Dataset Information

Inquiry-based learning: inflammation as a model to teach molecular techniques for assessing gene expression.

ABSTRACT: This laboratory module simulates the process used by working scientists to ask and answer a question of biological interest. Instructors facilitate acquisition of knowledge using a comprehensive, inquiry-based approach in which students learn theory, hypothesis development, experimental design, and data interpretation and presentation. Using inflammation in macrophages as a model system, students perform a series of molecular biology techniques to address the biological question: "Does stimulus 'X' induce inflammation?" To ask this question, macrophage cells are treated with putative inflammatory mediators and then assayed for evidence of inflammatory response. Students become familiar with their assigned mediator and the relationship between their mediator and inflammation by conducting literature searches, then using this information to generate hypotheses which address the effect of their mediator on induction of inflammation. The cellular and molecular approaches used to test their hypotheses include transfection and luciferase reporter assay, immunoblot, fluorescence microscopy, enzyme-linked immunosorbent assay, and quantitative PCR. Quantitative and qualitative reasoning skills are developed through data analysis and demonstrated by successful completion of post-lab worksheets and the generation and oral presentation of a scientific poster. Learning objective assessment relies on four instruments: pre-lab quizzes, post-lab worksheets, poster presentation, and posttest. Within three cohorts (n = 85) more than 95% of our students successfully achieved the learning objectives.

SUBMITTER: Gunn KE

PROVIDER: S-EPMC3867756 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Inquiry-based learning: inflammation as a model to teach molecular techniques for assessing gene expression.

Gunn Kathryn E KE McCauslin Christine Seitz CS Staiger Jennifer J Pirone Dana M DM

Journal of microbiology & biology education 20131202 2

This laboratory module simulates the process used by working scientists to ask and answer a question of biological interest. Instructors facilitate acquisition of knowledge using a comprehensive, inquiry-based approach in which students learn theory, hypothesis development, experimental design, and data interpretation and presentation. Using inflammation in macrophages as a model system, students perform a series of molecular biology techniques to address the biological question: "Does stimulus ...[more]

PMID: 24358382

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Project description:BackgroundModern high-throughput measurement technologies such as DNA microarrays and next generation sequencers produce extensive datasets. With large datasets the emphasis has been moving from traditional statistical tests to new data mining methods that are capable of detecting complex patterns, such as clusters, regulatory networks, or time series periodicity. Study of periodic gene expression is an interesting research question that also is a good example of challenges involved in the analysis of high-throughput data in general. Unlike for classical statistical tests, the distribution of test statistic for data mining methods cannot be derived analytically.ResultsWe describe the randomization based approach to significance testing, and show how it can be applied to detect periodically expressed genes. We present four randomization methods, three of which have previously been used for gene cycle data. We propose a new method for testing significance of periodicity in gene expression short time series data, such as from gene cycle and circadian clock studies. We argue that the underlying assumptions behind existing significance testing approaches are problematic and some of them unrealistic. We analyze the theoretical properties of the existing and proposed methods, showing how our method can be robustly used to detect genes with exceptionally high periodicity. We also demonstrate the large differences in the number of significant results depending on the chosen randomization methods and parameters of the testing framework.By reanalyzing gene cycle data from various sources, we show how previous estimates on the number of gene cycle controlled genes are not supported by the data. Our randomization approach combined with widely adopted Benjamini-Hochberg multiple testing method yields better predictive power and produces more accurate null distributions than previous methods.ConclusionsExisting methods for testing significance of periodic gene expression patterns are simplistic and optimistic. Our testing framework allows strict levels of statistical significance with more realistic underlying assumptions, without losing predictive power. As DNA microarrays have now become mainstream and new high-throughput methods are rapidly being adopted, we argue that not only there will be need for data mining methods capable of coping with immense datasets, but there will also be need for solid methods for significance testing.

Project description:Förster resonance energy transfer (FRET) techniques have proven invaluable for probing the complex nature of protein-protein interactions, protein folding, and intracellular signaling events. These techniques have traditionally been implemented with the use of one or more fluorescence band-pass filters, either as fluorescence microscopy filter cubes, or as dichroic mirrors and band-pass filters in flow cytometry. In addition, new approaches for measuring FRET, such as fluorescence lifetime and acceptor photobleaching, have been developed. Hyperspectral techniques for imaging and flow cytometry have also shown to be promising for performing FRET measurements. In this study, we have compared traditional (filter-based) FRET approaches to three spectral-based approaches: the ratio of acceptor-to-donor peak emission, linear spectral unmixing, and linear spectral unmixing with a correction for direct acceptor excitation. All methods are estimates of FRET efficiency, except for one-filter set and three-filter set FRET indices, which are included for consistency with prior literature. In the first part of this study, spectrofluorimetric data were collected from a CFP-Epac-YFP FRET probe that has been used for intracellular cAMP measurements. All comparisons were performed using the same spectrofluorimetric datasets as input data, to provide a relevant comparison. Linear spectral unmixing resulted in measurements with the lowest coefficient of variation (0.10) as well as accurate fits using the Hill equation. FRET efficiency methods produced coefficients of variation of less than 0.20, while FRET indices produced coefficients of variation greater than 8.00. These results demonstrate that spectral FRET measurements provide improved response over standard, filter-based measurements. Using spectral approaches, single-cell measurements were conducted through hyperspectral confocal microscopy, linear unmixing, and cell segmentation with quantitative image analysis. Results from these studies confirmed that spectral imaging is effective for measuring subcellular, time-dependent FRET dynamics and that additional fluorescent signals can be readily separated from FRET signals, enabling multilabel studies of molecular interactions. © 2013 International Society for Advancement of Cytometry.

Project description:Self-generation of knowledge can activate deeper cognitive processing and improve long-term retention compared to the passive reception of information. It plays a distinctive role within the concept of inquiry-based learning, which is an activity-oriented, student-centered collaborative learning approach in which students become actively involved in knowledge construction by following an idealized hypothetico-deductive method. This approach allows students to not only acquire content knowledge, but also an understanding of investigative procedures/inquiry skills - in particular the control-of-variables strategy (CVS). From the perspective of cognitive load theory, generating answers and solutions during inquiry-based learning is inefficient as it imposes an intrinsic and extraneous load on learners. Previous research on self-generation of content knowledge in inquiry-based learning has demonstrated that (1) a high cognitive load impairs retention of the generated information, (2) feedback is a fundamental requirement for self-generation of complex content knowledge, (3) self-generation success is key to long-term retention, and (4) generating and rereading place different demands on learners. However, there is still no research on the self-generation of scientific reasoning skills (procedural knowledge) and no knowledge of interaction between the (long-term) retention of these skills with prior knowledge, feedback and self-generation success. That is why this experiment was conducted. The focus of this research is to analyze the distinctive role of self-generation of scientific reasoning skills within the concept of inquiry-based learning and to identify the influence of prior knowledge and self-generation success on short-term and long-term retention. For this purpose, an experiment involving 133 6th and 7th graders was conducted. An inquiry activity that included the self-generation of scientific reasoning skills was compared to an inquiry task that had students simply read information about the experimental design. We used both an immediate and a delayed test to examine which treatment better developed a deeper understanding of CVS and an ability to apply this knowledge to novel problems (transfer). Direct instruction was clearly superior to self-generation in facilitating students' acquisition of CVS immediately after the inquiry task. However, after a period of 1 week had elapsed, both treatment conditions turned out to be equally effective. A generation effect was only found among students with high self-generation success after a 1-week delay.

Project description:RationaleThe most effective approach to teaching respiratory inhaler technique is unknown.ObjectivesTo evaluate the relative effects of two different educational strategies (teach-to-goal instruction vs. brief verbal instruction) in adults hospitalized with asthma or chronic obstructive pulmonary disease.MethodsWe conducted a randomized clinical trial at two urban academic hospitals. Participants received teach-to-goal or brief instruction in the hospital and were followed for 90 days after discharge. Inhaler technique was assessed using standardized checklists; misuse was defined as 75% steps or less correct (≤9 of 12 steps). The primary outcome was metered-dose inhaler misuse 30 days postdischarge. Secondary outcomes included Diskus technique; acute care events at 30 and 90 days; and associations with adherence, health literacy, site, and patient risk (near-fatal event).Measurements and main resultsOf 120 participants, 73% were female and 90% were African American. Before education, metered-dose inhaler misuse was similarly common in the teach-to-goal and brief intervention groups (92% vs. 84%, respectively; P = 0.2). Metered-dose inhaler misuse was not significantly less common in the teach-to-goal group than in the brief instruction group at 30 days (54% vs. 70%, respectively; P = 0.11), but it was immediately after education (11% vs. 60%, respectively; P < 0.001) and at 90 days (48% vs. 76%, respectively; P = 0.003). Similar results were found with the Diskus device. Participants did not differ across education groups with regard to rescue metered-dose inhaler use or Diskus device adherence at 30 or 90 days. Acute care events were less common among teach-to-goal participants than brief intervention participants at 30 days (17% vs. 36%, respectively; P = 0.02), but not at 90 days (34% vs. 38%, respectively; P = 0.6). Participants with low health literacy receiving teach-to-goal instruction were less likely than brief instruction participants to report acute care events within 30 days (15% vs. 70%, respectively; P = 0.008). No differences existed by site or patient risk at 30 or 90 days (P > 0.05).ConclusionsIn adults hospitalized with asthma or chronic obstructive pulmonary disease, in-hospital teach-to-goal instruction in inhaler technique did not reduce inhaler misuse at 30 days, but it was associated with fewer acute care events within 30 days after discharge. Inpatient treatment-to-goal education may be an important first step toward improving self-management and health outcomes for hospitalized patients with asthma or chronic obstructive pulmonary disease, especially among patients with lower levels of health literacy. Clinical trial registered with www.clinicaltrials.gov (NCT01426581).

Dataset Information

Inquiry-based learning: inflammation as a model to teach molecular techniques for assessing gene expression.

Publications

Inquiry-based learning: inflammation as a model to teach molecular techniques for assessing gene expression.

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