- Bioinformatics/Computational biology
- Molecular and cellular biology
Nature of the Research
- Wet lab/bench research
- Informatics/computational research
- Basic research
- Database research
- Structure and Function: Basic units of structure define the function of all living things.
- Information Flow and Exchange: The growth and behavior of organisms are activated through the expression of genetic information in context.
- Systems: Living systems are interconnected and interacting.
- Applying the process of science
- Using quantitative reasoning
- Using modeling and simulation
- Tapping into the interdisciplinary nature of science
- Communicating and collaborating
- What roles might uncharacterized proteins play in mitochondria of eukaryotic pathogens?
- Are there proteins unique to trypanosomatid mitochondria that represent potential drug targets?
- Do subcellular distributions of trypanosomatid proteins reflect in silico predictions?
- Develop a scientific argument and persuasviely express goals and findings in written and oral form.
- Identify and utilize computational and molecular biology resources to meet research goals.
- Comprehend and integrate primary literature in a research pipeline.
- Reflect upon challenges, troubleshoot, and implement solutions to research challenges.
- Participate collaboratively and interdependently in research environments.
Molecular Parasitology is a full-semester CURE in which students experience excitement and frustration of the discovery process as they analyze uncharacterized proteins in Crithidia fasciculata, a non-pathogenic model for protozoan parasites of humans. Molecular Parasitology uses a problem-based learning framework, and students must search for creative solutions to identify, characterize, and clone target genes with limited guidance regarding existing algorithms and tools. Our experience suggests students rapidly (~6 weeks) develop creativity, critical thinking, and self-confidence in this context.
We focus on three learning goals: development of core bioinformatics and molecular biology competencies, self-directed learning, and scientific literacy. To provide tools and structure for positive outcomes, students iteratively progress toward these goals through assignments including journal club sessions, completing safety and ethics certifications (e.g. CITI Responsible Conduct of Research, lab safety) weekly submission of learning logs, and extensive writing projects with opportunities for feedback and revision. Though students maintain ownership of individual research projects, we cultivate collaboration through group activities including group presentation, mini-projects, information sharing, and load-sharing of lab maintenance (e.g. washing dishes, waste management, racking tips).
The research focus blends traditional molecular biology and bioinformatics to investigate mitochondria. Each student selects a gene of their choice from the C. fasciculata genome (~11,000 gene calls) that must encode a protein that is (1) currently uncharacterized and (2) has a strong likelihood of mitochondrial localization. Students develop individual written proposal and a group oral presentation to support their goal of confirming mitochondrial localization via expression as a GFP-fusion. Following selection of targets, students isolate gDNA, design PCR primers, subclone, and sequence their amplicons. We provide basic background on topics (sequencing, PCR, subcloning) but prioritize and encourage collaborative discovery and problem-solving. Because protein targets vary considerably, each research project progresses at a different pace and presents opportunities for extensive trouble-shooting. At the end of the course, each student submits a formal, individual research report and participates in a group presentation of results. Students participating a second semester have opportunity to ligate gene targets into a GFP-fusion vector and transfect C. fasciculata to verify mitochondrial localization.
We host this CURE in an prototype learning space we developed at Georgia State University (GSU) for undergraduate research environments that he hope to implement more broadly. Our Collaborative Learning Lab is a remodeled space in Kell Hall, the oldest drive-in parking deck in the U.S. While this laboratory provide a unique learning space that blends a computer lab with wet-lab space, the CURE could be readily adapted using molecular biology laboratories and equipment found in most colleges and universities. Development of our laboratory was funded entirely through internal funding sources including the Technology Fee Program at GSU. Equipment, furniture, and workstation costs are available upon request.
Because we seek for students to effectively leverage computational tools to collaborate and facilitate research, we focused on configuring robust, computer workstations for student usage. Each student in our laboratory is assigned to a computer workstation (Lenovo ThinkCentre, 29” LED monitor, Windows 8.1) with standard office software installed. We rely on Geneious Pro R7 (Biomatters, Inc) as a platform for managing and analyzing molecular data because the software couples data management, molecular analysis, and basic bioinformatic capabilities with a cost-effective ($300 per license), permanent licensing structure. Student researchers learn to store and share results and data via a MySQL server residing on the instructor workstation.
Operational costs for the course consist solely of consumables typically used in molecular biology courses. Disposable resources such as pipette tips and tubes represent a small proportion of our budget. The most costly resources are PCR components, agarose gel stain, and competent cells. While these costs are necessary, they can be constrained by buying in bulk or production in house.