The Adventure of linc(RNAs): Building Confidence in Bioinformatics with lincRNA Identification
Rebecca Murphy, Centenary College of Louisiana
As the ability to generate large datasets becomes more accessible in many areas of biology, proficiency in computational tools that can manage these data becomes increasingly important. Computational biology and large dataset management are universally applicable skills in many subfields of the life sciences including medicine, molecular and cell biology, environmental, and geological sciences. While biology students may not develop expertise in informatics over the course of a semester, relevant exposure to these tools can help them develop confidence to try these analyses and build self-efficacy in the discipline for future work. Here we present an open-sourced laboratory module that can be used to identify certain types of RNA transcripts from a larger pool of high-throughput RNAseq data. This experiment uses publicly available gene expression data from environmental response in agriculturally relevant crop species. The core of this analysis pipeline utilizes Evolinc-I, which employs algorithms that capitalize on canonical protein-coding features, such as start codons, to identify transcripts that are expressed but likely not translated. Additionally, this module can be combined with other activities including reading related journal articles to help students understand how these large data sets are generated, exercises in initial transcriptome read mapping, and follow-up analyses to track differential gene expression. This module has been piloted as part of a Molecular Genetics course at Centenary College of Louisiana, and in addition to more traditional assessment, students were asked their confidence level with general biological concepts, genomics, computers, and large data sets both before and after the module. Data from this preliminary pilot are positive, indicating that deployment of this module show promising increases in confidence surrounding computer-based analysis and general biology (IRB Approval number 19-002).
Are CUREs enhanced by returning to a familiar model system? A case study using Lake-in-a-Tube microcosms
Brian Swisher, Saint Michael’s College
The curriculum in Biology at Saint Michael’s College features student research experiences in the classroom laboratory CUREs. This includes unique CUREs across 9 different courses from 100 to 400 levels. Among these, ecology students’ coursework may include two CUREs that both use Lake-in-a-Tube (LIAT) microcosms. LIAT is a system that first-year students use during a case study of lake algae blooms and use to conduct a CURE as a final project. Upper-level ecology students use LIAT to test a novel question about factors that affect exploitation competition within plankton assemblages in lakes. Data from a previous two-year assessment showed that student attitudes about conducting research and gaining skills increased with “dosage” of the number of CUREs completed over time. The implementation of LIAT in upper-level courses allowed me to test possible enhancement of this dosage effect when students use a familiar model system- a Cross-Curricular CURE. During the 2023 and 2024 fall semesters, I used this survey to test the hypothesis that a Cross-Curricular CURE experience enhanced student outcomes over those of students who experienced wholly independent CUREs with no common study systems. I predicted that in the Cross-Curricular CURE group would report higher Likert scores than students in the independent CURE group. My results indicated that both CURE types showed moderately increasing Likert scores of positive attitudes towards skills acquisition and conducting research with dosage. Comparison between CURE types showed support for my hypothesis, with scores on questions regarding student attitudes toward conducting research increasing more with dosage for Cross-Curricular CUREs than Independent CUREs. Attitudes toward research skill acquisition did not differ, with both CURE groups experiencing similar moderate gains in attitude with dosage. Together, these results suggest that Cross-Curricular CUREs hold unique benefits that should be considered when expanding CUREs within a Biology curriculum.
Student-designed experiments fill knowledge gaps about caterpillar-ant symbiosis
Lauren Lucas & Zachariah Gompert, Utah State University
Research-based learning is among the highest impact experiences college students can have. For the last four years, undergraduate students from the Honors Program enrolled in the introductory-level biology lab course at Utah State University have been filling gaps in the scientific community’s knowledge about abiotic and biotic factors that affect a mutualistic relationship between caterpillars and ants. Sugar-loving ants protect caterpillars from predators and parasitoids, and the caterpillars feed the ants honeydew from a dorsal organ and communicate with them through skin chemicals (cuticular hydrocarbons or CHCs). Students begin by learning about the scientific method, as well as developing collaboration and communication skills, through instructional videos and standalone experiments, which they then apply to this 7-week research experience. They work in small groups to make general observations about the study system, search and read the published literature, build off of what previous students have learned, and write a short research proposal. One of the proposed experiments is chosen for the class. Students use caterpillars hatched from hibernating eggs collected from multiple Lycaeides populations the previous summer by scientists. A small support team rears the caterpillars until they have developed their ant-tending organs. This ensures students have adequate sample sizes for data analysis (linear regression). Through these experiments, the students have shown that Lycaeides population affects the amount of attention received by ants, and that different ant species interact with the caterpillars to different extents. The project concludes when students individually record themselves giving a 5-minute “lightning talk”. This classroom research filters into a larger project about the long-term effects of natural selection in wild Lycaeides populations, funded by an NSF CAREER grant. The student discoveries have indicated that Lycaeides ant-tending traits are good candidates for studying rapid evolution. Students have felt this experience prepares them for their future STEM careers.
Salad BOL: An Investigation into the Efficacy of DNA Barcoding in Salad Greens
Katherine Wydner, Vasilios Orologas, Jill Callahan & Frances Raleigh, Saint Peter’s University
DNA Barcoding is a molecular approach to identifying groups of organisms using gene sequences. A gene useful for DNA barcoding at the species level should be highly conserved among a wide range of taxonomic groups yet just variable enough that a species’ gene pool contains one unique allele that differs from other species’ alleles. A gene that has been useful for this purpose in plants is rbcL which codes for the large subunit of ribulose 1,5 bisphosphate carboxylase/oxygenase (RUBISCO), an enzyme used in photosynthesis. We have developed a lab activity that introduces students to the Barcode of Life (BOL) Project while teaching them basic skills in both the laboratory and computer-based bioinformatics. Starting with a mix of salad greens obtained from a supermarket, each student pair selects a leaf and follows a protocol involving extraction of DNA, polymerase chain reaction (PCR), cleanup of rbcL amplicons, and set-up of sequencing reactions that are sent away to be processed. Once each student receives their DNA sequence, that sequence can then be BLASTed to reveal the most probable candidate species in the NCBI database. If students have collectively sampled a variety of different leaves, they can do pairwise BLAST comparisons of sequences obtained from both the same type of leaf and different types to assess the usefulness of the rbcl gene for DNA Barcoding among plants. Distance Trees can also be created to investigate phylogenetic relationships.
Using alkaline phosphatase extracted from bean beetles to introduce enzyme characteristics in introductory biology
Fardad Firooznia, The City College of New York
Here we present an investigative enzyme lab using alkaline phosphatase extracted from bean beetles (Callosobruchus maculatus). We are extracting the enzyme from beetles instead of using pre-purified alkaline phosphatases purchased from chemical companies. The simple extraction method does not require dissection of the insects and isolation of the digestive organs. In the process of performing this exercise, students will a) learn about the life cycle of the beetles and how to identify different genders and how to culture the beetles, b) gain experience in designing a study using basic biochemical techniques such as simple extractions, standard curves, and colorimetric assays, and collecting, analyzing, and reporting data for such a study, and c) discuss and study the factors that affect the activity of enzymes. Depending on the level at which the course is taught, longer term projects may include optimizing pH and temperature conditions, determining Km and Vmax, and investigating the effects of potential inhibitors identified through a literature review.
Effects of creatine monohydrate on Brassica rapa growth
Juan Aldana, Medicine Hat College
Creatine monohydrate has demonstrated ergogenic benefits in numerous human studies, prompting investigation into its potential effects on plant systems. This study explored the impact of creatine monohydrate on Brassica rapa (fast plants), a model organism suitable for rapid growth experiments. The investigation was motivated by as a small project in a first year biology class. The experiment, conducted in a controlled laboratory environment, aimed to determine the optimal concentration of creatine monohydrate for promoting growth. Two thousand five hundred and twenty B. rapa plants were divided into seven treatment groups, each further subdivided into five trays of 72 plants. Plants were watered weekly for seven weeks with varying creatine monohydrate concentrations: a control group (water only) and six treatment groups (0.10, 0.12, 0.14, 0.16, 0.18, and 0.20 g/mL). Twelve plants per tray were randomly selected for weekly height measurements to monitor growth progression. At the conclusion of the seven-week growth period, all plants were harvested and weighed to determine the final biomass. Phenological data, including observations of leaf development, stem structure, and overall plant health, were also collected to assess the impact of creatine monohydrate on overall growth and development. Results indicated that the 0.12 g/mL creatine monohydrate concentration yielded the highest increase in both plant height and weight compared to the control and other treatment groups. These findings suggest a potential positive effect of creatine monohydrate on B. rapa growth at this specific concentration. Future research will involve chemical analysis of plant tissue samples to quantify creatine uptake and explore the underlying mechanisms responsible for the observed growth enhancement. This analysis will provide a more comprehensive understanding of creatine monohydrate’s influence on plant physiology and potentially reveal its role in plant growth regulation.
Exploring Biodiversity Indexes: Laboratory Applications in Ecology, Epidemiology and Beyond
Erick Caamano & Brandy Garrett Kluthe, Saint Peter’s University
Biodiversity indexes are essential for quantifying species diversity within ecosystems providing valuable insights into ecological health, conservation efforts, and epidemiological patterns. This laboratory explores the fundamental biodiversity indexes which include species richness, Simpson’s index, Shannon’s index, dominant species index, and biodiversity evenness detailing how to use and interpret them. The laboratory exercises assign different student groups predetermined data with the color of the bead representing the species and the number of beads representing abundance. This laboratory aims to expose students, through hands-on simulations, to a comprehensive resource that looks at calculating and defining these indexes and shows how to integrate these metrics in their ecological or epidemiological research such as monitoring habitat changes, assessing ecosystem stability, and tracking the spread of vector-borne diseases. Understanding and utilizing biodiversity indexes allows researchers and practitioners to make informed decisions in environmental management, conservation biology, and public health. This laboratory activity utilizes critical thinking skills and can be adapted for introductory or advanced levels courses.
Female Anatomy and Physiology “Street Interview” Activity
Lisa Prowant, Culver-Stockton College
We have all seen late-night style shows with segments where a correspondent interviews people on the street to see what they know about a topic. That is the idea behind this anatomy activity, which explores female reproductive anatomy and physiology through one-on-one interviews between students. This activity was heavily inspired by the Roe v. Bros videos on social media (https://linktr.ee/roevbros), but was expanded to include a research component so students could increase their knowledge. In the Roe v. Bros videos, people walking by the interviewer are asked questions about female anatomy and reproduction. Questions examples include “what is a placenta?” and “can a woman hold her period like pee?” Students are each given notecards with one question on each notecard. Students then interview other members of the class, asking the questions on their notecards and recording the answers they receive. Once they have interviewed a predetermined number of other students, they return to their seat for research. They investigate the correct answer to each of their questions, with the answers taken from reliable sources. This portion of the exercise should include a discussion of what a “reliable” source is and how you can tell. After their research, students each make a PowerPoint or Google Slides presentation with 3 slides for each question they had. The first slide, per question, states the question, the second includes the list of answers they received, and the third includes the answer and the source of that answer. They are also encouraged to include any useful images, diagrams, or fun facts. The students then present their slides to the class, including a discussion on if each source is reliable, and how to tell. This activity provides a fun, interactive way to teach the intricacies of female anatomy and physiology, human reproduction, and birth control.
Making connections between PCR primer design theory and application using root transformation of soybeans as a model system
Laurie Pacarynuk, University of Lethbridge
PCR is a powerful tool used to confirm presence of DNA sequences and PCR primer design is key to success in DNA amplification. Students often struggle with aspects of primer design such as figuring out where primers should bind, on what DNA strand the primers should bind to, and how to ensure replication of their region of interest. To help students with these concepts, I have incorporated primer design, group evaluation, and then use of student designed primers into a third-year molecular techniques laboratory. Students use Agrobacterium rhizogenes containing vector pCAMGUSGFP to transform soybean roots. To confirm success, they use fluorescence microscopy and GUS staining to provide phenotypic evidence of transformation. I then have students design primers to amplify either GUS or GFP as neither of these sequences are found in plant cells. These primer sequences are submitted to the entire class anonymously and then students work in groups to evaluate each pair of primers dealing with questions such as “Do the primers bind? Do they amplify what they are supposed to? Do they fulfill conditions for successful primers – eg length, GC content”. Students are also asked to predict the results from PCR of transformed plants by drawing the results of agarose gel electrophoresis. Students then submit their top three primer pairs along with their group evaluations. We order the top ranked primers and use them in PCRs of root tissue showing evidence via microscopy and staining of transformation to confirm transformation success. Students then reflect on their choice of primers and their understanding of primer design in a written assessment.
Level Up Your Soil Respiration Knowledge: Gamifying Soil Respiration Lab Activities for Engagement and Active Learning
Manon Lepage, University of Alberta
Soil respiration is an important process for the cycling of carbon in ecosystems and contributes significantly to the global carbon cycle. The respiration rate of different plant litter and environmental conditions is studied during a 200-level ecology lab using sodium hydroxide traps and statistical analysis. Despite successfully completing the practical components of the activity, students struggle with the counterintuitive analysis of the C:N ratio and the daily respiration rate when announcing their hypothesis, the two parameters being inversely proportional. A gamification approach based on the board game Timeline® was used to allow students to familiarize themselves with the relationship between the two parameters. In small groups, students need to sort different substrates (examples: cow manure, tree leaves, pine needles, general food waste) in terms of their C:N ratios. This activity is a valuable way to help students understand the impact of molecular structure of the available litter and the important relationship between nutrient availability and microbial activity.
DNA Repair as a Model to Challenge Student Inquiry and Experimental Design
Christopher Day, Claire Meaders & Lisa McDonnell, University of California San Diego
Using CRISPR-cas9 as a tool to generate double stranded breaks in yeast, students can explore the processes involved in DNA repair. We describe an experimental package that allows students to learn valuable tool building skills but with an emphasis on hypothesis driven research and experimental design. This platform inspires students to generate diverse hypotheses and allows for the collection of unique data sets for analysis. Our approach is to target the ADE2 gene that has a distinct red colour for loss of function alleles. Students design and utilse homology directed repair (HDR) templates to create a wide range of edits to the ADE2 gene; this can range from point mutations to much larger insertions and deletions. Students take ownership of their designs, and gain confidence to plan, implement, and execute a real experiment.We will review several examples of experimental predictions and outcomes that have allowed students to see the scientific process unfold. Students make unanticipated discoveries that lead to fertile discussions regarding models of DNA repair and CRISPR function. Through data analysis, students refine their understanding and challenge their assumptions, and this is a launchpad for conversations to consider more applied applications for gene therapy.
Explorations in genetics research – broadening access to undergraduate research through a one-semester course
Megan K. Dennis & Madison McCarthy, Marist University
Like most small to midsize institutions, Marist has far more students who desire research opportunities than there are positions via traditional apprenticeship models. We are beginning to implement large-scale efforts (i.e. SEA-PHAGES) to address this, but students who arrive as transfers are still missing these important experiences. In this work, we describe the creation of a 1-semester lab course designed to provide students an opportunity to learn important skills and build their scientific identities. Students are introduced to the model organism Caenorhabditis elegans which are durable, have a short life cycle, and are budget-friendly, making them ideal for student research. C. elegans also possess observable phenotypes and contain many homologs of human genes, allowing for study of disease-related mutations in individual genes, including let-418/chd3 which was analyzed here. Students learn basic worm husbandry and utilize a variety of phenotypic assays and molecular techniques throughout the term. They gain wet lab experience, as well as modules designed to develop scientific communication skills, data analysis, and reading the primary literature. Students completed a short questionnaire to assess their scientific self-efficacy, scientific identity, and how much they valued the objectives of the scientific community. Additionally, the Test of Scientific Literacy Skills was administered before and after the course to determine if students developed skills relating to scientific literacy and data interpretation. We found a small but significant increase in scientific self-efficacy and scientific identity among students at the end of the course – both of which are linked to persistence minoritized students in STEM. Additionally, more students reported being interested in pursuing a career involving scientific research. Thus, this course not only provides an accessible research opportunity for more students, but it also develops many of the soft skills which promote persistence in STEM and motivates students to pursue careers in the sciences.
A multi-pronged approach to building visual literacy skills in a senior biochemistry course
Nina Bernstein & Amy Tessier, MacEwan University
One of the central themes in biochemistry is the intricate relationship between molecular structure and function. Therefore, developing a comprehensive knowledge of biomolecular structures is crucial for advancing our understanding of biochemical processes. The ability to visualize and interpret molecular structures in three dimensions is essential for this pursuit. A key attribute of “thinking like a biochemist” involves always considering biological and biochemical phenomena in the context of molecular structure. More generally, visual objects are often used to represent complex concepts and processes. The ability to interpret and create visual representations is defined as visual literacy and has been identified as a critical skill for undergraduate students in biochemistry1,2. We aimed to integrate visual literacy training into a senior biochemistry laboratory, focusing on both molecular and conceptual visualization. Students developed molecular visualization skills through interactive exploration of protein structures using FirstGlance in Jmol. Conceptual visualization was encouraged through hands-on demonstrations, as well as the creation, interpretation, and critique of graphical outlines and infographics. By incorporating visual literacy training into the laboratory curriculum, we aimed to enhance students’ ability to think critically and communicate effectively in the context of biochemical concepts and processes.
Integrating Active Learning Through Case Studies in Developmental Biology
Emily Shultz & Jennifer Liang, University of Minnesota Duluth
The Developmental Biology is an upper-level undergraduate lecture and laboratory course at the University of Minnesota Duluth. This course challenges undergraduate students with many new concepts. Implementing the case studies is an effective way to connect the active laboratory section to the lecture. Not only can the case studies be used as a strategy to learn in a lecture but, also can be used in a laboratory setting. We have developed “Case Studies” as a way to bring in real-world applications and encourage critical thinking. For instance, students are challenged to answer open ended questions, such as forming hypotheses that could explain real world data.
To determine the effects of using Case Studies, students in the class completed a Likert scale-style survey at the end of the semester. 88.2% of students reported that the Case Studies improved/greatly improved their level of understanding of concepts in developmental biology. 82.3% of students found they improved or greatly improved their confidence with answering open ended questions. . The second year of the study employs paired pre- and post-surveys to assess changes in student confidence and engagement with the material. Adding Case Studies to existing courses, including biology laboratory courses, diversifies teaching methods which has been shown to foster student success. This evaluation of Case Studies can inform future curriculum development, potentially creating a more effective learning environment. Additionally, incorporating Case Studies with hands-on experiences in the laboratory could help increase participation and increase confidence.
Implementation of a Puerto Rican Parrot Genomics CURE into an Upper-Level Biotechnology Course
Don Paetkau, Saint Mary’s College
Juan Carlos Martinez-Cruzado, Alondra Díaz Lameiro, University of Puerto Rico at Mayagüez
Wilson Leung, Washington University
Sheylda Díaz-Méndez, University of Puerto Rico at Ponce
The Puerto Rican Parrot Project of the Genomics Education Partnership (GEP; thegep.org) is a conservation-based bioinformatics Classroom Undergraduate Research Experience (CURE). The Puerto Rican Parrot (Amazona vittata), the only parrot native to a U.S. jurisdiction, has been listed as critically endangered since 1967; by 1975, only 13 individuals remained. Conservation efforts have been hampered by a weak egg-shell phenotype, likely due to the increase or fixation of deleterious alleles during the population bottleneck. This project trains students in bioinformatics while they perform comparative gene annotations and search for candidate mutations in the coding sequences of ~1,512 genes expressed in the uterus. Students use a standard set of practices to construct gene models that satisfy basic biological constraints; start/stop codons and compatible splice donor and acceptor sites to maintain the open reading frame. In order to construct these gene models, students learn how to interpret multiple lines of experimental (RNA-Seq data) and computational (transcript and protein sequence alignments against chicken and other avian species, gene predictions) evidence that are potentially contradictory. To ensure gene models are high quality, each gene is annotated by at least two students working independently at different institutions, before being reconciled by a third individual. Students identify potentially deleterious mutations using SIFT and Polyphen-2. The phenotypic effect of these mutations might be tested in vivo using CRISPR editing in chicken embryos. The expansion of this CURE from a single course (University of Puerto Rico at Mayagüez), to a second course (Saint Mary’s College), to current beta-testing with a larger group of GEP members in preparation for release to a wider public audience, has identified implementation challenges. I am particularly interested in connecting with others who are interested in expanding access to CUREs/CUR-like experiences to students in introductory-level and non-science major courses.
Portable inexpensive microscopes for large classes and STEAM (Science Technology Engineering Art and Mathematics) outreach
Sabrina Segar, University of Minnesota Duluth
The microscopic world has the potential to engage a wide variety of people with the beauty of science. However, microscopes have been largely limited to laboratory and classroom settings. Recent technological advancements have facilitated the development of portable, cost-effective microscopes and imaging devices ranging from 15 to 250 US dollars. This project aims to identify the best portable microscope options for K-12 outreach events based on image clarity and user-friendliness. I hypothesize that the microscopes with built-in digital screens will be the most favored. Data was collected by gathering responses from school-aged participants at a variety of community outreach events. Participants recorded their age range and their level of experience with microscopes. They then completed a survey with a Likert-type scale while observing live planaria under each of the four microscope options (cell phone clip microscope, endoscope with built-in screen, dissecting microscope, compound microscope with built-in screen), rating each microscope. Preliminary results suggest that the compound microscope will be the highest rated for both criteria. Seventy percent of respondents have used a microscope occasionally and twenty-three percent have never used a microscope before, and both groups rated the compound microscope the most highly. We hypothesize that the high rating of the compound microscope is due to the large viewing screen and the compound magnification being similar to the microscopes that participants have used before. Observations during the outreach events indicate that the screens are more accessible than eyepieces, especially for younger students, and improve collaboration. Based on these findings, educators and outreach coordinators should prioritize microscopes that include screens. Screened microscopes not only have the potential to enhance accessibility in community outreach and biology laboratories but also spark curiosity and engagement making hands-on learning more inclusive and impactful.
Impactful hands-on pre-labs using 3D paper models
Sarah Ruffell, University of Waterloo
In introductory 1st year biology labs, students often enter with varying levels of prior knowledge, creating challenges in maintaining a consistent laboratory understanding. To address this, we implemented impactful hands-on pre-labs using 3D paper models designed to reinforce and refresh key biological concepts. These interactive models allowed students to actively engage with fundamental topics such as cell structure, macromolecules, and genetic processes before entering the laboratory setting. The pre-labs were completed outside of lab time and aimed to bridge gaps in prior knowledge, ensuring all students, regardless of their high school biology background, started on more equal footing. Student feedback indicated high engagement and perceived learning benefits, with many reporting increased confidence in applying concepts during lab exercises. Furthermore, in-lab quizzes assessing introductory knowledge demonstrated a measurable improvement in student performance, highlighting the effectiveness of this approach. By integrating 3D paper-based activities as a preparatory tool, we enhanced student comprehension and participation, ultimately fostering a more effective and inclusive learning environment in first-year biology labs.