Undergraduate Laboratory Research Articles

Applying Beer's Law in the undergraduate cell biology laboratory: examining the mathematical relationship between optical density, cell concentration, and cell size using budding yeast.

Undergraduate students majoring in the life sciences benefit from experience with data analyses that connect mathematical calculations to the biological systems they are studying. Monitoring the optical density and cell number of Saccharomyces cerevisiae liquid cultures allows students to gain quantitative experience generating standard curves and trendlines that capture the relationship between optical density and cell concentration for a given S. cerevisiae strain. Data comparisons across multiple strains can yield insights into the biophysical properties of cells that drive light absorbance and scattering. In this Tips and Tools article, we share a laboratory module that allows students to experience cell biology tools, laboratory measurements, and data analysis to determine the mathematical relationship between optical density and cell concentration in liquid microbial cultures. This module could be integrated into undergraduate classes ranging from general biology to upper-level cell biology or microbiology and can be a starting point for more complex investigations of microbial growth.

No Experience Required: Inclusive Undergraduate Research in Computational Biophysical Chemistry

ABSTRACT Undergraduate research is a key tool for recruitment and, more importantly, retention of science, technology, engineering, and math students. Unfortunately, many students are not aware of or do not take advantage of these opportunities and, at best, often wait until late in their college careers. For my undergraduate computational biophysical chemistry research lab I have established a no-experience-required policy that allows me to recruit and mentor more research students. It also allows me to be more inclusive and expand the pool of students who have access to research. This also results in a more diverse research group, which is particularly important at a primarily undergraduate institution that has a diverse population with a high percentage of first-generation students. Here, I lay out the procedures I use to recruit and train students of all levels for my research lab, as well as the research products produced by students and myself.

Some educational uses of EDXRF for technologists in health science

Abstract Physicists teach physics to students of various academic disciplines such as physics, chemistry, health sciences, biology, geology, environmental sciences, etc. Energy dispersive X-ray fluorescence spectroscopy (EDXRF) is a case of application of atomic physics in the real world. Students, through applications of EDXRF, may find out how the basic concepts of atomic physics can be used for elemental analysis of samples of their scientific interest and everyday life. This paper presents some educational implementations of EDXRF and highlights the importance of incorporating this spectroscopic method in undergraduate or postgraduate labs or lectures in the field of health sciences. Five experimental activities, a general one for understanding X-ray spectra and the others for the analysis of substances/materials related to chemistry/toxicology, dentistry, optics, and cosmetics, are presented and discussed.

A PBL strategy for incorporating 3D cell culture into the classrooms of undergraduate biotechnology engineering students

ABSTRACT Background In Mexico, the undergraduate curriculum in biological, biomedical and related sciences only gives hands-on experience in 2D cell culture due to its low cost and ease of implementation. These traditional lecture-based cell culture courses are often limited to routine learning methods and fail to demonstrate alternative culture strategies that would be needed to realistically mimic the processes occurring within the human body and be used to solve relevant medical problems. The use of 3D cell culture, on the other hand, makes it possible to recreate a microenvironment similar to that of living tissue, which is extremely useful for physicochemical studies. Moreover, the incorporation of problem-based learning (PBL) techniques to teach 3D cell culture has the potential to greatly enhance student learning. Purpose The objective of the work herein was to evaluate the success of implementing a 3D cell culture technique using the PBL method of teaching. Sample In this pilot study, eight students attended a traditionally structured cell culture course to learn cell culture techniques (control group), and six students were taught using a PBL model. Design and methods The activities were carried out either with the guidance of an instructor (traditional learning) or through an autonomous search for information (PBL).3D cell culture and scaffold printing exercises were incorporated into the course schedule, fostering in our students the ability to solve real world problems within a team. Results With the PBL teaching method, students displayed a slight tendency to better interpret and discuss their results (P = 0.436). Conclusion This pilot study highlights the usefulness of self-learning through a PBL system and warrants larger-scale research to better examine the potential benefits of incorporating a PBL strategy for teaching 3D cell culture in undergraduate biotechnology engineering laboratories.

A Citrus Serenade: An Improved Procedure for the Imine Condensation Reaction in Undergraduate Laboratories

A Citrus Serenade: An Improved Procedure for the Imine Condensation Reaction in Undergraduate Laboratories

Reaction Optimization Experiment for Undergraduate Capstone Organic Chemistry Laboratory Course

Reaction Optimization Experiment for Undergraduate Capstone Organic Chemistry Laboratory Course

Evidence for validity and reliability of a research-based assessment instrument on measurement uncertainty

The Survey of Physics Reasoning on Uncertainty Concepts in Experiments (SPRUCE) was designed to measure students’ proficiency with measurement uncertainty concepts and practices across ten different assessment objectives to help facilitate the improvement of laboratory instruction focused on this important topic. To ensure the reliability and validity of this assessment, we conducted a comprehensive statistical analysis using classical test theory. This analysis includes an evaluation of the test as a whole, as well as an in-depth examination of individual items and assessment objectives. We make use of a previously reported on scoring scheme involving pairing items with assessment objectives, creating a new unit for statistical analysis referred to as a “couplet.” The findings from our analysis provide evidence for the reliability and validity of SPRUCE as an assessment tool for undergraduate physics labs. This increases both instructors’ and researchers’ confidence in using SPRUCE for measuring students’ proficiency with measurement uncertainty concepts and practices to ultimately improve laboratory instruction. Additionally, our results using couplets and assessment objectives demonstrate how these can be used with traditional classic test theory analysis. Published by the American Physical Society 2024

Uncovering malate dehydrogenase: structure, function and role in disease.

Malate dehydrogenases (MDHs) have been extensively studied since the 1960s due to their key roles in carbon metabolism and pathways such as redox balance and lipid synthesis. Recently, there has been renewed interest in these enzymes with the discovery of their role in the metabolic changes that occur during cancer and a widespread community of undergraduate teaching laboratories addressing MDH research questions, the Malate Dehydrogenase CUREs Community (MCC). This special issue describes different facets of MDH, including its physiological role, its structure-function relationships, its regulation through post-translational modifications, and perspectives on its evolutionary history. There are two human isoforms: a cytoplasmic isoform that carries out formation of NAD+ for glycolysis, and a mitochondrial isoform that plays a major role in the citric acid cycle. Although the sequences of these two isoforms vary, the structures of the enzymes are similar, and studies suggest that each isoform may form complexes with other enzymes in common pathways. Experimental and theoretical advances have helped to characterize the post-translational modifications of MDH, allowing us to ask more complex questions involving the regulation of the enzyme and substrate promiscuity in the context of cancer. Additionally, there are many unresolved questions on the role of malate dehydrogenase in other organisms, especially in parasites. The review articles in this issue seek to shed light on the latest advances in our understanding of MDH and highlight areas for future studies.

Undergraduate Laboratory Experiment Examining Free-Radical and Copper(0)-Mediated Polymerization and Postpolymerization Modification

Undergraduate Laboratory Experiment Examining Free-Radical and Copper(0)-Mediated Polymerization and Postpolymerization Modification

Increased Reaction Vessel Surface Area Decreases the Overall Mortality Rate of Rana catesbeiana Larvae during Chemically Induced Metamorphosis

Stimulating precocious metamorphosis in anuran larvae is an important pedagogical tool for understanding vertebrate development. However, historically, artificially provoking metamorphosis by immersing tadpoles in exogenous inducing agents (e.g., thyroxine, and iodine) compromises the longevity of the experimental animals, resulting in up to 100% mortality within a week. In our undergraduate teaching lab, we house our experimental tadpoles in circular glass dishes having a surface area of 182 cm2. Over the past four academic years this lab was performed, we observed 100% mortality of experimental animals within 10, 12, or 15 days when treated with 10-5 M, 10-6 M, or 10-7 M thyroxine, respectively. Here, we investigated whether increasing the surface area to 413 cm2 using square glass dishes would reduce the mortality of the treated animals. Omnibus Kaplan-Meier survival analysis demonstrates a statistically significant decrease in mortality in tadpoles reared in the larger square dishes compared to those housed in the smaller round dishes (P < 0.05). However, increasing the surface area of our reaction vessels could not rescue survivability of those tadpoles immersed in thyroxine, but did increase survivability of control tadpoles maintained in pond water (P < 0.01), tadpoles subjected to iodine (P < 0.05) or treated with actinomycin D (P < 0.05). These data demonstrate that increasing available reaction vessel surface area reduces overall tadpole mortality during chemically modified metamorphosis in an undergraduate teaching lab setting.

Sternalis featuring tendomuscular fusion to the contralateral sternocleidomastoid: a cadaveric case report.

To report the morphologic and spatial relationships of a bilateral sternalis muscle variant. Routine cadaveric dissection in an undergraduate anatomy laboratory revealed two sternalis muscles parasternal to the sternal body. Subsequent fine prosection of the anterior thoracic wall and neck was carried out to uncover the soft tissue attachments of both sternalis muscles. Positional relationship to neighboring anterior thoracic and neck structures, and geometric dimensions of the muscle bellies and tendons, were documented. Both sternalis muscles were imbedded in the pectoral fascia, with their muscle fibers running obliquely to the midsternal line. The right sternalis muscle was notably larger in length, width, and thickness compared to the sternalis muscle on the left. The right sternalis muscle featured a distinct superior cord-like intermediate tendon that traversed superolateral and fused directly with the contralateral sternomastoid and sterno-occipital portions of the left sternocleidomastoid muscle. The superior tendon of the left sternalis muscle was aponeurotic and affixed to the cord-tendon of the right sternalis muscle. A distinct tendinous entheses for the sternal head for both sternocleidomastoid muscles were noted at the manubrial body. This case report describes a unique bilateral sternalis muscle variant with conjoined sternocleidomastoid muscle integration. This anatomical description of a sternalis-sternocleidomastoid muscle morphology may supplement radiographic interpretations and support diagnostic accuracy.

Development of a global landscape of undergraduate physics laboratory courses

Physics education research (PER) is a global endeavor, with a wealth of work performed at a variety of institutions worldwide. However, results from research into undergraduate physics laboratory courses are often difficult to compare due to the broad variations in courses. We report here how we developed and validated a survey to classify these courses, as well as compare and contrast them. This will be useful in two key endeavors: comparisons between PER studies and providing useful data for individual instructors hoping to improve their courses. While we are still in the process of collecting sufficient data to create a full taxonomy of laboratory courses, we present here details of the survey creation itself, including its face, construct, and content validation, as well as a first look at the data collected, which includes a broad landscape of lab courses in 41 countries. We used both quantitative and qualitative methods to analyze the data collected. Some of these results include similarities between courses, such as students often using preconstructed apparatuses and instructors hoping for students to learn technical skills. We also find differences in courses, such as in the number and types of goals of the course, as well as the activities students participate in. Thus, this survey and its results can provide information relevant to both researchers and instructors. Published by the American Physical Society 2024

Complementary Instrumental Techniques Applied to Pain Relieving Tablets in an Undergraduate Laboratory Experiment

Complementary Instrumental Techniques Applied to Pain Relieving Tablets in an Undergraduate Laboratory Experiment

Virtual Reality in an Eco-Niche Undergraduate Organic Chemistry Laboratory Course: New Practice in Chemistry Lab Teaching

Virtual Reality in an Eco-Niche Undergraduate Organic Chemistry Laboratory Course: New Practice in Chemistry Lab Teaching

Social and Emotional Learning as Experienced by Students in Undergraduate General Chemistry Labs

Students can meticulously perform laboratory techniques and be proficient in writing lab reports yet report negative affective experiences within the chemistry teaching labs. This study addresses this contradiction by studying students’ experiences using a Social and Emotional Learning (SEL) framework to qualitatively and deductively analyze semi-structured student interviews (N=15). The interviews followed the students’ completion of introductory chemistry and focused on their experiences with the laboratories. What emerged from this analysis were the SEL competencies intertwining with all aspects of the teaching labs as students worked with their lab partners, peers, and teaching assistants. The labs provide a unique environment for students to apply their SEL skills, including effective relationship and self-management skills. Despite students using and relying on their SEL skills, they are not always supported in lab design, and this presents a barrier to student success and a positive learning experience associated with the teaching labs. Given this, there is a need to change chemistry laboratory teaching practices and curricula to emphasize support and learning outcomes related to SEL. These findings were used to implement changes to the first-year labs to support SEL competencies, such as designing and implementing a TA manual, providing students with tips for dividing lab procedures, and offering more resources including rubrics.

A genetic screen of transcription factors in the Drosophila melanogaster abdomen identifies novel pigmentation genes.

Gene regulatory networks specify the gene expression patterns needed for traits to develop. Differences in these networks can result in phenotypic differences between organisms. Although loss-of-function genetic screens can identify genes necessary for trait formation, gain-of-function screens can overcome genetic redundancy and identify loci whose expression is sufficient to alter trait formation. Here, we leveraged transgenic lines from the Transgenic RNAi Project at Harvard Medical School to perform both gain- and loss-of-function CRISPR/Cas9 screens for abdominal pigmentation phenotypes. We identified measurable effects on pigmentation patterns in the Drosophila melanogaster abdomen for 21 of 55 transcription factors in gain-of-function experiments and 7 of 16 tested by loss-of-function experiments. These included well-characterized pigmentation genes, such as bab1 and dsx, and transcription factors that had no known role in pigmentation, such as slp2. Finally, this screen was partially conducted by undergraduate students in a Genetics Laboratory course during the spring semesters of 2021 and 2022. We found this screen to be a successful model for student engagement in research in an undergraduate laboratory course that can be readily adapted to evaluate the effect of hundreds of genes on many different Drosophila traits, with minimal resources.

Probing coherent phonons in the advanced undergraduate laboratory

Probing coherent phonons in the advanced undergraduate laboratory

The Neuroscience Research Opportunities to Increase Diversity Program: Transformative and Successful Research Training Strategies for Undergraduate Students within Hispanic Serving Institutions.

Over the past 14 years, the Neuroscience Research Opportunities to Increase Diversity (NeuroID) program, funded by the National Institute of Neurological Diseases and Stroke (NINDS), has played a transformative role in training numerous undergraduate Hispanic students within The University of Puerto Rico-Rio Piedras (UPR-RP). This innovative Neuroscience-based research training initiative has successfully guided dozens of Hispanic students toward graduate programs in Neuroscience, significantly contributing to the enhancement of diversity within the academic and scientific fields. The achievements of the NeuroID program can be attributed to three key objectives. Firstly, the establishment of a comprehensive and innovative program has provided Hispanic undergraduate students with invaluable insights into various facets of a research career in neuroscience. Secondly, the program has fostered a robust mentorship network that supports selected students throughout their journey to become neuroscientists. Thirdly, it has strengthened the neuroscience network in Puerto Rico by bridging the gap between undergraduate teaching universities and research laboratories in top-tier institutions across the mainland United States.

A Multiweek Experimental Project Bringing Real-World Lithium Batteries into a Third-Year Undergraduate Analytical Chemistry Laboratory

A Multiweek Experimental Project Bringing Real-World Lithium Batteries into a Third-Year Undergraduate Analytical Chemistry Laboratory

Fostering scientific reasoning competencies: investigating impacts of cross- and within-content area experimentation using the competency triad

ABSTRACT Educational standards and science education research suggest that experiments can be used to foster scientific reasoning competencies. So far, little is known about whether to sequence experiments from one or multiple content areas for this purpose. Therefore, we compared two sequences in an experimental study to investigate the influence of content areas of experiments on competencies’ development: Based on the same underlying structure, the first, homogeneous sequence includes four kinetics experiments. The second, heterogeneous sequence involves experiments from kinetics, thermodynamics, and redox chemistry. A total of 97 students participating in undergraduate chemistry lab courses were randomly assigned to one of the sequences. The changes in competencies within the sequences were compared based on the ‘competency triad’ differentiating between underlying knowledge (dispositions), the use of this knowledge (processes), and the quality of the resulting investigations (products). The results show that both sequences are comparably suitable to foster scientific reasoning competencies. However, in the post-experiments, we found a tendency of increased inadequate or irrelevant content-related reasoning by bringing in and conflating concepts from previous experiments such as activation energy or the chemical equilibrium (in particular Le Chatelier's principle). We discuss these findings concerning the consequences of sequencing experiments for fostering scientific reasoning.