Development of a Lac Operon Concept Inventory (LOCI)

Missed connections: Exploring features of undergraduate biology students' knowledge networks relating gene regulation, cell-cell communication, and phenotypic expression

Explaining biological phenomena requires understanding how different processes function and describing interactions between components at various levels of organization over time and space in biological systems. This is a desired competency yet is a complicated and often challenging task for undergraduate biology students. Therefore, we need a better understanding of their integrated knowledge regarding important biological concepts. Informed by the theory of knowledge integration and mechanistic reasoning, in this qualitative case study, we elicited and characterized knowledge networks of nine undergraduate biology students. We investigated students' conceptions of and the various ways they connect three fundamental subsystems in biology: 1) gene regulation, 2) cell-cell communication, and 3) phenotypic expression. We found that only half of the conceptual questions regarding the three subsystems were answered correctly by the majority of students. Knowledge networks tended to be linear and unidirectional, with little variation in the types of relationships displayed. Students did not spontaneously express mechanistic connections, mainly described undefined, cellular, and macromolecular levels of organization, and mainly discussed unspecified and intracellular localizations. These results emphasize the need to support students' understanding of fundamental concepts, and promoting knowledge integration in the classroom could assist students' ability to understand biological systems.

Learning and STEM identity gains from an online module on sequencing-based surveillance of antimicrobial resistance in the environment: An analysis of the PARE-Seq curriculum

COVID-19 necessitated the rapid transition to online learning, challenging the ability of Science, Technology, Engineering, and Math (STEM) professors to offer laboratory experiences to their students. As a result, many instructors sought online alternatives. In addition, recent literature supports the capacity of online curricula to empower students of historically underrepresented identities in STEM fields. Here, we present PARE-Seq, a virtual bioinformatics activity highlighting approaches to antimicrobial resistance (AMR) research. Following curricular development and assessment tool validation, pre- and post-assessments of 101 undergraduates from 4 institutions revealed that students experienced both significant learning gains and increases in STEM identity, but with small effect sizes. Learning gains were marginally modified by gender, race/ethnicity, and number of extracurricular work hours per week. Students with more extracurricular work hours had significantly lower increase in STEM identity score after course completion. Female-identifying students saw greater learning gains than male-identifying, and though not statistically significant, students identifying as an underrepresented minority reported larger increases in STEM identity score. These findings demonstrate that even short course-based interventions have potential to yield learning gains and improve STEM identity. Online curricula like PARE-Seq can equip STEM instructors to utilize research-driven resources that improve outcomes for all students, but support must be prioritized for students working outside of school.

LacOp: A free web-based lac operon simulation that enhances student learning of gene regulation concepts

Here, we describe a free, web-based simulation of the lac operon, "LacOp," that is designed to enhance the learning of prokaryotic gene regulation and pathways in advanced high school and undergraduate genetics courses. This new electronic resource was created by a team of students in an advanced undergraduate course and is hosted online (http://flask-env.rnwhymamqf.us-west-2.elasticbeanstalk.com/lacop). LacOp has a simple web interface compatible with a range of devices, including smartphones. To determine whether the LacOp simulation enhances student learning from traditional instruction, we introduced the lac operon to undergraduate genetics students through a traditional classroom experience followed by use of the LacOp simulation. Students worked on their own using the included tutorial to create and test the effect of various genotypes on E. coli lactose metabolism and regulation. Upon completion of the tutorial, students showed measurable gains in conceptual understanding of the lac operon. These students also reported a generally favorable opinion of the LacOP simulation as a use of their instructional time.

Building the lac Operon: A Guided-Inquiry Activity Using 3D-Printed Models

Undergraduate biology courses rely heavily on visual representation of information. Students view images of plants, animals, and microbes, interpret data presented in graphs, and use drawings to understand how cells and molecules interact in three dimensions. Traditional teaching approaches exclude students with visual impairments and disadvantage students with disabilities that affect their interpretation and processing of visual and spatial information, and also students who simply do not identify as "visual learners." By using new technologies to develop tactile teaching tools (TTTs) that can be employed in classrooms, we aim to create inclusive learning environments and more effectively instruct diverse learners. The advent of affordable and accessible 3D printing technology makes it possible to create tactile models that represent molecules, cells, and entire organisms more accurately than traditional visual representations. We describe the assessment of a 3D gene expression puzzle as a guided inquiry learning activity in which students must correctly assemble a series of components in order to achieve an output. Upon completion of the puzzle, the TTT provides tactile feedback through vibration to signal transcriptional activation. Analysis of pre- and postassessment performance demonstrated statistically significant increases in individual students' paired assessment scores in two different classroom implementations, with a greater effect size at a rural minority-serving institution than an urban R1 university. These encouraging preliminary data suggest that TTTs with guided-inquiry learning disproportionately benefit disadvantaged student populations and could serve as a tool in leveling the playing field when teaching abstract biological concepts in diverse educational settings.

Riboflavin Riboswitch Regulation: Hands-On Learning about the Role of RNA Structures in the Control of Gene Expression in Bacteria

American Society for Microbiology (ASM) Curriculum Guidelines highlight the importance of instruction about informational flow in organisms, including regulation of gene expression. However, foundational central dogma concepts and more advanced gene regulatory mechanisms are challenging for undergraduate biology students. To increase student comprehension of these principles, we designed an activity for upper-level biology students centered on construction and analysis of physical models of bacterial riboswitches. Students manipulate an inexpensive bag of supplies (beads, pipe cleaners) to model two conformations of a riboswitch in a bacterial transcript. After initial pilot testing, we implemented the activity in three upper-level classes at one research-intensive and two primarily undergraduate institutions. To assess student perceptions of learning gains, we utilized a pre/post-activity 5-point Likert-type survey instrument to characterize student perceptions of confidence in both their understanding of riboswitches and their ability to apply the central dogma to riboswitches. Median post-test ranks were significantly higher than median pre-test ranks (p < 0.0001) when compared by the Wilcoxon signed-rank test (n = 31). Next, we assessed post-activity knowledge via use of a rubric to score student responses on exam questions. More than 80% of students could correctly describe and diagram examples of riboswitches; data from initial iterations were used to enhance curriculum materials for subsequent implementations. We conclude that this riboswitch activity leads to both student-reported increases in confidence in the ASM curriculum dimension of gene regulation, including central dogma concepts, and demonstrated student ability to diagram riboswitches, predict outcomes of riboswitches, and connect riboswitches to evolutionary roles.

Development and Validation of the Microbiology for Health Sciences Concept Inventory

Identifying misconceptions in student learning is a valuable practice for evaluating student learning gains and directing educational interventions. By accurately identifying students' knowledge and misconceptions about microbiology concepts, instructors can design effective classroom practices centered on student understanding. Following the development of ASM's Curriculum Guidelines in 2012, we developed a concept inventory, the Microbiology for Health Sciences Concept Inventory (MHSCI), that measures learning gains and identifies student misconceptions in health sciences microbiology classrooms. The 23-question MHSCI was delivered to a wide variety of students at multiple institution types. Psychometric analysis identified that the MHSCI instrument is both discriminatory and reliable in measuring student learning gains. The MHSCI results correlated with course outcomes, showing the value of using the instrument alongside course level assessments to measure student learning. The MHSCI is a reliable and efficient way to measure student learning in microbiology and can be used both as a faculty development tool and an effective student assessment tool.

Development, Validation, and Application of the Microbiology Concept Inventory

If we are to teach effectively, tools are needed to measure student learning. A widely used method for quickly measuring student understanding of core concepts in a discipline is the concept inventory (CI). Using the American Society for Microbiology Curriculum Guidelines (ASMCG) for microbiology, faculty from 11 academic institutions created and validated a new microbiology concept inventory (MCI). The MCI was developed in three phases. In phase one, learning outcomes and fundamental statements from the ASMCG were used to create T/F questions coupled with open responses. In phase two, the 743 responses to MCI 1.0 were examined to find the most common misconceptions, which were used to create distractors for multiple-choice questions. MCI 2.0 was then administered to 1,043 students. The responses of these students were used to create MCI 3.0, a 23-question CI that measures students' understanding of all 27 fundamental statements. MCI 3.0 was found to be reliable, with a Cronbach's alpha score of 0.705 and Ferguson's delta of 0.97. Test item analysis demonstrated good validity and discriminatory power as judged by item difficulty, item discrimination, and point-biserial correlation coefficient. Comparison of pre- and posttest scores showed that microbiology students at 10 institutions showed an increase in understanding of concepts after instruction, except for questions probing metabolism (average normalized learning gain was 0.15). The MCI will enable quantitative analysis of student learning gains in understanding microbiology, help to identify misconceptions, and point toward areas where efforts should be made to develop teaching approaches to overcome them.

Teaching Genetics: Past, Present, and Future

Genetics teaching at the undergraduate level has changed in many ways over the past century. Compared to those of 100 years ago, contemporary genetics courses are broader in content and are taught increasingly differently, using instructional techniques based on educational research and constructed around the principles of active learning and backward design. Future courses can benefit from wider adoption of these approaches, more emphasis on the practice of genetics as a science, and new methods of assessing student learning.

Diagnostic of students' misconceptions using the Biological Concepts Instrument (BCI): A method for conducting an educational needs assessment

Concept inventories, constructed based on an analysis of students’ thinking and their explanations of scientific situations, serve as diagnostics for identifying misconceptions and logical inconsistencies and provide data that can help direct curricular reforms. In the current project, we distributed the Biological Concepts Instrument (BCI) to 17-18-year-old students attending the highest track of the Swiss school system (Gymnasium). Students’ performances on many questions related to evolution, genetics, molecular properties and functions were diverse. Important common misunderstandings were identified in the areas of evolutionary processes, molecular properties and an appreciation of stochastic processes in biological systems. Our observations provide further evidence that the BCI is efficient in identifying specific areas where targeted instruction is required. Based on these observations we have initiated changes at several levels to reconsider how biological systems are presented to university biology studies with the goal of improving student’s foundational understanding.