Alison J. Crowe

Sequence and Spacing of TATA Box Elements Are Critical for Accurate Initiation from the β-Phaseolin Promoter

The β-phaseolin (phas) gene, which encodes one of the major seed storage proteins of P. vulgaris, is tightly regulated at the transcription level resulting in strict tissue-specific and spatial expression during embryonic development. The phas proximal promoter contains a complex arrangement of core promoter elements including three TATA boxes as well as several putative initiator elements. To delineate the respective contributions of the core promoter elements to transcription initiation we have performed site-directed mutagenesis of the phas promoter. In vivo expression studies were performed on transgenic Arabidopsis harboring phas promoter mutants driving expression of the β-glucuronidase (gus) reporter gene. Quantitative assessment of GUS activity in seeds bearing the promoter mutants indicated that both sequence and spacing of the TATA elements influenced the efficiency of transcription. Substitution, insertion or deletion mutations had no effect on histochemical staining patterns indicating that strict spacing requirements are not essential for correct spatial expression of phas during embryogenesis. Further evaluation of the phas promoter by in vitro transcription analysis revealed the presence of multiple TATA-dependent transcription initiation start sites. The distance between TATA elements and transcription start sites was maintained in insertion and deletion mutants through the creation of novel initiation sites, indicating that positioning of the TATA elements rather than DNA sequence was the primary determinant of start site location. We conclude that, while dispensable for proper spatial distribution, the complex architecture of the phas promoter is required to ensure high levels of accurate phas transcription initiation in the developing embryo.

Males Under-Estimate Academic Performance of Their Female Peers in Undergraduate Biology Classrooms.

Women who start college in one of the natural or physical sciences leave in greater proportions than their male peers. The reasons for this difference are complex, and one possible contributing factor is the social environment women experience in the classroom. Using social network analysis, we explore how gender influences the confidence that college-level biology students have in each other’s mastery of biology. Results reveal that males are more likely than females to be named by peers as being knowledgeable about the course content. This effect increases as the term progresses, and persists even after controlling for class performance and outspokenness. The bias in nominations is specifically due to males over-nominating their male peers relative to their performance. The over-nomination of male peers is commensurate with an overestimation of male grades by 0.57 points on a 4 point grade scale, indicating a strong male bias among males when assessing their classmates. Females, in contrast, nominated equitably based on student performance rather than gender, suggesting they lacked gender biases in filling out these surveys. These trends persist across eleven surveys taken in three different iterations of the same Biology course. In every class, the most renowned students are always male. This favoring of males by peers could influence student self-confidence, and thus persistence in this STEM discipline.

BioCore Guide: A Tool for Interpreting the Core Concepts of Vision and Change for Biology Majors

Using a grassroots approach to incorporate feedback from more than 240 biologists, the authors have taken the core concepts of Vision and Change and created the BioCore Guide—a set of general principles and specific statements that expand upon the core concepts, creating a framework that biology departments can use to align with the goals of Vision and Change.

How should we teach tree-thinking? An experimental test of two hypotheses

BackgroundPhylogenies are ubiquitous in college-level biology textbooks, yet many college students continue to struggle to interpret them correctly. Multiple activities and frameworks for teaching phylogenies have been proposed to address this problem. In an introductory biology course for majors, we tested two contrasting hypotheses about the best way for students to learn the basic principles of ‘tree-thinking’.MethodsWe constructed two 30-minute, pencil-and-paper-based guided group activities: one focused on using a character matrix to build a tree and one focused on analyzing an existing tree. Groups of three students completed one of these activities during one class session of a large lecture course. All students completed an identical assessment the night of the activity.ResultsWe confirmed that students in the two groups were of equal academic ability, and found that students in the ‘build your own tree’ treatment performed significantly better on the assessment than students in the ‘analyze an existing tree’ treatment. We also had first-year graduate students in a Biology PhD program complete the assessment, without doing the activity beforehand. The scores of undergraduates who had done a modified version of the tree building activity were indistinguishable from those of the graduate students.ConclusionWe recommend simple tree-building activities be a standard part of training for tree-thinking in introductory biology.

Chromatin alteration, transcription and replication: What's the opening line to the story?

Polymerase accessibility to chromatin is a limiting step in both RNA and DNA synthesis. Unwinding DNA and nucleosomes during polymerase complex binding and processing likely requires priming by chromatin restructuring. The initiating step in these processes remains an area of speculation. This review focuses on the physical handling of chromatin during transcription and replication, the fate of nucleosomes assembled on DNA during unwinding and processing the chromatin substrate, and how these alterations in chromatin structure may affect gene expression. Transcription or replication may alter chromatin structure during synthesis, enabling regulatory factor binding and, potentially, future rounds of transcription. As chromatin remodeling and transcription factor binding augment transcription and replication, and are themselves increased by these processes, a temporal model of structural alterations and gene activation is built that may be more circular than linear.

Student perception of group dynamics predicts individual performance: Comfort and equity matter

Active learning in college classes and participation in the workforce frequently hinge on small group work. However, group dynamics vary, ranging from equitable collaboration to dysfunctional groups dominated by one individual. To explore how group dynamics impact student learning, we asked students in a large-enrollment university biology class to self-report their experience during in-class group work. Specifically, we asked students whether there was a friend in their group, whether they were comfortable in their group, and whether someone dominated their group. Surveys were administered after students participated in two different types of intentionally constructed group activities: 1) a loosely-structured activity wherein students worked together for an entire class period (termed the ‘single-group’ activity), or 2) a highly-structured ‘jigsaw’ activity wherein students first independently mastered different subtopics, then formed new groups to peer-teach their respective subtopics. We measured content mastery by the change in score on identical pre-/post-tests. We then investigated whether activity type or student demographics predicted the likelihood of reporting working with a dominator, being comfortable in their group, or working with a friend. We found that students who more strongly agreed that they worked with a dominator were 17.8% less likely to answer an additional question correct on the 8-question post-test. Similarly, when students were comfortable in their group, content mastery increased by 27.5%. Working with a friend was the single biggest predictor of student comfort, although working with a friend did not impact performance. Finally, we found that students were 67% less likely to agree that someone dominated their group during the jigsaw activities than during the single group activities. We conclude that group activities that rely on positive interdependence, and include turn-taking and have explicit prompts for students to explain their reasoning, such as our jigsaw, can help reduce the negative impact of inequitable groups.

In vitro reconstitution of nuclei for replication and transcription.

Publisher Summary This chapter discusses the in vitro reconstitution of nuclei for replication and transcription. Reconstitution of synthetic nuclei provides an accessible, dynamic in vitro system that integrates higher order protein–DNA structure with multiple nuclear functions. As synthetic nuclei formed in the Xenopus egg extract are transcriptionally quiescent, ascertaining the role of DNA replication in mediating changes in chromatin structure in the absence of ongoing transcription is possible. DNA replication may be necessary to mediate the derepression of chromatin-repressed genes by facilitating the competition between trans -acting factors and histones during the repackaging of the newly replicated daughter strands. Thus, the relative local concentration of activating factors at the time of replication may determine whether a given chromatin structure is maintained or converted to an alternate conformation. The studies discussed in the chapter illustrate the potential of using the solid-phase nuclei assembly system to identify the responsible tumorigenic factors as well as the contribution of cellular proliferation to the activation of gene expression.

ASPECT: A Survey to Assess Student Perspective of Engagement in an Active-Learning Classroom

This paper describes the development and validation of a survey to measure students’ self-reported engagement during a wide variety of in-class active-learning exercises. The survey provides researchers and instructors alike with a tool to rapidly evaluate different active-learning strategies from the perspective of the learner.

Likes attract: Students self-sort in a classroom by gender, demography, and academic characteristics:

Although a growing literature has documented the effectiveness of informal group work during class sessions, virtually no data exist on which students are collaborating. As a result, instructors rarely know whether students are self-sorting in ways that maximize learning. This article explores which undergraduate students worked together on each of five exercises scheduled throughout the term, in a large-enrollment course for majors that emphasized intensive peer interaction. Pairwise logistic regression models were used to assess the likelihood that students collaborated based on shared demographic characteristics, socioeconomic status, and academic performance. In almost all cases, students self-sorted by ethnicity and gender. In addition, students who were predicted to do well in the course, based on their academic history, worked together initially; students who actually did well in the course, based on their final grade, were working together at the end; and students who were predicted to struggle in the course began collaborating late in the term.

The ICAP Active Learning Framework Predicts the Learning Gains Observed in Intensely Active Classroom Experiences

STEM classrooms (science, technology, engineering, and mathematics) in postsecondary education are rapidly improved by the proper use of active learning techniques. These techniques occupy a descriptive spectrum that transcends passive teaching toward active, constructive, and, finally, interactive methods. While aspects of this framework have been examined, no large-scale or actual classroom-based data exist to inform postsecondary education STEM instructors about possible learning gains. We describe the results of a quasi-experimental study to test the apex of the ICAP framework (interactive, constructive, active, and passive) in this ecological classroom environment. Students in interactive classrooms demonstrate significantly improved learning outcomes relative to students in constructive classrooms. This improvement in learning is relatively subtle; similar experimental designs without repeated measures would be unlikely to have the power to observe this significance. We discuss the importance of seemingly small learning gains that might propagate throughout a course or departmental curriculum, as well as improvements with the necessity for faculty to develop and implement similar activities.