Undergraduate Laboratory Classes Research Articles

Post-COVID-19 approach to teaching an undergraduate laboratory class focused on experimental design and data interpretation.

To best prepare students for the real-world research environment, key skills, including experimental design, data analysis, communication of results, and critical thinking, should be key components of undergraduate science courses. Furthermore, the impact of the COVID-19 pandemic on in-person teaching has resulted in a need to develop courses that enable flexible learning. This paper details the laboratory component of a senior-level toxicology class that was developed to emphasize all these skills and allow for flexible learning. The aim of the laboratory class was for students to determine how curcumin protected against acetaminophen-induced hepatoxicity. To stimulate critical thinking, students were required to choose a maximum of four experiments from the six on offer. Before conducting an experiment, students stated a hypothesis and selected the appropriate treatment groups. Once an experiment was completed, students were given access to a complete dataset, on which they performed statistical analysis and drew conclusions. Students who were unable to attend the laboratory session in person were able to complete the required pre-lab work and access the dataset. Following each experiment, students could write a lab summary, and receive thorough feedback. The final assessment was a written manuscript of their findings as well as a chance to respond to reviewer comments. This teaching approach prioritized the critical thinking, analysis, and experimental design aspects of scientific research. Overall, this structure was well received by students and it could easily be adapted for use on other life science courses.

A simple, robust, broadly applicable insertion mutagenesis method to create random fluorescent protein: target protein fusions.

A simple, broadly applicable method was developed using an in vitro transposition reaction followed by transformation into Escherichia coli and screening plates for fluorescent colonies. The transposition reaction catalyzes the random insertion of a fluorescent protein open reading frame into a target gene on a plasmid. The transposition reaction is employed directly in an E. coli transformation with no further procedures. Plating at high colony density yields fluorescent colonies. Plasmids purified from fluorescent colonies contain random, in-frame fusion proteins into the target gene. The plate screen also results in expressed, stable proteins. A large library of chimeric proteins was produced, which was useful for downstream research. The effect of using different fluorescent proteins was investigated as well as the dependence of the linker sequence between the target and fluorescent protein open reading frames. The utility and simplicity of the method were demonstrated by the fact that it has been employed in an undergraduate biology laboratory class without failure over dozens of class sections. This suggests that the method will be useful in high-impact research at small liberal arts colleges with limited resources. However, in-frame fusion proteins were obtained from 8 different targets suggesting that the method is broadly applicable in any research setting.

Identifying new small proteins through a molecular biology course-based undergraduate research experience laboratory class.

We developed a curriculum for an upper-level molecular biology course-based undergraduate research laboratory class funded by a National Science Foundation CAREER grant that focuses on identifying new small proteins in the bacterium, Escherichia coli. Our CURE class has been continually offered each semester for the last 10 years, with multiple instructors collaboratively developing and implementing their own pedagogical approach while maintaining the same overall scientific goal and experimental strategy. In this paper, we delineate the experimental strategy for our molecular biology CURE laboratory class, describe a range of pedagogical approaches implemented by multiple instructors, and provide recommendations for teaching the class. The purpose of our paper is to share our experiences both in developing and teaching a molecular biology CURE laboratory class based on small protein identification and in creating a curriculum and support system that allows traditional, non-traditional, and under-represented students to participate in authentic research projects.

Development of YOLOv5-Based Real-Time Smart Monitoring System for Increasing Lab Safety Awareness in Educational Institutions.

The term "smart lab" refers to a system that provides a novel and flexible approach to automating and connecting current laboratory processes. In education, laboratory safety is an essential component of undergraduate laboratory classes. The institution provides formal training for the students working in the labs that involve potential exposure to a wide range of hazards, including chemical, biological, and physical agents. During the laboratory safety lessons, the instructor explains the lab safety protocols and the use of personal protective equipment (PPE) to prevent unwanted accidents. However, it is not always guaranteed that students follow safety procedures throughout all lab sessions. Currently, the lab supervisors monitor the use of PPE, which is time consuming, laborious, and impossible to see each student. Consequently, students may unintentionally commit unrecognizable unsafe acts, which can lead to unwanted situations. Therefore, the aim of the research article was to propose a real-time smart vision-based lab-safety monitoring system to verify the PPE compliance of students, i.e., whether the student is wearing a mask, gloves, lab coat, and goggles, from image/video in real time. The YOLOv5 (YOLOv5l, YOLOv5m, YOLOv5n, YOLOv5s, and YOLOv5x) and YOLOv7 models were trained using a self-created novel dataset named SLS (Students Lab Safety). The dataset comprises four classes, namely, gloves, helmets, masks, and goggles, and 481 images, having a resolution of 835 × 1000, acquired from various research laboratories of the United Arab Emirates University. The performance of the different YOLOv5 and YOLOv7 versions is compared based on instances' size using evaluation metrics such as precision, F1 score, recall, and mAP (mean average precision). The experimental results demonstrated that all the models showed promising performance in detecting PPE in educational labs. The YOLOv5n approach achieved the highest mAP of 77.40% for small and large instances, followed by the YOLOv5m model having a mAP of 75.30%. A report detailing each student's PPE compliance in the lab can be prepared based on data collected in real time and stored in the proposed system. Overall, the proposed approach can be utilized to make laboratories smarter by enhancing the efficacy of safety in research settings; this, in turn, will aid the students in establishing a health and safety culture among students.

Quinone Synthesis and a Visual Introduction to Column Chromatography: An Undergraduate Experiment

An introductory normal phase column chromatography experiment is described and evaluated for second year undergraduate chemistry laboratory class. The experiment involves a nucleophilic substitution yielding a crude mixture of reactant and one product, both of which are brightly colored and contrasting, creating a clearly visual separation when purified using column chromatography. A student survey was conducted which showed that 75.4% of students (n = 53, approximately 50% of year group) agreed or strongly agreed that the experiment worked well for them, and 88.7% agreed or strongly agreed that the experiment was enjoyable. Every student was also assessed in the lab on their practical technique, with the year group achieving an average of 72.1% in this assessment.

The use of isothermal titration calorimetry for the assay of enzyme activity: Application in higher education practical classes.

Determination of enzyme activity is crucial for discovery, research, and development in life sciences. The activity of enzymes is routinely determined using spectrophotometric assays that measure rates of substrate consumption or product formation. Though colorimetric-based detection systems are simple, rapid, and economical to perform, the majority of enzymes are unsuitable for this technique as their substrates/products do not absorb in the UV or visible range. This limitation can be addressed by the use of coupled-enzyme assays or artificial chromogenic substrates; however these approaches have their own drawbacks. Here, we describe a method based on the use of an isothermal titration calorimeter (ITC) to measure the heat produced or absorbed during any enzyme-catalyzed reaction. The concept of calorimetric enzyme assays was demonstrated for the determination of enzyme hexokinase activity, which cannot be monitored colorimetrically without first coupling it to another enzymatic reaction. The assay is suitable for incorporation into undergraduate laboratory classes, providing students with an appreciation for; the versatility and ease of use of ITC assays; ITC as a flexible generic method for exploring the functional characteristics of uncharacterized enzymes; an activity detection parameter suitable for enzymes that either have no straightforward colorimetric methods available or require the use of nonartificial chromogenic substrates.

Microcontroller based study of diode thermometers for online demonstration of undergraduate laboratory classes in COVID-19 lockdown

At constant current (I) the forward bias potential (V) of a pn junction diode may be considered to vary linearly with temperature (t) within a temperature range. Based on this property we have constructed diode thermometer using germanium (Ge) and silicon (Si) diodes. The experimental data at constant forward current have been fitted to a straight line for calibration of the diode thermometers using the least square method. Furthermore, the fitting parameters of the straight line have also been used to determine the band gap energy of germanium and silicon and experimental values of band gap for both the semiconductor materials are found to agree well with accepted values.

“Half-wet-half-dry”: an innovation in undergraduate laboratory classes to generate transgenic mouse models using CRISPR/Cas9 and computer simulation

ABSTRACT Animal models are widely used in laboratory practicals in biomedical disciplines. However, experiments involving animal work are usually time-and-labor consuming. It is also costly to run an animal lab and the animal caring/holding request special training. Here we present a laboratory course design that provides students with wet lab experience in gene editing in mouse stem cell lines using CRSISPR/Cas9 and dry lab experience in generating transgenic mouse models using computer simulation. This workshop is for senior undergraduates as well as graduate students and is designed to help them understand the application of gene editing in biomedical research. The virtual simulation is incorporated as a computer-based alternative to using mice for embryo transplantation, breeding, and characterization. The integrated curriculum of wet and dry laboratories enabled us to complete this complicate multi-disciplinary experiment in one semester. In addition, the computer-based alternatives reduce the unnecessary animal tests down to zero and errors during practice are well-tolerated without raising any ethical issues. The survey and student’s feedback showed overall satisfaction in their learning experiences and learning benefits. The evaluation of the outcomes of learning objectives on the completion of this course revealed positive achievements in bioinformatics, molecular biology, and in general animal work

Facile Grignard Reaction Demonstration Using Molecular Sieved Dried Solvent

Methods involving C–C bond formation are continuously being innovated due to their importance in the creation and modification of important organic molecules. The classic Grignard reaction demonstrates C–C bond formation with reagents that are usually accessible in undergraduate laboratory classes. Oftentimes, to make the Grignard reaction viable, the reactions are assisted by heating at elevated temperatures or with the use of a catalyst accompanied by solvents that have been dried using highly reactive sodium metal (Na0)─conditions which increase the risk of a laboratory fire or explosion. For this work, a method to conduct Grignard reactions under mild conditions utilizing sand-paper-polished Mg ribbons and solvent dried using molecular sieves was developed. The conscientious, accessible, and easy-to-follow preparation of both the solvent and the Mg ribbons is found to contribute more to the percent conversion of reagents to products. The average percent conversion with the proposed method ranged from 76.8% to 99.5% based on 1H NMR results. This makes the Grignard demonstration possible even for the most humid, tropical locations.

Flipped laboratory classes: Student performance and perceptions in undergraduate food science and technology

AbstractIn STEM (science, technology, engineering, and mathematics) courses, undergraduate laboratory classes are vital for students to develop competencies such as critical observation, collaboration, critical thinking, technical, and problem‐solving skills. Thus, for students to successfully acquire these competencies, preparation for laboratory classes is essential. This study aimed to explore the students' performance and perceptions of online pre‐laboratory videos and quizzes in undergraduate food science and technology. Quantitative data on student usage statistics of the videos, student performance in online quizzes and practical reports scores and student perceptions were analysed to provide a detailed perspective of the course. The students' performance was above 60% in all pre‐lab quizzes for both the 2018 and 2019 cohorts. The average pre‐lab video views were higher in the 2019 cohorts compared to the 2018 cohort. The majority of the students felt that the topics were well explained in the videos (M = 4.25 ± 0.84) and it was easy to learn from the videos (M = 4.31 ± 0.76). In terms of students perceptions, a strong positive correlations were found between course organisation and motivation and self‐efficacy (r = 0.86, p < 0.05); course engagement and motivation and self‐efficacy (r = 0.82, p < 0.05). The strongest positive correlation was between course organisation and online engagement (r = 0.95, p < 0.05). The results of this study suggest that the introduction of multimodal/digital preparation resources (pre‐lab videos and online quizzes) was positively received and benefited the students. Students have engaged enthusiastically with these resources and completed the majority of the tasks set. These findings will further expand research directed towards student perception of the lab experience and aid in the adaptation of food science and technology curriculums to accommodate both student and university needs.

Staff-student interactions in a physiology laboratory class: What do they involve and are they important?

Although considerable staff resources are often allocated to the teaching of undergraduate laboratory classes, there is a paucity of discussion regarding the extent and substance of the staff-student interactions that occur within classes and also whether these interactions benefit student learning in any way. Performed across four undergraduate laboratory sessions, this exploratory study aimed to quantify the interactions in terms of frequency, duration, and initiation of interactions, as well as gathering staff and student perceptions of the impact of the interactions. Staff gathered descriptive data by completing an observation checklist after each interaction and also provided their own perceptions of the interaction focus and outcome. Student perceptions were collected using an online survey after each class. Staff perceived that the most frequent achievement of the interactions was to enable students to progress with work. However, students' perceptions suggested that staff may underestimate the impact of staff-student interactions on conceptual learning. The most striking findings were the students' perceptions of the impact of interactions on their affective domain. On average, 93% of students agreed that when staff take an interest in their work, it motivates them to work hard, and 78% agreed that interactions with staff made the classes more enjoyable. With evidence that positive affect such as enjoyment is positively associated with aspects of learning, this is a salient finding. The study underscores the value of staff availability within the laboratory class and provides impetus to reevaluate how we perceive these interactions and their impact on student learning.

Application of DNA Fingerprinting using the <em>D1S80</em> Locus in Lab Classes

In biological sciences, DNA fingerprinting has been widely used for paternity testing, forensic applications and phylogenetic studies. Here, we describe a reliable and robust method for genotyping individuals by Variable Number of Tandem Repeat (VNTR) analysis in the context of undergraduate laboratory classes. The human D1S80 VNTR locus is used in this protocol as a highly polymorphic marker based on variation in the number of repetitive sequences. This simple protocol conveys useful information for teachers and the implementation of DNA fingerprinting in practical laboratory classes. In the presented laboratory exercise, DNA extraction followed by PCR amplification is used to determine genetic variation at the D1S80 VNTR locus. Differences in the fragment size of PCR products are visualized by agarose gel electrophoresis. The fragment sizes and repeat numbers are calculated based on a linear regression of the size and migration distance of a DNA size standard. Following this guide, students should be able to: • Harvest and extract DNA from buccal mucosa epithelial cells • Perform a PCR experiment and understand the function of various reaction components • Analyze the amplicons by agarose gel electrophoresis and interpret the results • Understand the use of VNTRs in DNA fingerprinting and its application in biological sciences

Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes.

In biological sciences, DNA fingerprinting has been widely used for paternity testing, forensic applications and phylogenetic studies. Here, we describe a reliable and robust method for genotyping individuals by Variable Number of Tandem Repeat (VNTR) analysis in the context of undergraduate laboratory classes. The human D1S80 VNTR locus is used in this protocol as a highly polymorphic marker based on variation in the number of repetitive sequences. This simple protocol conveys useful information for teachers and the implementation of DNA fingerprinting in practical laboratory classes. In the presented laboratory exercise, DNA extraction followed by PCR amplification is used to determine genetic variation at the D1S80 VNTR locus. Differences in the fragment size of PCR products are visualized by agarose gel electrophoresis. The fragment sizes and repeat numbers are calculated based on a linear regression of the size and migration distance of a DNA size standard. Following this guide, students should be able to: • Harvest and extract DNA from buccal mucosa epithelial cells • Perform a PCR experiment and understand the function of various reaction components • Analyze the amplicons by agarose gel electrophoresis and interpret the results • Understand the use of VNTRs in DNA fingerprinting and its application in biological sciences.

“Reprocessable Thermosets”: Synthesis and Characterization of Vitrimer in the Undergraduate Lab Course

This article introduces a novel experiment that involves vitrimers, a new type of polymer, in polymer chemistry and physics lab courses for undergraduate students. Vitrimers are permanently cross-linked networks that can be reprocessed under certain external stimuli. Therefore, they combine the advantages of traditional thermoplastics (excellent reprocessability) with thermosets (outstanding mechanical properties and environmental stability). They can be regarded as a kind of “special thermoset”, which moves this industry toward a more sustainable path, as they are conducive to decreasing thermosetting wastes, reducing environmental pollution, and cutting down the waste of resources. From this lab class, students obtained more experience in the preparation and characterization of polymers. They also learned the concepts of dynamic chemistries and vitrimers and gained a better understanding of the advantages and limitations of thermosets and thermoplastics, as well as a strategy for making a reprocessable thermoset polymeric material. It also fostered students’ interest in functional materials and inspired them to design other functional materials. Moreover, this experimental setup is convenient and safe for implementation and dissemination in most undergraduate laboratory classes.

Design and Validation of an Instrument to Measure Students’ Interactions and Satisfaction in Undergraduate Chemistry Laboratory Classes

This paper describes the development, final design and validation of an instrument that measures a range of student interactions and satisfaction in undergraduate chemistry laboratories. Student surveys or conceptual and attitudinal instruments are widely used techniques for collecting relevant information on student learning. However, there is a lack of specific instruments for collecting data on the relationships between social factors and learning. Consequently, this study attempted to fill this gap by introducing an instrument—the Interactions in Undergraduate Laboratory Classes (IULC). The design of the IULC instrument is based on the theory of distributed cognition, meaning that knowledge is not rooted in an individual’s mind, but develops in the process of interacting with the environment. The instrument covers three aspects: (i) frequency of interactions, (ii) satisfaction and (iii) importance of interactions for the specific laboratory. Undergraduate students (N = 204) enrolled in a first-year chemistry course participated in a test case for the instrument and the corresponding data were analysed using different methods for each of the three parts. The factor structure of the data obtained from the first part of the instrument and internal consistency measures are discussed. Among findings captured by the instrument, student-teacher (instructors in the university context) interactions correlated positively with students’ satisfaction levels. Implications and suggestions for the use of the instrument are discussed.

Bringing immersive science to undergraduate laboratory courses using CRISPR gene knockouts in frogs and butterflies.

The use of CRISPR/Cas9 for gene editing offers new opportunities for biology students to perform genuine research exploring the gene-to-phenotype relationship. It is important to introduce the next generation of scientists, health practitioners and other members of society to the technical and ethical aspects of gene editing. Here, we share our experience leading hands-on undergraduate laboratory classes, where students formulate hypotheses regarding the roles of candidate genes involved in development, perform loss-of-function experiments using programmable nucleases and analyze the phenotypic effects of mosaic mutant animals. This is enabled by the use of the amphibian Xenopus laevis and the butterfly Vanessa cardui, two organisms that reliably yield hundreds of large and freshly fertilized eggs in a scalable manner. Frogs and butterflies also present opportunities to teach key biological concepts about gene regulation and development. To complement these practical aspects, we describe learning activities aimed at equipping students with a broad understanding of genome editing techniques, their application in fundamental and translational research, and the bioethical challenges they raise. Overall, our work supports the introduction of CRISPR technology into undergraduate classrooms and, when coupled with classroom undergraduate research experiences, enables hypothesis-driven research by undergraduates.

University of Manchester School of Biological Sciences launches a blueprint for drastic laboratory plastic reduction

The University of Manchester has pledged to eliminate ‘avoidable’ single-use plastic by 2022. To contribute, Dr Maggy Fostier and Dr Ruth Grady from the School of Biological Sciences (SBS) have launched a project to reduce the amount of plastic in their undergraduate laboratory classes. These classes involve thousands of students per year who require pipettes, weighing boats, stirrers, gloves and other plastic implements which sometimes can have usage lifespans that are less than a minute.

Capacitance-voltage profiling of MOS capacitors: A case study of hands-on semiconductor testing for an undergraduate laboratory

Catering to a large undergraduate laboratory class requires the experiments to be robust, low maintenance, and easy to set up with low cost test equipment at the disposal of most university laboratories. Most introductory undergraduate semiconductor device laboratory courses utilize packaged semiconductor integrated circuit chips to illustrate the functioning and applications of fundamental semiconductor devices such as diodes and transistors. While such methods do justice to the illustration of device concepts, the packages abstract the device physics and manufacturing and promote a “black-box” mentality towards device engineering. We have proposed and implemented a novel undergraduate device laboratory experiment, where metal oxide semiconductor capacitor (MOSCAP) devices were designed and fabricated at our university cleanroom and provided to students to perform basic capacitance-voltage profile measurements. To allow over a hundred students to simultaneously perform the experiments, we fabricated miniature test jigs that served as probe stations with spring-loaded pogo pins to make electrical contact with the devices. Using a simple op-amp based circuit that is easy for second year undergraduates to analyze, students are able to successfully extract device parameters such as substrate doping density and flat-band voltage using this experiment, and visualize the different modes of operation of a MOSCAP.

Integration of a faculty's ongoing research into an undergraduate laboratory teaching class in developmental biology

Traditional developmental biology laboratory classes have utilized a number of different model organisms to allow students to be exposed to diverse biological phenomena in developing organisms. This traditional approach has mainly focused on the diverse morphological and anatomical descriptions of the developing organisms. However, modern developmental biology is focusing more on conserved genetic networks which are responsible for generating conserved body patterns in developing organisms. Therefore, it is necessary to develop a new pedagogical tool to educate undergraduate biology students in the laboratory class of developmental biology with the genetic principles which are responsible for generating and controlling the developing body patterns. A new undergraduate laboratory class for developmental biology was developed in order to offer students the opportunity to explore a wide range of experimental procedures, also incorporating the instructor's on-going research. Thereby the course can serve as a bridge between research and education by combining both into a single theme. The course design involves a sequence of exercises which can be easily adapted to the faculty's ongoing research. This style of laboratory coursework could be a transitional form between a regular laboratory course and a discovery-based laboratory course. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(2):141-150, 2018.

Birdcage volume coils and magnetic resonance imaging: a simple experiment for students

BackgroundThis article explains some simple experiments that can be used in undergraduate or graduate physics or biomedical engineering laboratory classes to learn how birdcage volume radiofrequency (RF) coils and magnetic resonance imaging (MRI) work. For a clear picture, and to do any quantitative MRI analysis, acquiring images with a high signal-to-noise ratio (SNR) is required. With a given MRI system at a given field strength, the only means to change the SNR using hardware is to change the RF coil used to collect the image. RF coils can be designed in many different ways including birdcage volume RF coil designs. The choice of RF coil to give the best SNR for any MRI study is based on the sample being imaged.ResultsThe data collected in the simple experiments show that the SNR varies as inverse diameter for the birdcage volume RF coils used in these experiments. The experiments were easily performed by a high school student, an undergraduate student, and a graduate student, in less than 3 h, the time typically allotted for a university laboratory course.ConclusionsThe article describes experiments that students in undergraduate or graduate laboratories can perform to observe how birdcage volume RF coils influence MRI measurements. It is designed for students interested in pursuing careers in the imaging field.