Path 1
Research Lab
Plan I—Research Immersion Laboratory
Path 1 is an authentic research experience in which students participate in all aspects of the scientific process, from sample collection through preparation of data for publication. Students choose to enroll in one of three laboratory courses referred to as Research Immersion Labs (course AL). The process of discovery is demonstrated through a guided, inquiry-based experience organized around team research projects. Activities span two consecutive quarters with each Research Immersion Lab followed by an Advanced Research Analysis course (BL). The first course offers hands-on experience collecting data, analyzing preliminary results, and reading the scientific literature, while the second course emphasizes rigorous quantitative and computational analysis of data, oral presentation and discussion of research ideas, and written documentation of research accomplishments.
In 103AL/BL, students collect samples from natural environments and design experiments to discover and characterize novel bacterial viruses (phages). Students then sequence and annotate the genomes of the phages they discover, and perform comparative genomics analyses. This is an authentic research experience in which students participate in all aspects of the scientific process, from sample collection through preparation of data for publication.
Working in teams, students conduct self-directed research projects that incorporate techniques in microbiology, virology, and molecular biology in order to characterize the life cycle and phage-host dynamics of the phages they isolate. Students get to name their phages and select which phages are the best candidates for whole-genome sequence analysis.
The emphasis of this course is on reading and understanding scientific literature as well as improving critical thinking skills such as ability to evaluate hypotheses or experimentally address scientific questions. Class activities also highlight critical aspects of the research process, including record keeping, ethics, laboratory safety and citizenry, mechanics of scientific writing, and project responsibilities and ownership. In addition, students are introduced to the use of bioinformatics tools and computational analysis software necessary to genomic analyses.
In 103BL, students use bioinformatics and/or mathematical modeling software to interpret, expand, or refine the genome annotations of the phages isolated in MIMG 103AL for comparative genome analyses. The final deliverable is a fully annotated phage genome ready for publication to Genbank, with the students as submission authors.
Students learn to use graphics software to prepare figures and illustrations for presentations, posters, reports, and websites (database entries). Primary literature is discussed in Journal Club-style meetings in which students create PowerPoint slides and formally present results to the class. Production of a research seminar presentation, team poster, and final report describing the entire research project are required to complete the two-course series.
Research Objectives:
- Discover a unique bacterial virus (phage)
- Characterize viral particles using standard Electron Microscopy techniques
- Sequence phage genomes using Next-Gen technology
- Investigate organization of viral genomes and functions of virus genes using computational tools
- Publish phage genomes in GenBank
In 109AL/BL, students investigate the microbiomes of natural environments, asking the questions “Who’s there?” and “What are they doing there?” by isolating and performing functional characterization on bacteria from different samples, as well as using metageomics to compare community and functional profiles. This is an authentic research experience in which students participate in all aspects of the scientific process, from sample collection through preparation of data for publication.
Working in teams, students conduct self-directed research projects designed to promote discovery of novel microorganisms involved in antibiotic production and resistance, plant growth promotion, biofuel production, and other scientifically relevant questions. Student research projects incorporate techniques in microbiology and molecular biology and involve use of bioinformatics tools and phylogenetics software for data analysis.
The emphasis of this course is on reading and understanding scientific literature as well as improving critical thinking skills such as ability to evaluate hypotheses or experimentally address scientific questions. Class activities also highlight critical aspects of the research process, including record keeping, ethics, laboratory safety and citizenry, mechanics of scientific writing, and project responsibilities and ownership. In addition, students are introduced to the use of bioinformatics tools and computational analysis software necessary for phylogenetic and metagenomics studies.
In 109BL, students use bioinformatics and/or mathematical modeling software to interpret, expand, or refine datasets generated in MIMG 109AL. Students generate 16S phylogenetic trees to assign identities to their isolates and use statistical tools to make comparisons of the microbial communities from different environments. The final deliverables are 16S sequences ready for publication to Genbank, with the students as submission authors.
Students learn to use graphics software to prepare figures and illustrations for presentations, posters, reports, and websites (database entries). Primary literature is discussed in Journal Club-style meetings in which students create PowerPoint slides and formally present results to the class. Production of a research seminar presentation, team poster, and final report describing the entire research project are required to complete the two-course series.
Research Objectives:
- Discover new microbes, novel DNA sequences, and previously unknown phenotypes
- Identify bacteria using standard molecular, microbiological, and bioinformatics techniques
- Generate phylogenetic trees from nucleotide sequence data
- Use bacterial community profiles (metagenomics) for comparative analysis of different environments
- Publish 16S sequence data in Genbank