Undergraduate Laboratory Course Research Articles

Study on the LED Light Induced Cyanomethylation of Imidazopyridine Used in the Teaching of Undergraduate Laboratory Course

Study on the LED Light Induced Cyanomethylation of Imidazopyridine Used in the Teaching of Undergraduate Laboratory Course

Determining the Effect of pH on Iron Oxidation Kinetics in Aquatic Environments: Exploring a Fundamental Chemical Reaction To Grasp the Significant Ecosystem Implications of Iron Bioavailability

Understanding the controls of the oxidation rate of iron (Fe) in oxygenated aquatic systems is fundamental for students of the Earth and Environmental Sciences as it defines the bioavailability of Fe, a trace metal essential for life. The laboratory experiment presented here was successfully developed and used during a third-year undergraduate lab course at Imperial College London for several years. It employs ultraviolet–visible (UV–vis) spectroscopy calibrated externally with 0 to 50 μM Fe2+ standards created in a 492 μM ferrozine and 0.43 M acetate matrix. The students conducted the oxidation experiments in stirred batch reactors at equilibrium with atmospheric oxygen. The solution contained 40.5 μM initial Fe2+ concentration and a 5.1 mM imidazole buffer. The pH was adjusted to values between 7.22 and 7.77. The students observed a pseudo-first-order reaction with respect to Fe2+ concentration. Plotting the logarithms of the apparent rate constants (k′) at different pH values leads to a gradient of 2.2 ± 0.2 min–1 pH–1, indicating a second-order reaction with respect to OH– concentration, in agreement with published literature. The oxidation reaction occurred rapidly (tens of seconds to tens of minutes) indicating that in oxygenated aquatic systems, Fe3+ will be the dominant oxidation state, significantly reducing the bioavailability of Fe. The simple laboratory experiment presented here allows the students to learn about kinetic parameters for a fundamental chemical reaction. It allows the students to explore the significant implications this has for aquatic ecosystems.

A guided-inquiry investigation of bacterial membrane potential using flow cytometry for an undergraduate biochemistry laboratory course.

Flow cytometry has become an important tool in the life sciences and medical fields, yet there are often few opportunities for undergraduate students to receive training with this type of instrumentation as part of life science curricula at many colleges and universities. We describe a straightforward laboratory exercise designed for a college-level biochemistry course that uses flow cytometry to investigate changes in bacterial membrane potential and cell viability in response to various treatments. Anecdotally, we have noticed that many students often have difficulty understanding the concept of membrane potential and the essential role that it plays in cellular processes. Therefore, this exercise also provides a pedagogical tool for visualizing changes in cellular membrane potential as way to enhancing students' comprehension of this abstract concept. Students' understanding of flow cytometry and membrane potential was assessed using a preactivity and postactivity quiz; the results indicate that the students' understanding of these concepts significantly improved after they completed this laboratory exercise. © 2019 International Union of Biochemistry and Molecular Biology, 48(1):61-66, 2020.

Biology Student Perceptions of Information Literacy Instruction in the Context of an Essential Skills Workshop Series

The University Libraries at the University of New Mexico reconfigured their established library instruction program for biology as part of a broader grant-funded essential skills workshop series for STEM students. This initiative standardized supplementary instruction through seven in-person and online workshops delivered to students through the Biology Department’s four core undergraduate laboratory courses. Post-workshop feedback data were gathered from students throughout the two-year grant period. The present study analyzes this data set—including 3,797 completed student surveys from both library and non-library workshops over the course of four semesters—with the goal of understanding STEM student perceptions of the value of information literacy skills as compared to the general and disciplinary value of other essential intellectual and practical skills. The findings suggest that undergraduate biology students generally perceive information literacy to be among the most valuable and relevant skills introduced through the workshop series. The results have the potential to inform information literacy instruction practices and collaborative efforts with broader essential skills education programs.

Biology Student Perceptions of Information Literacy Instruction in the Context of an Essential Skills Workshop Series

The University Libraries at the University of New Mexico reconfigured their established library instruction program for biology as part of a broader grant-funded essential skills workshop series for STEM students. This initiative standardized supplementary instruction through seven in-person and online workshops delivered to students through the Biology Department’s four core undergraduate laboratory courses. Post-workshop feedback data were gathered from students throughout the two-year grant period. The present study analyzes this data set—including 3,797 completed student surveys from both library and non-library workshops over the course of four semesters—with the goal of understanding STEM student perceptions of the value of information literacy skills as compared to the general and disciplinary value of other essential intellectual and practical skills. The findings suggest that undergraduate biology students generally perceive information literacy to be among the most valuable and relevant skills introduced through the workshop series. The results have the potential to inform information literacy instruction practices and collaborative efforts with broader essential skills education programs.

Using think-aloud interviews to characterize model-based reasoning in electronics for a laboratory course assessment

Models of physical systems are used to explain and predict experimental results and observations. The Modeling Framework for Experimental Physics describes the process by which physicists revise their models to account for the newly acquired observations, or change their apparatus to better represent their models when they encounter discrepancies between actual and expected behavior of a system. While modeling is a nationally recognized learning outcome for undergraduate physics lab courses, no assessments of students' model-based reasoning exist for upper-division labs. As part of a larger effort to create two assessments of students' modeling abilities, we used the Modeling Framework to develop and code think-aloud problem-solving activities centered on investigating an inverting amplifier circuit. This study is the second phase of a multiphase assessment instrument development process. Here, we focus on characterizing the range of modeling pathways students employ while interpreting the output signal of a circuit functioning far outside its recommended operation range. We end by discussing four outcomes of this work: (1) Students engaged in all modeling subtasks, and they spent the most time making measurements, making comparisons, and enacting revisions; (2) Each subtask occurred in close temporal proximity to all over subtasks; (3) Sometimes, students propose causes that do not follow logically from observed discrepancies; (4) Similarly, students often rely on their experiential knowledge and enact revisions that do not follow logically from articulated proposed causes.

Combining novel research and community-engaged learning in an undergraduate physiology laboratory course.

To better prepare physiology students for 21st century careers, we incorporated classroom-based undergraduate research experiences and service learning/community-engaged learning (SLCE) into a college-level physiology laboratory course. The interventions were incorporated over 4 yr and assessed using validated surveys of student-reported learning gains related to attitudes toward science, the scientific process, and career paths. Students reported the greatest learning gains in those years when students did novel research oriented around a common theme of water quality. The gains were greater than those of a matched cohort that participated in an apprentice-style summer undergraduate research experience. With respect to the SLCE related to youth science literacy, students provided evidence of learning related to academics, personal growth, and civic mindedness. For example, many expressed discomfort about being in a new situation, often describing the differences between themselves and the youth with whom they interacted. However, students also grew in confidence about collaborating with people who were different from them and in their role as the "scientist." Limitations of the study include the quasi-experimental design and the incorporation of multiple interventions at the same time. Future studies should examine improvement in content acquisition and competency-based learning skills. Nonetheless, these results suggest that both novel research and SLCE increase student learning in the context of an undergraduate physiology laboratory course. Many of the learning gains observed with the SLCE are particularly important for physiology students, many of whom aspire to careers in health sciences, where they will be regularly working with nonscientists.

Perceived Student Benefits of an Undergraduate Physiological Psychology Laboratory Course

Undergraduate research (UR) is a high-impact practice associated with many positive student outcomes. However, extending UR opportunities to all students is not practical for all psychology program...

Enhancing Motivation To Learn In A Biology Laboratory Course Through Gaming

In this design case, we describe our work to develop a gameful learning design for use in an introductory, undergraduate biology laboratory course for science majors. Our design team included three university-based mathematics and science educators and a biologist responsible for the management of curriculum and instruction in the course under study. The gameful learning design was employed during the four weeks of plant evolutionary life history instruction. Key challenges to the design and implementation of gameful learning included the adaptation of instruction from teacher-centered to student-centered and establishing novel learning conditions in the eight laboratory sections so as to determine the value of two different elements of game design, repeat-testing and leaderboard with badges.

Serum albumin as a model protein in designing an undergraduate laboratory course in biochemistry

A previous work on the design of an undergraduate laboratory course in biochemistry using serum albumin as model protein, presented at the EB 2017 conference was widely accepted. Based on comments and suggestions from faculty colleagues, we are extending the project. Extensions to the course include using fluorescence spectroscopy to monitor and determine the kinetic parameters of chemically induced unfolding of serum albumin. Serum albumin has desirable properties that make the protein a suitable model for the laboratory course design. The protein is highly abundant in blood plasma or serum; it is very soluble and stable in a wide range of buffer, pH and salt conditions. The structure of albumin makes it an ideal candidate for students to study protein structure‐function relationship using spectroscopic methods such as fluorescence, circular dichroism, infrared and UV‐Visible spectroscopies. Of particular note is the robustness of the course in terms of cost‐effectiveness, skill‐sets and pedagogical aims. All the data presented herein were generated and analyzed by students under the guidance of the professor. This is a classic example of using faculty research as a teaching tool.Support or Funding InformationWelch Foundation Grant # AN‐0008This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Using Educational Escape Room Activities to Teach Teamwork Skills and Build Effective Teams

Teamwork involves a set of skills used by a group of people who are working together towards a common goal. It is one of the most important skill sets for many careers; however, undergraduate students report that opportunities to develop teamwork skills are limited. Additionally, knowing the criteria that should be used to build effective teams of students can be challenging for instructors. In response to these problems, our aim was to develop and evaluate a low‐stakes team‐based activity that provides students with an opportunity to practice and develop teamwork skills. We also used the activity to investigate the criteria required to select effective student teams. To do this, we collaborated with a local escape room design team to develop a novel educational escape room activity (escape activity) that could be implemented in upper year science laboratory courses. Briefly, the activity requires students to work in teams and consists of various thematic challenges, such as visual and numerical puzzles. It requires collaboration amongst team members, each with their own strengths and perspectives, to solve a series of challenges and “break‐in” to the box within a limited amount of time.Currently, a longitudinal study approved by our institutional review board is being completed in a fourth‐year undergraduate laboratory course, which requires students to work in teams throughout the semester on a research project. The escape activity was run during the first lab session and students were randomly placed in small groups. Following the activity, students completed a validated self‐efficacy of teamwork skills survey and reported on their past research experiences. The results of the surveys allowed us to build teams that had strengths in teamwork skills, research experience, or both. When building teams, we ensured that they all represented a diversity of skills so that no teams were disadvantaged. An additional survey on self and peer evaluations of teamwork behaviours will also be administered at the end of the semester to evaluate the effectiveness of these teams. This will be done using a t‐distribution test on the teams' scores. The results of these surveys could inform the criteria that are used to select effective student teams in the future. Individual and group‐based reflections completed after the activity and at the end of the semester will be analyzed to identify themes related to teamwork concepts that students learned and compared to surveys on past teamwork experiences. These will assess the students' development of teamwork skills and their perceptions of its importance throughout the semester, which could inform the effectiveness of the escape activity as a pedagogical tool to teach teamwork skills. The data is in the process of being collected and analyzed.The escape activity is generalizable to any course or discipline. Thereby, validation of the escape activity as an effective pedagogical tool to teach teamwork skills could provide educators with an innovative opportunity to address the lack of opportunities for teamwork development in the undergraduate curriculum. It could also enhance students' self‐efficacy of teamwork skills which could provide educators with criteria to develop more effective student teams.Support or Funding InformationWestern CTLThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Integration of Authentic Research into an Undergraduate Laboratory Course: Design and Synthesis of a Gene Therapy Vector

Undergraduate Biology students often graduate without exposure to authentic research experiences. Laboratory courses often follow a one or two week fail‐proof experiment resembling a cookbook recipe, lacking the uncertainty of genuine research. Techniques in genetics and molecular biology cover a wide array of skills that are essential to succeed in a biotechnological laboratory today. Can we design a lab course based on the teaching of concepts while imparting the skills and applications of modern techniques to undergraduate students? In our experimental laboratory course, we focus on the implementation of genetics and molecular biology lab techniques, thus providing students with theoretical concepts and laboratory skills. We prepare students to carry‐out scientific protocols that can be applied to a future workforce setting. Students are immersed in an 11‐week series of labs with the objective to use molecular cloning to make a gene therapy vector; therapies are designed to inhibit the overexpression of oncogenes in brain tumors. Students in the laboratory are introduced to PubMed and Genbank to research the background of the target gene. Students use DNA analysis software, Serial Cloner, as an interactive tool to evaluate DNA sequences and visualize therapy design, with each student generating their own therapy vector. Students isolate and purify DNA using a plasmid purification protocol, and measure quantity and quality using a spectrophotometer. They are introduced to molecular cloning and the value of master mixes, beginning with the digestion of their DNA plasmid using restriction enzymes. Students, making their own buffers and gels, perform gel electrophoresis and subsequently cut‐out the appropriate bands. Students purify bands and clean‐up DNA with magnetic beads, preparing samples for the next step. Students perform DNA ligation with proper controls and transform ligations into DH5‐α super competent cells. To verify successful transformation, students make Luria Broth ampicillin plates and spread transformed bacteria onto plates; ligation efficiency is measured based on bacterial colony count. The students then use colony PCR and agarose gel analysis to verify successful ligations. At the end of the semester, students compile results from each step during the 11‐week lab series and integrate learning from the lecture to synthesize a comprehensive lab report. Student evaluation is based on connecting lecture concepts to laboratory experiments, including clearly stating lab objectives, writing protocols in own words, accurately recording results in notebook (in pen), labeling of figures, analysis of data, and comprehension of results. Properly recording and understanding results is more highly valued over expected results. Successful experiments carried‐out in the course are used to contribute to authentic research projects. The goal of this lab course is to integrate authentic research into the undergraduate learning experience, preparing students for graduate school and employment in a modern biotechnological lab; establishing the next generation of scientist.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Structural Studies of GMP Reductase from Escherichia coli

Guanosine Monophosphate Reductase (GMPR) is an NADPH‐dependent enzyme that catalyzes the reductive deamination of guanosine (G) monophosphate nucleotides into their corresponding inosine (I) monophosphate derivatives. GMPR plays an important role in purine salvage, re‐utilization of free intracellular bases, and contributes overall to the intracellular balance of G and adenine (A) nucleotides. As with many other enzymes in the purine salvage or biosynthesis pathways, GMPR is widespread in nature across eukaryotic and prokaryotic taxa. Given the interest in purine metabolism as a potential target for drug design, GMPR has been characterized both structurally and kinetically in different studies using GMPR derived from several species. We report progress towards solving the crystal structure of GMPR from Escherichia coli in order to extend the insight from existing studies of the E. coli GMPR kinetic and thermodynamic characteristics. Additionally, lessons learned from integrating related research activities into an undergraduate laboratory course will be presented in order to promote adoption of similar course‐based research practices at other primarily‐undergraduate institutions.Support or Funding InformationIthaca College Department of ChemistryThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Augmenting the fine beam tube: From hybrid measurements to magnetic field visualization

Since the emergence of augmented reality (AR), it has been a constant subject of educational research, as it can improve conceptual understanding and generally promote learning. In addition, a motivational effect and improved interaction and collaboration through AR were observed. Recently, AR technologies have taken a major leap forward in development, such that head-mounted devices or smartglasses in particular are now finding their first applications in STEM education, especially in experiments. In line with these developments, we here present an AR experiment in electrodynamics for undergraduate laboratory courses in physics using real-time physical data from and virtual tools on mobile devices to both analyze and visualize physical phenomena.

Bacterial cellobiose metabolism: An inquiry-driven, comprehensive undergraduate laboratory teaching approach to promote investigative learning.

Technique-centered biochemistry or molecular biology undergraduate laboratory curricula do not offer significant opportunities for thoughtful, in-depth exploration of the science to foster investigative learning. To demonstrate inclusion of inquiry-driven laboratory experiments into the undergraduate biochemistry and molecular biology curricula, a comprehensive set of laboratory experiments, covering several principles of biochemistry and molecular biology, have been developed under a single theme. The laboratory curriculum described here comprehensively investigates bacterial cellobiose metabolism using multiple biochemical, molecular biological (RNA isolation, RT-PCR, PCR, and enzyme assay), and analytical techniques (High Performance Liquid Chromatography, NMR, spectrophotometry, and thin-layer chromatography) to explore the principles of metabolomics and genomics in a single undergraduate laboratory course setting using Caulobacter crescentus as the model organism. This laboratory module serves as a model for educators to develop easy-to-implement laboratory curricula incorporating contemporary biochemistry and molecular biology concepts and techniques to provide a course-based undergraduate research experiences (CUREs) with defined learning objectives. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):438-445, 2019.

Plagiarism or not? investigation of Turnitin®-detected similarity hits in biology laboratory reports.

In undergraduate biology laboratory courses, laboratory reports can be a useful tool for teaching scientific writing, integration of source material, and information literacy; however, these teaching objectives are at times undermined by students' plagiarism. Laboratory instructors often use similarity-matching software to detect plagiarism in laboratory reports, yet similarity hits detected with such software remain poorly characterized. In the upper division molecular biology laboratory course described here, Turnitin® routinely detected dozens of similarity hits in laboratory reports. To determine whether this abundance of similarity hits was indicative of widespread plagiarism, we analyzed similarity hits detected in 255 laboratory reports written by 135 students. Only a small minority of Turnitin® similarity matches were problematic, but over half of the laboratory reports contained at least one problem with incorporation of scientific sources (e.g., laboratory manual and scientific articles). We identified four common types of such writing problems: patchwriting, technical parroting, copying, and falsification of sources. In 18% of the laboratory reports, we detected an alarmingly superficial use of primary literature. Most of the source incorporation problems did not rise to the level of plagiarism. As a result of this study, we recommend changes in scientific writing instruction and a transition to laboratories providing more authentic research experiences. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):370-379, 2019.

Teaching an Undergraduate Organic Chemistry Laboratory Course with a Tailored Problem-Based Learning Approach

This article presents the structure of the organic chemistry laboratory Course “Synthesis and Extraction of Drugs” that is included in Modena University (Italy) in the third year of the five-year “Chemistry and Pharmaceutical Technologies” degree program. This course is unique in its kind, and it aims to provide students with the critical-thinking skills required to face practical organic synthesis. Because the “problem-based learning” approach ensures a high level of learning, we modified this approach to reconcile the students’ knowledge, the resources available compared with the number of students, and the purpose of a deep learning. Accordingly, tailored academic materials have been prepared (a textbook, a laboratory notebook, and a selection of primary literature), appropriate in-class and laboratory activities have been set up, and a grading pattern that promotes the active learning process has been defined. Although the number of students is high, following this approach, very positive results with...

Self-Propagating High-Temperature Synthesis of Titanium Carbide: An Educational Module using a Wooden Block Reactor

Self-propagating high-temperature synthesis is an effective method for preparing refractory ceramic materials, especially carbides and borides as fine powders. The common perception that a pressurized stainless steel reactor is necessary for conducting the synthesis has, until now, excluded it from undergraduate laboratory courses. Our students performed this synthesis using a simple and inexpensive wooden block reactor to prepare TiC, using TiO2, C and Mg as the reactants. The product at this stage is contaminated with Mg2TiO4 which forms through a side-reaction during this highly exothermic reaction. The factors that caused this provoked a stimulating class discussion and led to a method for recovering the TiC as a monophasic powder. The crude and purified product materials were characterized by powder X-ray diffraction. All in all, these aspects make this synthesis an ideal experiment for undergraduate laboratory in chemistry or materials science courses. Moreover, the skills and methods learned through this experiment ensure that students are better equipped to tackle the self-propagating high-temperature synthesis of more complex carbides and refractory ceramic materials in conventional reactors.

Laboratory Exercise To Measure Restriction Enzyme Kinetics.

Enzymes are ubiquitous in the fields of biology and microbiology, catalyzing critical reactions and enabling a broad range of biotechnological applications. Despite the important role that enzyme catalysis plays in biological processes, undergraduate students often struggle to understand enzyme kinetics in the classroom. In an attempt to improve students’ understanding of the topic, we present a relatively short and inexpensive laboratory activity designed to give students hands-on experience with generating and manipulating enzyme kinetic data. Students perform restriction digests of DNA at various time points, visualize the reaction products on an agarose gel, and quantify their data in order to construct Lineweaver-Burk plots which compare the effects of a restriction enzyme and its engineered version. The activity may be completed in a single two-hour lab session and, unlike other enzyme assays designed for laboratory courses, does not require a microplate reader to complete. The activity allows students to see connections between a visual data set and quantitative kinetic data, in order to solidify their understanding of enzyme kinetics. Students also learn the skills of gel electrophoresis and image quantification using ImageJ software. This lab activity is ideal for undergraduate laboratory courses which address enzyme kinetics and DNA technology.

Plot Twist: Changing the Story in Graphing Skills with an Open-Ended Approach

Two of the most fundamental skills that students acquire in introductory undergraduate physics laboratory courses are how to accurately plot data and interpret the physical meaning of linear graphs. We redesigned our graphing skills lab with an open-ended approach designed to promote inquiry in graphical analysis and to address specific areas of weakness in students’ understanding of graphs. Students had to decide on their own how to graph data in order to promote understanding of linear relationships between variables and slope. Students completing the new open-ended lab developed and retained better graphing skills than students that were taught the lab with a more traditional cookbook approach.