Establishment of an Engaged and Active Learning Community in the Biology Classroom and Lab with Discord.

Discord is an instant messaging platform that facilitates voice and video calls and media exchanges. Although Discord was initially developed for video gaming, it is currently used by other communities where voice chatting is frequent. Here, Discord is described as a useful tool in the science classroom. We implemented Discord in several biology labs and classes and gained experience using it as a professor (AW) and as both a teaching assistant and a student (SS). In this Discord-enhanced learning space, students seemed to be more engaged with the subject material, their peers, and their instructors in comparison with a more traditional physical classroom and an entirely online classroom. In addition, real-time communication was augmented in a physical lab or classroom by Discord's interconnectivity. Discord facilitated real-time peer and instructor discussion and provided opportunities for group interaction outside conventional science teaching spaces. These increased connections also extended to the lab setting, both in and out of scheduled class time, providing a space to build community within and between groups and between students and instructors. Introducing Discord to a physical classroom or using it for an online class provided us with opportunities for a more engaged and active student, and they found it may lead to greater productivity and learning.

Conjuring up creativity: the effect of performing magic tricks on divergent thinking.

Research suggests that learning to perform magic tricks can promote both physical and psychological wellbeing. The current study extended this work by examining the impact of learning magic tricks on divergent thinking. A group of 10- to 11-year-old children completed Guilford's Alternate Uses Test both before and after participating in either a magic-based, or art-based, activity. As predicted, compared to the art-based activity, the magic-based activity resulted in a significantly greater increase in both AUT Fluency and AUT Originality scores. Rosenberg's Self-Esteem Scale and Dweck's Implicit Theories of Intelligence Scale for Children was also completed after each activity, and participants' self-esteem scores were higher after the art-based activity than the magic-based activity. In an exploratory aspect of the study, the AUT was re-administered to both groups three weeks later, and yielded no significant differences. The practical and theoretical implications of these findings are discussed, along with recommendations for future research.

Figure analysis: A teaching technique to promote visual literacy and active Learning.

Learning often improves when active learning techniques are used in place of traditional lectures. For many of these techniques, however, students are expected to apply concepts that they have already grasped. A challenge, therefore, is how to incorporate active learning into the classroom of courses with heavy content, such as molecular-based biology courses. An additional challenge is that visual literacy is often overlooked in undergraduate science education. To address both of these challenges, a technique called figure analysis was developed and implemented in three different levels of undergraduate biology courses. Here, students learn content while gaining practice in interpreting visual information by discussing figures with their peers. Student groups also make connections between new and previously learned concepts on their own while in class. The instructor summarizes the material for the class only after students grapple with it in small groups. Students reported a preference for learning by figure analysis over traditional lecture, and female students in particular reported increased confidence in their analytical abilities. There is not a technology requirement for this technique; therefore, it may be utilized both in classrooms and in nontraditional spaces. Additionally, the amount of preparation required is comparable to that of a traditional lecture. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):336-344, 2016.

Figure analysis: An implementation dialogue.

Figure analysis is a novel active learning teaching technique that reinforces visual literacy. Small groups of students discuss diagrams in class in order to learn content. The instructor then gives a brief introduction and later summarizes the content of the figure. This teaching technique can be used in place of lecture as a mechanism to deliver information to students. Here, a "how to" guide is presented in the form of an in-class dialogue, displaying the difficulties in visual interpretation that some students may experience while figure analysis is being implemented in an upper-level, cell biology course. Additionally, the dialogue serves as a guide for instructors who may implement the active learning technique as they consider how to respond to students' concerns in class. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):345-348, 2016.

Ethical dilemmas in the biology undergraduate classroom: role-playing congressional testimony.

Students often struggle with weighing multiple sides of bioethical dilemmas. The assignment described here incorporates discussion of ethical dilemmas in an upper-level undergraduate biology course. Students are introduced to ethical dilemmas in genetics through discussion of issues in small groups. They are then polled as to what positions they take on each dilemma and are assigned to argue a side opposite of one of their choices. Each student receives a subpoena to appear before a Senate subcommittee to give testimony as an expert witness. This role-play provides students with a starting point and motivation for developing their argument as well as a way to distance themselves from their own opinions by acting as someone holding the opposite stance. At the end of the presentations, students are required to reflect on the experience.

Building and analyzing protein interactome networks by cross-species comparisons.

BACKGROUND: A genomic catalogue of protein-protein interactions is a rich source of information, particularly for exploring the relationships between proteins. Numerous systems-wide and small-scale experiments have been conducted to identify interactions; however, our knowledge of all interactions for any one species is incomplete, and alternative means to expand these network maps is needed. We therefore took a comparative biology approach to predict protein-protein interactions across five species (human, mouse, fly, worm, and yeast) and developed InterologFinder for research biologists to easily navigate this data. We also developed a confidence score for interactions based on available experimental evidence and conservation across species. RESULTS: The connectivity of the resultant networks was determined to have scale-free distribution, small-world properties, and increased local modularity, indicating that the added interactions do not disrupt our current understanding of protein network structures. We show examples of how these improved interactomes can be used to analyze a genome-scale dataset (RNAi screen) and to assign new function to proteins. Predicted interactions within this dataset were tested by co-immunoprecipitation, resulting in a high rate of validation, suggesting the high quality of networks produced. CONCLUSIONS: Protein-protein interactions were predicted in five species, based on orthology. An InteroScore, a score accounting for homology, number of orthologues with evidence of interactions, and number of unique observations of interactions, is given to each known and predicted interaction. Our website http://www.interologfinder.org provides research biologists intuitive access to this data.

A network of conserved damage survival pathways revealed by a genomic RNAi screen.

Damage initiates a pleiotropic cellular response aimed at cellular survival when appropriate. To identify genes required for damage survival, we used a cell-based RNAi screen against the Drosophila genome and the alkylating agent methyl methanesulphonate (MMS). Similar studies performed in other model organisms report that damage response may involve pleiotropic cellular processes other than the central DNA repair components, yet an intuitive systems level view of the cellular components required for damage survival, their interrelationship, and contextual importance has been lacking. Further, by comparing data from different model organisms, identification of conserved and presumably core survival components should be forthcoming. We identified 307 genes, representing 13 signaling, metabolic, or enzymatic pathways, affecting cellular survival of MMS-induced damage. As expected, the majority of these pathways are involved in DNA repair; however, several pathways with more diverse biological functions were also identified, including the TOR pathway, transcription, translation, proteasome, glutathione synthesis, ATP synthesis, and Notch signaling, and these were equally important in damage survival. Comparison with genomic screen data from Saccharomyces cerevisiae revealed no overlap enrichment of individual genes between the species, but a conservation of the pathways. To demonstrate the functional conservation of pathways, five were tested in Drosophila and mouse cells, with each pathway responding to alkylation damage in both species. Using the protein interactome, a significant level of connectivity was observed between Drosophila MMS survival proteins, suggesting a higher order relationship. This connectivity was dramatically improved by incorporating the components of the 13 identified pathways within the network. Grouping proteins into "pathway nodes" qualitatively improved the interactome organization, revealing a highly organized "MMS survival network." We conclude that identification of pathways can facilitate comparative biology analysis when direct gene/orthologue comparisons fail. A biologically intuitive, highly interconnected MMS survival network was revealed after we incorporated pathway data in our interactome analysis.

An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme.

Genome-wide RNA interference (RNAi) screening allows investigation of the role of individual genes in a process of choice. Most RNAi screens identify a large number of genes with a continuous gradient in the assessed phenotype. Screeners must decide whether to examine genes with the most robust phenotype or the full gradient of genes that cause an effect and how to identify candidate genes. The authors have used RNAi in Drosophila cells to examine viability in a 384-well plate format and compare 2 screens, untreated control and treatment. They compare multiple normalization methods, which take advantage of different features within the data, including quantile normalization, background subtraction, scaling, cellHTS2 (Boutros et al. 2006), and interquartile range measurement. Considering the false-positive potential that arises from RNAi technology, a robust validation method was designed for the purpose of gene selection for future investigations. In a retrospective analysis, the authors describe the use of validation data to evaluate each normalization method. Although no method worked ideally, a combination of 2 methods, background subtraction followed by quantile normalization and cellHTS2, at different thresholds, captures the most dependable and diverse candidate genes. Thresholds are suggested depending on whether a few candidate genes are desired or a more extensive systems-level analysis is sought. The normalization approaches and experimental design to perform validation experiments are likely to apply to those high-throughput screening systems attempting to identify genes for systems-level analysis.

Nutrient regulation of oligopeptide transport in Saccharomyces cerevisiae.

Small peptides (2-5 amino acid residues) are transported into Saccharomyces cerevisiae via two transport systems: PTR (Peptide TRansport) for di-/tripeptides and OPT (OligoPeptide Transport) for oligopeptides of 4-5 amino acids in length. Although regulation of the PTR system has been studied in some detail, neither the regulation of the OPT family nor the environmental conditions under which family members are normally expressed have been well studied in S. cerevisiae. Using a lacZ reporter gene construct fused to 1 kb DNA from upstream of the genes OPT1 and OPT2, which encode the two S. cerevisiae oligopeptide transporters, the relative expression levels of these genes were measured in a variety of environmental conditions. Uptake assays were also conducted to measure functional protein levels at the plasma membrane. It was found that OPT1 was up-regulated in sulfur-free medium, and that Ptr3p and Ssy1p, proteins involved in regulating the di-/tripeptide transporter encoding gene PTR2 via amino acid sensing, were required for OPT1 expression in a sulfur-free environment. In contrast, as measured by response to toxic tetrapeptide and by real-time PCR, OPT1 was not regulated through Cup9p, which is a repressor for PTR2 expression, although Cup9p did repress OPT2 expression. In addition, all of the 20 naturally occurring amino acids, except the sulfur-containing amino acids methionine and cysteine, up-regulated OPT1, with the greatest change in expression observed when cells were grown in sulfur-free medium. These data demonstrate that regulation of the OPT system has both similarities and differences to regulation of the PTR system, allowing the yeast cell to adapt its utilization of small peptides to various environmental conditions.

N-Arachidonyl-glycine inhibits the glycine transporter, GLYT2a.

N-arachidonyl-glycine is one of a series of N-arachidonyl-amino acids that are derived from arachidonic acid. N-arachidonyl-glycine is produced in a wide range of tissues with greatest abundance in the spinal cord. Here we report that N-arachidonyl-glycine is a reversible and non-competitive inhibitor of glycine transport by GLYT2a, but has little effect on glycine transport by GLYT1b or gamma-amino butyric acid transport by GAT1. It has previously been reported that the activity of GLYT2a is down-regulated by protein kinase C and therefore we investigated whether the actions of N-arachidonyl-glycine on GLYT2a are mediated by second messenger systems that lead to the activation of protein kinase C. However, the protein kinase C inhibitor, staurosporine, had no effect on the actions of N-arachidonyl-glycine on GLYT2a. Thus, the actions of N-arachidonyl-glycine are likely to be mediated by a direct interaction with the transporter. We have further defined the pharmacophore by investigating the actions of other N-arachidonyl amino acids as well as the closely related compounds arachidonic acid, anandamide and R1-methanandamide. Arachidonic acid, anandamide and R1-methanandamide have no effect on glycine transport, but N-arachidonyl-l-alanine has similar efficacy at GLYT2a to N-arachidonyl-glycine, and N-arachidonyl-gamma-amino butyric acid is less efficacious. These observations define a novel recognition site for the N-arachidonyl amino acids.

Transmembrane domain prediction and consensus sequence identification of the oligopeptide transport family.

Few polytopic membrane proteins have had their topology determined experimentally. Often, researchers turn to an algorithm to predict where the transmembrane domains might lie. Here we use a consensus method, using six different transmembrane domain prediction algorithms on six members of the oligopeptide transport family, all of which have been experimentally characterized. PSI-BLAST results indicate that the six chosen oligopeptide transport family members are distributed throughout most branches of the phylogram, suggesting that these members represent a broad view of the oligopeptide transport family. We combined the prediction algorithms with a multiple sequence alignment, and consensus transmembrane domains were assigned not only based on algorithmic output, but also based on conserved familial motifs found by analysis of the PSI-BLAST results. The consensus method combined with the "charge-difference rule" yields a model topology for the family containing 12 transmembrane domains with the N- and C-termini facing extracellular.

An oligopeptide transporter gene family in Arabidopsis.

We have identified nine oligopeptide transporter (OPT) orthologs (AtOPT1 to AtOPT9) in Arabidopsis. These proteins show significant sequence similarity to OPTs of Candida albicans (CaOpt1p), Schizosaccharomyces pombe (Isp4p), and Saccharomyces cerevisiae (Opt1p and Opt2p). Hydrophilicity plots of the OPTs suggest that they are integral membrane proteins with 12 to 14 transmembrane domains. Sequence comparisons showed that the AtOPTs form a distinct subfamily when compared with the fungal OPTs. Two highly conserved motifs (NPG and KIPPR) were found among all OPT members. The identification of multiple OPTs in Arabidopsis suggests that they may play different functional roles. This idea is supported by the fact that AtOPTs have a distinct, tissue-specific expression pattern. The cDNAs encoding seven of the AtOPTs were cloned into a yeast vector under the control of a constitutive promoter. AtOPT4 expressed in S. cerevisiae mediated the uptake of KLG-[3H]L. Similarly, expression of five of the seven AtOPT proteins expressed in yeast conferred the ability to uptake tetra- and pentapeptides as measured by growth. This study provides new evidence for multiple peptide transporter systems in Arabidopsis, suggesting an important physiological role for small peptides in plants.