students use a centrifuge to spin down cells as a way to determine the phenotype of cells.
- Students analyze various data sets to determine a bacteriorhodopsin network and to determine the importance of compiling multiple sets of data.
- Students compare, contrast and critique divergent results from their investigations and discuss/identify possible errors/sources of variation.
- Students use a simulation to verify and/or correct their network understanding.
- Students plan the steps needed for scientists to determine and verify a question using systems methods.
- Students analyze the role the environment has on gene expression. In this analysis, recognize the components, structure, and organization of systems and the interconnections within and among them.