Course-Based Undergraduate Research

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Phage Hunters

Dr. Sarah Ball has been involved with our Science Education Alliance (SEA) Phages CURE since its inception at OSU in 2011. Together, with Dr. Caroline Breitenberger, and Dr. Charles Daniels, SEA Phages lab began with an original cohort of 25 students. A part of some sections of Biology 1113, hundreds of students have participated in this CURE since that initial cohort. A national project, numerous universities and colleges across the United States are participating in this Phage-hunting.

In this CURE, students isolate bacteriophages (viruses that infect bacteria) from soil samples collected from locations around campus, in Columbus, and beyond! Students purify their phage populations, and along the way learn important lab techniques, such as direct plating, and 3-phase streaks. Students then amplify the isolated sample of interest, and isolate DNA from the phage. They also conduct gel electrophoresis to characterize the bacteriophages. The DNA is then sequenced for a few of the phages isolated that semester.

Because this is a national project, information about the student isolated phages is added to a national database, called Phages DB. As part of this course, 2-3 students a semester are selected to present results at an HHMI symposium in Northern Virginia. As of June 2019, 18 students have presented at HHMI, and 171 phages have been contributed to Phage DB. After completion of the phage hunter CURE, students can enroll in Biology 2200 in a subsequent semester. In this course, the sequenced genome from a phage isolated the previous semester is annotated by students using DNAMaster and 42 completed genomes have been submitted to GenBank.

Interestingly, the types of bacteria hosts are varied. So far, students in Biology 1113 have isolated bacteriophages from Arthrobacter sp., Mycobacterium smegmatis, and Gordonia terrae. Phages representing 12 different clusters have been sequenced giving us just a small glimpse at the incredible diversity waiting to be uncovered. There are always more interesting phages to be discovered!

We have also developed a helper program in which students who successfully complete the course, and its associated genome course become student assistants in the classroom. These helpers have been invaluable assistants to our Teaching Assistants. Other undergraduate students have been instrumental on our lab prep team, making sure that students in the course have the supplies they need.

Gel electrophoresis showing DNA ladder and several DNA bands
Gel electrophoresis

Prevalence of Antibiotic Resistance in the Environment (PARE)

Common infections are becoming hard to treat due to the increase in antibiotic-resistant strains of bacteria. Antibiotics are over-prescribed for human illnesses and administered to livestock to promote health and growth of animals. Once ingested, they are excreted and end up in sewage systems and in the environment. Very little is known about how the presence of antibiotics in the environment affects the prevalence of antibiotic-resistant bacteria in the environment. The Prevalence of Antibiotic Resistance in the Environment (PARE) project is harnessing the work of students in a nationwide experiment to track and report antibiotic resistant bacteria in the soil and compile the data in the PARE Global database. Developed by Carol Bacsom-Slack, the PARE CURE has been implemented at many different types of institutions in over 30 states (Genné-Bacon & Bascom-Slack, 2018)

PARE is a CURE for students enrolled in non-majors Bio1110 and majors Bio1113 and Bio1113H courses. Students are given a unique chance to conduct authentic research and learn a variety of laboratory techniques and professional skills. They are using scientific processes to determine if the bacteria they’ve found in the environment are resistant to antibiotics. Students learn microbiology plating techniques, conduct bacterial colony counting, and practice molecular biology techniques such as DNA extraction, PCR, gel electrophoresis and bioinformatics analysis. Students analyze and interpret their results as well as read and discuss primary literature sources. Finally, their results are included in the national PARE database.

Nine agar plates with bacteria growth on a lab bench
Plates from a PARE experiment

 

Dr. Jennifer Larson started this project in 2016 and since then every semester multiple CLSE instructors guided by Dr. Lubomira Cubonova have implemented PARE in their courses. As of now, the database contains 85 clean and statistically valid entries of the relative frequencies of antibiotic resistant microbes reported by our OSU students. As in any authentic research, this laboratory study can be “messy,” but students appreciate the notion of ownership of the project. They choose their own soil sample locations, such as their hometowns or even their family backyards. They analyze their own data and they share their experiences and knowledge in the classroom setting as well as in departmental poster presentation sessions.

Endophytes

Endophytes—fungal and bacterial species that reside within plant tissues—form part of the plant microbiome and may confer benefits to their plant hosts. In academic year 2013-2014, a CURE on fungal endophytes (Bascom-Slack et al., 2012) was introduced into BIO 1114H, the honors section of an Introductory Biology course for STEM majors focused on evolution, organismal biology, and ecology. In Autumn 2018 the endophytes CURE was incorporated into a non-honors section of BIO 1114.

Students in BIO 1114/BIO 1114H labs conduct a term-long research project to characterize the fungal endophytes present in plant tissues. In small research groups, students develop a research question, design a research study, and select plant species and plant tissues to sample for their project.

Students have ownership over the project through the development of their research questions, and the collection of plant material for this CURE from a variety of sources, including:

  • Ohio State’s Waterman Agricultural and Natural Resources Laboratory
  • Ohio State’s Biological Sciences Greenhouses
  • The Oval and other parts of the OSU campus
  • Crop plants grown on students’ family farms
  • Students’ homes, gardens, and dorm rooms
  • Commercial sources including grocery stores, farmers markets, and flower shops

The endophytes CURE bridges microbiology and ecology. In addition to developing lab skills and techniques, students engage with all aspects of the scientific process. The project culminates when the research team synthesizes their results, evaluates their research question, and develops a research poster or paper following the style of a scientific conference or journal. Students present their findings at a multi-course poster session at the end of the semester, in which they gain experience communicating scientific results to a broader audience.