Helping undergraduates repair faulty mental models in the student laboratory

Over half of the undergraduate students entering physiology hold a misconception concerning how breathing pattern changes when minute ventilation increases. Repair of this misconception was used as a measure to compare the impact of three student laboratory protocols on learning by 696 undergraduate students at 5 institutions. Students were tested for the presence of the misconception before and after performing a laboratory activity in which they measured the effect of exercise on tidal volume and breathing frequency. The first protocol followed a traditional written "observe and record" ("cookbook") format. In the second treatment group, a written protocol asked students to complete a prediction table before running the experiment ("predictor" protocol). Students in the third treatment group were given the written "predictor" protocol but were also required to verbalize their predictions before running the experiment ("instructor intervention" protocol). In each of the three groups, the number of students whose performance improved on the posttest was greater than the number of students who performed less well on the posttest (P < 0.001). Thus the laboratory protocols helped students correct the misconception. However, the remediation rate for students in the "instructor intervention" group was more than twice that observed for the other treatment groups (P < 0.001). The results indicate that laboratory instruction is more effective when students verbalize predictions from their mental models than when they only "discover" the outcome of the experiment.     

Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses

An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.     

Multiweek cell culture project for use in upper-level biology laboratories

This article describes a laboratory protocol for a multiweek project piloted in a new upper-level biology laboratory (BIO 426) using cell culture techniques. Human embryonic kidney-293 cells were used, and several culture media and supplements were identified for students to design their own experiments. Treatments included amino acids, EGF, caffeine, epinephrine, heavy metals, and FBS. Students researched primary literature to determine their experimental variables, made their own solutions, and treated their cells over a period of 2 wk. Before this, a sterile technique laboratory was developed to teach students how to work with the cells and minimize contamination. Students designed their experiments, mixed their solutions, seeded their cells, and treated them with their control and experimental media. Students had the choice of manipulating a number of variables, including incubation times, exposure to treatment media, and temperature. At the end of the experiment, students observed the effects of their treatment, harvested and dyed their cells, counted relative cell numbers in control and treatment flasks, and determined the ratio of living to dead cells using a hemocytometer. At the conclusion of the experiment, students presented their findings in a poster presentation. This laboratory can be expanded or adapted to include additional cell lines and treatments. The ability to design and implement their own experiments has been shown to increase student engagement in the biology-related laboratory activities as well as develop the critical thinking skills needed for independent research.     

An at‐home laboratory in plant biology designed to engage students in the process of science

The COVID‐19 pandemic prompted a transition to remote delivery of courses that lack immersive hands‐on research experiences for undergraduate science students, resulting in a scientific research skills gap. In this report, we present an option for an inclusive and authentic, hands‐on research experience that all students can perform off‐campus. Biology students in a semester‐long (13 weeks) sophomore plant physiology course participated in an at‐home laboratory designed to study the impacts of nitrogen addition on growth rates and root nodulation by wild nitrogen‐fixing Rhizobia in Pisum sativum (Pea) plants. This undergraduate research experience, piloted in the fall semester of 2020 in a class with 90 students, was created to help participants learn and practice scientific research skills during the COVID‐19 pandemic. Specifically, the learning outcomes associated with this at‐home research experience were: (1) generate a testable hypothesis, (2) design an experiment to test the hypothesis, (3) explain the importance of biological replication, (4) perform meaningful statistical analyses using R, and (5) compose a research paper to effectively communicate findings to a general biology audience. Students were provided with an at‐home laboratory kit containing the required materials and reagents, which were chosen to be accessible and affordable in case students were unable to access our laboratory kit. Students were guided through all aspects of research, including hypothesis generation, data collection, and data analysis, with video tutorials and live virtual sessions. This at‐home laboratory provided students an opportunity to practice hands‐on research with the flexibility to collect and analyze their own data in a remote setting during the COVID‐19 pandemic. This, or similar laboratories, could also be used as part of distance learning biology courses.     

T-DNA插入突变在植物功能基因组学中的应用

T-DNA插入突变在植物功能基因组学研究中发挥着重要作用,广泛应用于大规模植物基因功能分析,是分离新基因、研究基因功能的有效工具。我们简单介绍了T-DNA插入突变的原理,详细论述了3种T-DNA插入突变载体的应用,并综述了利用T-DNA插入突变克隆新基因的方法,同时指出了T-DNA插入突变存在的问题及其发展方向。     

Genetically altered mice: phenotypes,no phenotypes,and Faux phenotypes

Phenotype means different things, but whatever the measure, phenotype can be profoundly influenced by genetic, environmental and infectious variables. The laboratory mouse is a complex multisystemic organism which, despite its genetically inbred nature, as highly variable pathophysiologic characteristics. Mouse strains have background characteristics that can influence genomics research. In addition to the mouse itself, different approaches toward creating mutant mice each create variables that influence phenotype. Different background strains of mice are utilized for these different approaches, and various strains are preferred among different laboratories. Background genotype significantly influences phenotype of gene mutations, as can insufficient genetic stabilization of a mutation. Research programs engaged in functional mouse genomics not only must use genetically well-defined mice, but also must incorporate environmental and infectious disease quality assurance/prevention programs. Laboratory mice are subject to over 60 different infectious disease agents, including a wide variety of viruses, bacteria, protozoa, and metazoa. Although these agents can be readily diagnosed and prevented, a number of forces are resulting in their rise in prevalence in mouse colonies. Infectious disease, including clinically silent infections, can and do influence phenotype, and can jeopardize research considerably through lost time, wasted effort, cost, and even loss of valuable strains.     

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental activity that are common across different technologies, including protocols, samples and data. FuGE provides a foundation for describing entire laboratory workflows and for the development of new data formats. The Microarray Gene Expression Data society and the Proteomics Standards Initiative have committed to using FuGE as the basis for defining their respective standards, and other standards groups, including the Metabolomics Standards Initiative, are evaluating FuGE in their development efforts. Adoption of FuGE by multiple standards bodies will enable uniform reporting of common parts of functional genomics workflows, simplify data-integration efforts and ease the burden on researchers seeking to fulfill multiple minimum reporting requirements. Such advances are important for transparent data management and mining in functional genomics and systems biology.     

Rice functional genomics research in China

Rice functional genomics is a scientific approach that seeks to identify and define the function of rice genes, and uncover when and how genes work together to produce phenotypic traits. Rapid progress in rice genome sequencing has facilitated research in rice functional genomics in China. The Ministry of Science and Technology of China has funded two major rice functional genomics research programmes for building up the infrastructures of the functional genomics study such as developing rice functional genomics tools and resources. The programmes were also aimed at cloning and functional analyses of a number of genes controlling important agronomic traits from rice. National and international collaborations on rice functional genomics study are accelerating rice gene discovery and application.     

功能基因组学的研究方法

基因组学的研究已从结构基因组学转向功能基因组学,功能基因组学时代对于基因功能的研究也由单一基因转向大规模,批量分析,本综述了功能基因组学的研究内容与方法,主要包括：差异显示反转录PCR,基因表达序列分析（SAGE）,微点阵,遗传足迹法,反求遗传学,蛋白质组学和生物信息学等新方法。     

Detection and location of OP-degrading activity: A model to integrate education and research

The Environmental Sampling Research Module (ESRM) is an investigative/discovery module that provides undergraduate research experiences for students as part of an interdisciplinary research-based biotechnology curriculum at the University of Houston campus. As part of the ESRM, students collect soil samples from various locations to test for the presence of organophosphorous (OP) degrading bacteria. At the end of this research project students submit a research paper on their field and laboratory activities and discuss their experimental data and observations. Students also record the date, location of collection, and the results of testing the sample for the degradation of two pesticides, methyl parathion or paraoxon, in an electronic laboratory notebook (ELN). Each collection site is recorded on a Google Maps module and the data from student research activities is made available to other undergraduate students. This data is then used to generate a microorganism database of pesticide degrading activity and promote reading, critical thinking, and analytical skills as part of the curriculum. Our sampling of agricultural sites and wastewater within and around the city of Houston has identified seven distinct genera of OP degrading organisms, including Pseudomonas, Stenotrophomonas, Exiguobacterium, Delftia, Agrobacterium, Aeromonas, and Rhizobium. Collected strains exhibit phosphotriesterase-like enzymatic activity with isolates of Pseudomonas putida and Stenotrophomonas maltophilia capable of degrading both the phosphotriester paraoxon and the phosphorothioate methyl parathion. Using this collection of OP-degrading microorganisms, undergraduate students have evaluated their potential for enhancing the removal of harmful organophosphates and their toxic metabolites from contaminated agricultural soil and adjacent bodies of water. This analytical data can potentially be utilized for environmental and industrial applications in bioremediation and ecology providing an innovative method for integrating education and research. In addition, the versatility of the ESRM itself provides for easy and rapid adaptation into varying environmental science courses with significant potential for the discovery and isolation of new and unique organisms to be used as part of ongoing research in the laboratory.     

Using the two-hybrid screen in the classroom laboratory

The National Science Foundation and others have made compelling arguments that research be incorporated into the learning of undergraduates. In response to these arguments, a two-hybrid research project was incorporated into a molecular biology course that contained both a lecture section and a laboratory section. The course was designed around specific goals for educational outcomes, including introducing research to a wide range of students, teaching students experimental design and data analysis, and enhancing understanding of course material. Additional goals included teaching students to search genomic databases, to access scientific articles, and to write a paper in scientific format. Graded events tested these goals, and a student evaluation indicated student perception of the project. According to our analysis of the data, the yeast two-hybrid screen was a success: several novel clones were identified; students met expectations on graded lab reports, the poster session, and the final paper; and evaluations indicated that students had achieved the outlined goals. Students indicated on the evaluations that the research project increased their interest in research and greatly improved understanding of the course material. Finally, several students in the course intend to submit the findings of the research project to an undergraduate research journal.     

Serotonergic genes modulate amygdala activity in major depression

Serotonergic genes have been implicated in the pathogenesis of depression probably via their influence on neural activity during emotion processing. This study used an imaging genomics approach to investigate amygdala activity in major depression as a function of common functional polymorphisms in the serotonin transporter gene (5-HTTLPR) and the serotonin receptor 1A gene (5-HT(1A)-1019C/G). In 27 medicated patients with major depression, amygdala responses to happy, sad and angry faces were assessed using functional magnetic resonance imaging at 3 Tesla. Patients were genotyped for the 5-HT(1A)-1019C/G and the 5-HTTLPR polymorphism, including the newly described 5-HTT-rs25531 single nucleotide polymorphism. Risk allele carriers for either gene showed significantly increased bilateral amygdala activation in response to emotional stimuli, implicating an additive effect of both genotypes. Our data suggest that the genetic susceptibility for major depression might be transported via dysfunctional neural activity in brain regions critical for emotion processing.     

Using "spinal shrinkage" as a trigger for motivating students to learn about obesity and adopt a healthy lifestyle

Obesity is a global problem; however, relatively little attention is directed toward preparing and inspiring students of medicine and allied medical sciences to address this serious matter. Students are not routinely exposed to the assessment methods for obesity, its overall prevalence, causative factors, short- and long-term consequences, and its management by lifestyle modification. This physiology laboratory exercise involving students of medicine (n = 106) was developed to 1) introduce medical students to methods of obesity assessment and to differentiate between general and abdominal obesity, 2) generate an interest and sensitivity about obesity, and 3) stimulate thinking about modification of their lifestyle in relation to eating habits, weight control, and physical activity. Spinal shrinkage (the difference between the standing height of a person and his/her recumbent length) was used as an immediate observable parameter to demonstrate the effect of adiposity. Spinal shrinkage is recognized as an index of the compressive forces acting on the spine and is related to body mass index. A positive correlation (r = 0.365, P < 0.05) was observed between body mass index and spinal shrinkage. A questionnaire was used to assess student responses to this exercise. Students were motivated to engage in more physical activity (74%), adopt healthier eating (63%), and enhance their knowledge about obesity (67%). They expressed keen interest in the laboratory exercise and found the sessions enjoyable (91%). The laboratory exercise proved to be a success in motivating the students to actively learn and inquire about obesity and to adopt a healthier lifestyle.     

How to engage medical students in chronobiology: an example on autorhythmometry

This contribution describes a new laboratory experience that improves medical students' learning of chronobiology by introducing them to basic chronobiology concepts as well as to methods and statistical analysis tools specific for circadian rhythms. We designed an autorhythmometry laboratory session where students simultaneously played the role of researchers and experimental subjects. During this session, which lasted 24 h, students recorded their own arterial pressure, heart rate, oral temperature, forced expiratory flow, glucose tolerance, muscular strength, reaction time, and sensorimotor coordination at regular intervals and also took the Horne and Ostberg test, after which they analyzed their own data. Furthermore, to gather information from subjects under normal sleep and eating schedules, some students acquired data at home. To guide and help students with their work, a dedicated web page was implemented with scientific references, cosinor analysis software, and other valuable information. All these "raw" data were combined into a single database that students could use to evaluate whatever aspect of the data they seemed fit. A number of suggestions were offered to them as guidance. Students were then instructed to write a scientific article on the subject they had chosen. The experience was highly rewarding for both instructors and students alike. In view of the high level of absenteeism in Spanish universities and the fact that 93% of the students attended the exam and 95% of these passed, the experience was considered a great success.     

Isolation and characterization of Saccharomyces cerevisiae mutants defective in chromosome transmission in an undergraduate genetics research course

An upper-level genetics research course was developed to expose undergraduates to investigative science. Students are immersed in a research project with the ultimate goal of identifying proteins important for chromosome transmission in mitosis. After mutagenizing yeast Saccharomyces cerevisiae cells, students implement a genetic screen that allows for visual detection of mutants with an increased loss of an ADE2-marked yeast artificial chromosome (YAC). Students then genetically characterize the mutants and begin efforts to identify the defective genes in these mutants. While engaged in this research project, students practice a variety of technical skills in both classical and molecular genetics. Furthermore, students learn to collaborate and gain experience in sharing scientific findings with others in the form of written papers, poster presentations, and oral presentations. Previous students indicated that, relative to a traditional laboratory course, this research course improved their understanding of scientific concepts and technical skills and helped them make connections between concepts. Moreover, this course allowed students to experience scientific inquiry and was influential for students as they considered future endeavors.     

Apoptosis: a four-week laboratory investigation for advanced molecular and cellular biology students

Over the past decade, apoptosis has emerged as an important field of study central to ongoing research in many diverse fields, from developmental biology to cancer research. Apoptosis proceeds by a highly coordinated series of events that includes enzyme activation, DNA fragmentation, and alterations in plasma membrane permeability. The detection of each of these phenotypic changes is accessible to advanced undergraduate cell and molecular biology students. We describe a 4-week laboratory sequence that integrates cell culture, fluorescence microscopy, DNA isolation and analysis, and western blotting (immunoblotting) to follow apoptosis in cultured human cells. Students working in teams chemically induce apoptosis, and harvest, process, and analyze cells, using their data to determine the order of events during apoptosis. We, as instructors, expose the students to an environment closely simulating what they would encounter in an active cell or molecular biology research laboratory by having students coordinate and perform multiple tasks simultaneously and by having them experience experimental design using current literature, data interpretation, and analysis to answer a single question. Students are assessed by examination of laboratory notebooks for completeness of experimental protocols and analysis of results and for completion of an assignment that includes questions pertaining to data interpretation and apoptosis.