Study strategies and beliefs about learning as a function of academic achievement and achievement goals.

Prior research by Hartwig and Dunlosky [(2012). Study strategies of college students: Are self-testing and scheduling related to achievement? Psychonomic Bulletin & Review, 19(1), 126-134] has demonstrated that beliefs about learning and study strategies endorsed by students are related to academic achievement: higher performing students tend to choose more effective study strategies and are more aware of the benefits of self-testing. We examined whether students' achievement goals, independent of academic achievement, predicted beliefs about learning and endorsement of study strategies. We administered Hartwig and Dunlosky's survey, along with the Achievement Goals Questionnaire [Elliot, A. J., & McGregor, H. A. (2001). A 2 × 2 achievement goal framework. Journal of Personality & Social Psychology, 80, 501-519] to a large undergraduate biology course. Similar to results by Hartwig and Dunlosky, we found that high-performing students (relative to low-performing students) were more likely to endorse self-testing, less likely to cram, and more likely to plan a study schedule ahead of time. Independent of achievement, however, achievement goals were stronger predictors of certain study behaviours. In particular, avoidance goals (e.g., fear of failure) coincided with increased use of cramming and the tendency to be driven by impending deadlines. Results suggest that individual differences in student achievement, as well as the underlying reasons for achievement, are important predictors of students' approaches to studying.

Prequestions do not enhance the benefits of retrieval in a STEM classroom.

Answering questions before a learning episode-"prequestions"-can enhance memory for that information. A number of studies have explored this effect in the laboratory; however, few studies have examined prequestions in a classroom setting. In the current study, the effects of prequestions were examined in an undergraduate course in chemical engineering. At the start of several class meetings, students were provided with a prequestion to answer about the upcoming lesson, and then were asked to provide ratings of confidence in their answers, familiarity with the content in the prequestion, and how much of the assigned reading they had completed. At the end of class, students were given the same question again (postquestion), along with a different question from the same lesson (new question). On a quiz at the end of each week, students were given the postquestions and new questions again, in addition to never-before-seen questions (quiz-only questions) from the same lessons. Performance on questions at the end of class revealed no difference in performance for postquestions vs. new questions. Although weekly quiz performance revealed an effect of retrieval practice-superior memory for material tested at the end of class (postquestions and new questions) compared to material not tested (quiz-only questions)-there was no difference in weekly quiz performance on postquestions vs. new questions. These results suggest that retrieval practice is beneficial to learning in the classroom. However, prequestions do not appear to enhance learning, nor to enhance the effects of retrieval practice.

Students' Use of Optional Online Reviews and Its Relationship to Summative Assessment Outcomes in Introductory Biology.

Retrieval practice has been shown to produce significant enhancements in student learning of course information, but the extent to which students make use of retrieval to learn information on their own is unclear. In the current study, students in a large introductory biology course were provided with optional online review questions that could be accessed as Test questions (requiring students to answer the questions before receiving feedback) or as Read questions (providing students with the question and correct answer up-front). Students more often chose to access the questions as Test compared with Read, and students who used the Test questions scored significantly higher on subsequent exams compared with students who used Read questions or did not access the questions at all. Following an in-class presentation of superior exam performance following use of the Test questions, student use of Test questions increased significantly for the remainder of the term. These results suggest that practice questions can be an effective tool for enhancing student achievement in biology and that informing students about performance-based outcomes coincides with increased use of retrieval practice.

Improved Student Learning through a Faculty Learning Community: How Faculty Collaboration Transformed a Large-Enrollment Course from Lecture to Student Centered.

Undergraduate introductory biology courses are changing based on our growing understanding of how students learn and rapid scientific advancement in the biological sciences. At Iowa State University, faculty instructors are transforming a second-semester large-enrollment introductory biology course to include active learning within the lecture setting. To support this change, we set up a faculty learning community (FLC) in which instructors develop new pedagogies, adapt active-learning strategies to large courses, discuss challenges and progress, critique and revise classroom interventions, and share materials. We present data on how the collaborative work of the FLC led to increased implementation of active-learning strategies and a concurrent improvement in student learning. Interestingly, student learning gains correlate with the percentage of classroom time spent in active-learning modes. Furthermore, student attitudes toward learning biology are weakly positively correlated with these learning gains. At our institution, the FLC framework serves as an agent of iterative emergent change, resulting in the creation of a more student-centered course that better supports learning.

Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure.

BACKGROUND: The arginine of the D/E/NRY motif in Rhodopsin family G protein-coupled receptors (GPCRs) is conserved in 96% of these proteins. In some GPCRs, this arginine in transmembrane 3 can form a salt bridge with an aspartic acid or glutamic acid in transmembrane 6. The Drosophila melanogaster GPCR Trapped in endoderm-1 (Tre1) is required for normal primordial germ cell migration. In a mutant form of the protein, Tre1sctt, eight amino acids RYILIACH are missing, resulting in a severe disruption of primordial germ cell development. The impact of the loss of these amino acids on Tre1 structure is unknown. Since the missing amino acids in Tre1sctt include the arginine that is part of the D/E/NRY motif in Tre1, molecular dynamics simulations were performed to explore the hypothesis that these amino acids are involved in salt bridge formation and help maintain Tre1 structure. RESULTS: Structural predictions of wild type Tre1 (Tre1+) and Tre1sctt were subjected to over 250 ns of molecular dynamics simulations. The ability of the model systems to form a salt bridge between the arginine of the D/E/NRY motif and an aspartic acid residue in transmembrane 6 was analyzed. The results indicate that a stable salt bridge can form in the Tre1+ systems and a weak salt bridge or no salt bridge, using an alternative arginine, is likely in the Tre1sctt systems. CONCLUSIONS: The weak salt bridge or lack of a salt bridge in the Tre1sctt systems could be one possible explanation for the disrupted function of Tre1sctt in primordial germ cell migration. These results provide a framework for studying the importance of the arginine of the D/E/NRY motif in the structure and function of other GPCRs that are involved in cell migration, such as CXCR4 in the mouse, zebrafish, and chicken.

ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms.

BACKGROUND: Zinc Finger Nucleases (ZFNs) have tremendous potential as tools to facilitate genomic modifications, such as precise gene knockouts or gene replacements by homologous recombination. ZFNs can be used to advance both basic research and clinical applications, including gene therapy. Recently, the ability to engineer ZFNs that target any desired genomic DNA sequence with high fidelity has improved significantly with the introduction of rapid, robust, and publicly available techniques for ZFN design such as the Oligomerized Pool ENgineering (OPEN) method. The motivation for this study is to make resources for genome modifications using OPEN-generated ZFNs more accessible to researchers by creating a user-friendly interface that identifies and provides quality scores for all potential ZFN target sites in the complete genomes of several model organisms. DESCRIPTION: ZFNGenome is a GBrowse-based tool for identifying and visualizing potential target sites for OPEN-generated ZFNs. ZFNGenome currently includes a total of more than 11.6 million potential ZFN target sites, mapped within the fully sequenced genomes of seven model organisms; S. cerevisiae, C. reinhardtii, A. thaliana, D. melanogaster, D. rerio, C. elegans, and H. sapiens and can be visualized within the flexible GBrowse environment. Additional model organisms will be included in future updates. ZFNGenome provides information about each potential ZFN target site, including its chromosomal location and position relative to transcription initiation site(s). Users can query ZFNGenome using several different criteria (e.g., gene ID, transcript ID, target site sequence). Tracks in ZFNGenome also provide "uniqueness" and ZiFOpT (Zinc Finger OPEN Targeter) "confidence" scores that estimate the likelihood that a chosen ZFN target site will function in vivo. ZFNGenome is dynamically linked to ZiFDB, allowing users access to all available information about zinc finger reagents, such as the effectiveness of a given ZFN in creating double-stranded breaks. CONCLUSIONS: ZFNGenome provides a user-friendly interface that allows researchers to access resources and information regarding genomic target sites for engineered ZFNs in seven model organisms. This genome-wide database of potential ZFN target sites should greatly facilitate the utilization of ZFNs in both basic and clinical research.ZFNGenome is freely available at: http://bindr.gdcb.iastate.edu/ZFNGenome or at the Zinc Finger Consortium website: http://www.zincfingers.org/.

An evolutionarily conserved arginine is essential for Tre1 G protein-coupled receptor function during germ cell migration in Drosophila melanogaster.

BACKGROUND: G protein-coupled receptors (GPCRs) play central roles in mediating cellular responses to environmental signals leading to changes in cell physiology and behaviors, including cell migration. Numerous clinical pathologies including metastasis, an invasive form of cell migration, have been linked to abnormal GPCR signaling. While the structures of some GPCRs have been defined, the in vivo roles of conserved amino acid residues and their relationships to receptor function are not fully understood. Trapped in endoderm 1 (Tre1) is an orphan receptor of the rhodopsin class that is necessary for primordial germ cell migration in Drosophila melanogaster embryos. In this study, we employ molecular genetic approaches to identify residues in Tre1 that are critical to its functions in germ cell migration. METHODOLOGY/PRINCIPAL FINDINGS: First, we show that the previously reported scattershot mutation is an allele of tre1. The scattershot allele results in an in-frame deletion of 8 amino acids at the junction of the third transmembrane domain and the second intracellular loop of Tre1 that dramatically impairs the function of this GPCR in germ cell migration. To further refine the molecular basis for this phenotype, we assayed the effects of single amino acid substitutions in transgenic animals and determined that the arginine within the evolutionarily conserved E/N/DRY motif is critical for receptor function in mediating germ cell migration within an intact developing embryo. CONCLUSIONS/SIGNIFICANCE: These structure-function studies of GPCR signaling in native contexts will inform future studies into the basic biology of this large and clinically important family of receptors.

Programmed cell death of primordial germ cells in Drosophila is regulated by p53 and the Outsiders monocarboxylate transporter.

Primordial germ cell development uses programmed cell death to remove abnormal, misplaced or excess cells. Precise control of this process is essential to maintain the continuity and integrity of the germline, and to prevent germ cells from colonizing locations other than the gonads. Through careful analyses of primordial germ cell distribution in developing Drosophila melanogaster embryos, we show that normal germ cell development involves extensive programmed cell death during stages 10-12 of embryogenesis. This germ cell death is mediated by Drosophila p53 (p53). Mutations in p53 result in excess primordial germ cells that are ectopic to the gonads. Initial movements of the germ cells appear normal, and wild-type numbers of germ cells populate the gonads, indicating that p53 is required for germ cell death, but not migration. To our knowledge, this is the first report of a loss-of-function phenotype for Drosophila p53 in a non-sensitized background. The p53 phenotype is remarkably similar to that of outsiders (out) mutants. Here, we show that the out gene encodes a putative monocarboxylate transporter. Mutations in p53 and out show nonallelic noncomplementation. Interestingly, overexpression of p53 in primordial germ cells of out mutant embryos partially suppresses the out germ cell death phenotype, suggesting that p53 functions in germ cells either downstream of out or in a closely linked pathway. These findings inform models in which signaling between p53 and cellular metabolism are integrated to regulate programmed cell death decisions.

G protein-coupled receptor roles in cell migration and cell death decisions.

Recognition of external conditions and the elicitation of appropriate responses are critical to a cell's ability to adjust to various developmental and environmental cues. G protein-coupled receptors (GPCRs) are a large class of receptors that act to relay external information into the cell by initiating signaling pathways that allow the cell to adapt to its present conditions. There are numerous ligands that activate GPCRs to initiate a multitude of intracellular signaling cascades involved in critical decisions including cell growth, differentiation, proliferation, migration, survival, and death. This article focuses on the signaling pathways involved in cell migration, survival, and death decisions with an emphasis on germ cells from various organisms.

DNA damage-induced programmed cell death: potential roles in germ cell development.

The detection of DNA damage is necessary to protect against proliferation of potentially harmful cells and often results in cell cycle arrest and programmed cell death. Key components of DNA damage signaling networks include ATM, CHK2, p53, and Bax. Mutations in these damage signaling systems are linked to tumorigenesis and developmental abnormalities. Expression of some of these genes in primordial germ cells (PGCs) argues that PGCs may utilize DNA damage-induced signaling mechanisms to select against germ cells that are genetically defective, thus maintaining the integrity of the germline. This paper summarizes the roles of these DNA damage signaling molecules and addresses their potential involvement in germ cell development.

Cell migration and programmed cell death of Drosophila germ cells.

Cell migration and programmed cell death are essential components of animal development and homeostasis, and the germ cells of Drosophila provide a simple genetic system to study the molecular mechanisms that govern these important cellular processes. Detailed descriptions of germ cell migration in Drosophila were accomplished long ago, but most genetic and molecular analyses of the process have occurred within the past 10 years. A few of the genes required for germ cell migration have been identified, and a very interesting picture is emerging. However, a process as complex as cell migration must involve the functions of many more molecules. In addition, cell migration and cell death mechanisms are often linked, as it is important to eliminate cells that are misplaced and could present a danger to the organism. In Drosophila, genes involved in germ cell migration can also affect programmed cell death. Currently, very little is known about how germ cells ectopic to the gonads are eliminated. To date, only four genes have been reported with roles in germ cell death, and three of these have additional functions in germ cell pathfinding. The nature of the cell death program has not been elucidated. Here, I provide a brief review of Drosophila germ cell migration and programmed cell death at both the descriptive and molecular levels. Many questions remain to be answered, but advances made in recent years are providing useful insights into these critical biological phenomena.

Identification of X-linked genes required for migration and programmed cell death of Drosophila melanogaster germ cells.

Drosophila germ cells form at the posterior pole of the embryo and migrate to the somatic gonad. Approximately 50% of the germ cells that form reach their target. The errant cells within the embryo undergo developmentally regulated cell death. Prior studies have identified some autosomal genes that regulate germ cell migration, but the genes that control germ cell death are not known. To identify X-linked genes required for germ cell migration and/or death, we performed a screen for mutations that disrupt these processes. Here we report the identification of scattershot and outsiders, two genes that regulate the programmed death of germ cells. The scattershot gene is defined by a mutation that disrupts both germ cell migration and the death of germ cells ectopic to the gonad. Maternal and zygotic expression of scattershot is required, but the migration and cell death functions can be genetically uncoupled. Zygotic expression of wild-type scattershot rescues germ cell pathfinding, but does not restore the programmed death of errant cells. The outsiders gene is required zygotically. In outsiders mutant embryos, the appropriate number of germ cells is incorporated into the gonad, but germ cells ectopic to the gonad persist.