Departmental Honors Ad Hoc

Student Name: Benjamin Brown
What is the standard coursework for this class? Include details about assignments, projects, and activities.
Biol 403, entitled ‘Knowledge Synthesis in Cell Biology’ is a course which aims to impart students with a range of critical thinking skills necessary for work in the sciences. These skills are built by interpreting experimental data, evaluating claims based on that data, constructing models of cell processes, and organizing current scientific findings. The main biological processes that will be examined include cytoskeleton structure and function, and the mechanics of viral entry.

This course emphasizes discussion in small groups and as a class. In class activities include the analysis of academic papers, as well as the study and use of modern methods to concatenate scientific thought. Additional time will be spent interpreting the results of and modifying several types of models of cell events. The goal of this effort is to create literate and discerning scientists capable of critiquing scientific works, interpreting results, and identifying gaps in current knowledge.

As such, evaluation of learning objectives will take place through scores on in-class engagement, paper annotations, and group quizzes. Outside of class, evaluation takes place through reflections on lecture activities and assignments based on course themes, including a project that synthesizes course content.

Outline your proposed ad hoc Honors Project, be sure to include the main topic, focus, and goal of the project. Please also include details about the deliverable of your project (i.e., if a video, how long will it be? If reviewing resources, how many minimum? how will you find them? etc.)
Cells transcribe DNA in a dynamic manner. The flexibility in gene transcription and translation allows the cell to respond to a changing environment, and undergo time dependent events like division.
In particular, chromatin is subject to modification by binding proteins, breakage, repair, and shape changes due to thermal fluctuations. These properties all affect what, and when proteins are expressed in the cell.

My project will seek to address how chromatin dynamics change and regulate gene transcription through the creation of a discourse graph. The project will have several phases beginning with the identification of 3 sub-questions that fit under the central theme. Examples of these questions include: how do the mechanics of chromatin structure affect gene expression, how do remodeling complexes affect DNA transcription, and how is genomic compartmentalization established?
After these questions are posed, ~ten primary research articles will be selected, and key details like evidence and the author’s claims will be gathered.
Next, the gathered information will be arranged in a discourse graph on the Roam platform. The umbrella question will form a central node, with sub-questions and associated information branching out from there in an informative and organic manner. The graph will be arranged to identify evidence that supports or refutes claims across the gathered literature. Related information will be grouped in clusters and identified with visual markers like color and title. Knowledge gaps or claims that need additional supporting evidence will be noted for further work, and hypotheses based on assembled knowledge will be posed.
A diagram will be created in a program like BioRender to arrange the assembled knowledge into a tangible representation of the key biological mechanisms at play in chromatin dynamics, and how these give rise to altered gene expression.
Lastly, a video tour (~10 min) will be used to present the graph and diagram.

Discuss your motivations for pursuing this ad hoc project. What do you hope to gain from completion of this project?
I currently work in Dr. Akamatsu’s lab studying the actin network structure and force generation during endocytosis. Additionally, my course background has included preparation not only in cell biology but in genetics, applied mathematics and physics. I’ve become interested in studying how “simple” physical interactions, even random and chaotic interactions, can give rise to complex and ordered phenomena.

In Biol 403, I’ll gain a deeper understanding of the actin cytoskeleton and the biological agents that harness it, but I’m also interested in looking one or two steps back, to the nuclear processes that ultimately create the pool of protein agents like actin monomers in the cell. Furthermore, a better understanding of the mathematical description of structures like rods, filaments, and fibers will allow me to pursue more theoretical biophysical questions about the mechanics of many biological structures, including filamentous actin.

This project will give me the opportunity to apply the knowledge synthesis methods taught in this course to a new biological topic, and through this project I hope to gain deeper insight into fascinating intracellular events, and increase my knowledge of the physical description of biological materials.

How does this additional work connect with the educational goals of the course and/or your professors area of expertise?
One main goal of the class is to prepare students with a set of skills for scientific work and critical thinking, rather than a specific list of biological facts. This project will extend the course material on discourse graph building and model creation towards a new biological research area, demonstrating their versatility in the field.

Dr. Akamatsu’s expertise in computational biology and biophysics will be a valuable resource as I interpret and synthesize physical modelling and mathematical biology papers. His career as a professor and scientist has contributed to expertise in many topics in advanced cell biology, including gene expression and intranuclear dynamics. Furthermore, he has collaborated extensively with Roam’s founders, and will be an excellent individual to aid in navigating its nuances to create the most beneficial synthesis from many knowledge sources.

Outline your project schedule. In your schedule be sure to include your plan for in-person meetings, when each component of your project is due (drafts, revisions, preliminary research), when you are hoping to receive feedback, and other relevant steps.
End of week 2: Identify the umbrella question in its final form, along with the rationale for its selection.
End of week 3: Identify three sub questions in their final forms, with rationale.
End of week 4: Identify all papers to be used in synthesis.
End of week 5: Extract evidence and claims from papers. Check-in meeting with Dr. Akamatsu
End of week 7: First draft of discourse graph, including hypothesis and knowledge gaps.
End of week 8: First draft of diagram. Meeting with Dr. Akamatsu to discuss revisions to graph and diagram.
End of week 10: Final draft of discourse graph, diagram, and video description.