"They Have Shown Me It Is Possible to Thrive within STEM": Incorporating Learning Assistants in General Chemistry Enhances Student Belonging and Confidence.

Students often experience social and psychological barriers to success in General Chemistry, which is a key gateway to many students' science pathways. Learning assistants (LAs) have the potential to reduce these barriers and to strengthen students' sense of belonging in General Chemistry and STEM more broadly. Here, we used a 17-item Likert scale to determine whether incorporating LAs into General Chemistry I and II enhances students' sense of belonging in these courses. The incorporation of LAs into General Chemistry I had a significant positive effect and a medium to large effect size for students in all student groups examined: women and men; students in both racially and ethnically underrepresented and well-represented groups; first- and continuing-generation students. In General Chemistry II, similar results were observed for women and men; students in well-represented racial and ethnic groups; continuing-generation students. Further, we asked students to reflect on the impact that working with LAs had on their sense of belonging in STEM and confidence in talking about science. Sixty percent of students indicated that working with LAs had a positive impact on their STEM belonging, with five themes describing LA impacts: reducing isolation, serving as inspirational role models, providing mentoring, increasing opportunities for engagement and confidence building, and serving as accessible and approachable sources of support. Sixty-one percent of students also indicated that working with LAs increased their confidence in talking about science, with three themes emerging: fostering an environment with a lower risk of negative judgment, providing increased opportunities for feedback, and supporting students as they practiced their growing skills. Together, these results indicate that LAs can be an important means to reduce social and psychological barriers for students in gateway science courses, increasing their sense that they belong to the class and STEM more broadly.

Teaching Discipline-Based Problem Solving.

Problem solving plays an essential role in all scientific disciplines, and solving problems can reveal essential concepts that underlie those disciplines. Thus, problem solving serves both as a common tool and desired outcome in many science classes. Research on teaching problem solving offers principles for instruction that are guided by learning theories. This essay describes an online, evidence-based teaching guide (https://lse.ascb.org/evidence-based-teaching-guides/problem-solving) intended to guide instructors in the use of these principles. The guide describes the theoretical underpinnings of problem-solving research and instructional choices that can place instruction before problem solving (e.g., peer-led team learning and worked examples) or problem solving before instruction (e.g., process-oriented guided inquiry learning, contrasting cases, and productive failure). Finally, the guide describes assessment choices that help instructors consider alternative outcomes for problem-solving instruction. Each of these sections consists of key points that can be gleaned from the literature as well as summaries and links to articles that inform these points. The guide also includes an instructor checklist that offers a concise summary of key points with actionable steps to direct instructors as they develop and refine their problem-solving instruction.

"It made me feel like a bigger part of the STEM community": Incorporation of Learning Assistants Enhances Students' Sense of Belonging in a Large Introductory Biology Course.

Large introductory science courses are a particularly important and challenging target for creating inclusive learning environments. In this study, we examined the impact of incorporating learning assistants (LAs) on the learning environment in an introductory biology course taught with two different structures: an in-person lecture with intermittent active-learning components and an online setting taught with a flipped instructional approach. Using a survey that measured sense of belonging in a single class, we found that students in sections with LAs reported greater sense of belonging than students in sections without LAs in both class structures. Further, student focus groups revealed that LAs promoted learning and engagement in the class by answering questions and providing clarity; allowing more use of active- and interactive-learning structures; and serving as accessible, approachable, and immediate sources of help. Student responses also indicated that LAs promoted a sense of belonging in science, technology, engineering, and mathematics (STEM) by decreasing feelings of isolation, serving as inspirational role models, clarifying progression through the STEM educational system, and helping students become more engaged and confident in their STEM-related knowledge and skills. These findings indicate that LAs can support multiple elements of inclusive STEM learning environments.

Framework for advancing rigorous research.

There is a pressing need to increase the rigor of research in the life and biomedical sciences. To address this issue, we propose that communities of 'rigor champions' be established to campaign for reforms of the research culture that has led to shortcomings in rigor. These communities of rigor champions would also assist in the development and adoption of a comprehensive educational platform that would teach the principles of rigorous science to researchers at all career stages.

Inclusive Teaching.

Over the past two decades, science, technology, engineering, and mathematics (STEM) faculty have been striving to make their teaching practices more inclusive and welcoming to the variety of students who enter college. However, many STEM faculty, even those at teaching-focused institutions, have been educated in a traditional environment that emphasizes research and may not include classroom teaching. This can produce a deficit in training that leaves many STEM faculty feeling uncertain about inclusive teaching practices and their essential undergirding principles. This essay describes an online, evidence-based teaching guide ( https://lse.ascb.org/evidence-based-teaching-guides/inclusive-teaching ) intended to help fill this gap, serving as a resource for science faculty as they work to become more inclusive, particular with regard to differences in race, ethnicity, and gender. The guide describes the importance of developing self-awareness and empathy for students as a precursor to considering classroom practices. It also explores the role of classroom climate before turning to pedagogical choices that can support students' sense of belonging, competence, and interest in the course. Finally, the guide suggests that true inclusivity is a community effort and that instructors should leverage local and national networks to maximize student learning and inclusion. Each of these essential points is supported by summaries of and links to articles that can inform these choices. The guide also includes an instructor checklist that offers a concise summary of key points with actionable steps that can guide instructors as they work toward a more inclusive practice. We hope that the guide will provide value for both faculty who are just beginning to consider how to change their teaching practices and faculty seeking to enrich their current efforts.

Peer Instruction.

Peer instruction, a form of active learning, is generally defined as an opportunity for peers to discuss ideas or to share answers to questions in an in-class environment, where they also have opportunities for further interactions with their instructor. When implementing peer instruction, instructors have many choices to make about group design, assignment format, and grading, among others. Ideally, these choices can be informed by research about the impact of these components of peer instruction on student learning. This essay describes an online, evidence-based teaching guide published by CBE-Life Sciences Education at http://lse.ascb.org/evidence-based-teaching-guides/peer-instruction . The guide provides condensed summaries of key research findings organized by teaching choices, summaries of and links to research articles and other resources, and actionable advice in the form of a checklist for instructors. In addition to describing key features of the guide, this essay also identifies areas in which further empirical studies are warranted.

Helping Practitioners and Researchers Identify and Use Education Research Literature.

Evidence-based teaching practices are being encouraged to increase student skills and understanding in the sciences. Finding, interpreting, and applying education literature to a specific context are barriers to adopting these evidence-based practices. Here, we introduce a new feature, Evidence-Based Teaching Guides This feature identifies literature associated with specific pedagogies, which we distill to practical recommendations for teaching. The goals of the feature are: to provide instructors with tools to make research-supported choices to implement the pedagogy in question, to articulate the reasons for their choices, and to develop increased awareness of biology education research. We think these guides may also be useful for biology education researchers in identifying critical components, adaptations, and contextual features that could be investigated for a given pedagogy. Each guide consists of a website with a visual map of instructional choices associated with the topic and linked pages that summarize findings from the literature and provide additional links to and summaries of key articles. Each guide will include an instructor checklist of recommendations consolidated from the entire guide in order to provide instructors with a snapshot of instructional choices and actionable advice.

Group Work.

Science, technology, engineering, and mathematics faculty are increasingly incorporating both formal and informal group work in their courses. Implementing group work can be improved by an understanding of the extensive body of educational research studies on this topic. This essay describes an online, evidence-based teaching guide published by CBE-Life Sciences Education (LSE). The guide provides a tour of research studies and resources related to group work (including many articles from LSE). Instructors who are new to group work, as well as instructors who have experienced difficulties in implementing group work, may value the condensed summaries of key research findings. These summaries are organized by teaching challenges, and actionable advice is provided in a checklist for instructors. Education researchers may value the inclusion of empirical studies, key reviews, and meta-analyses of group-work studies. In addition to describing key features of the guide, this essay also identifies areas in which further empirical studies are warranted.

Effective Educational Videos: Principles and Guidelines for Maximizing Student Learning from Video Content.

Educational videos have become an important part of higher education, providing an important content-delivery tool in many flipped, blended, and online classes. Effective use of video as an educational tool is enhanced when instructors consider three elements: how to manage cognitive load of the video; how to maximize student engagement with the video; and how to promote active learning from the video. This essay reviews literature relevant to each of these principles and suggests practical ways instructors can use these principles when using video as an educational tool.

Traditional Versus Online Biology Courses: Connecting Course Design and Student Learning in an Online Setting.

Online courses are a large and growing part of the undergraduate education landscape, but many biology instructors are skeptical about the effectiveness of online instruction. We reviewed studies comparing the effectiveness of online and face-to-face (F2F) undergraduate biology courses. Five studies compared student performance in multiple course sections at community colleges, while eight were smaller scale and compared student performance in particular biology courses at a variety of types of institutions. Of the larger-scale studies, two found that students in F2F sections outperformed students in online sections, and three found no significant difference; it should be noted, however, that these studies reported little information about course design. Of the eight smaller scale studies, six found no significant difference in student performance between the F2F and online sections, while two found that the online sections outperformed the F2F sections. In alignment with general findings about online teaching and learning, these results suggest that well-designed online biology courses can be effective at promoting student learning. Three recommendations for effective online instruction in biology are given: the inclusion of an online orientation to acclimate students to the online classroom; student-instructor and student-student interactions facilitated through synchronous and asynchronous communication; and elements that prompt student reflection and self-assessment. We conclude that well-designed online biology courses can be as effective as their traditional counterparts, but that more research is needed to elucidate specific course elements and structures that can maximize online students' learning of key biology skills and concepts.

Test-enhanced learning: the potential for testing to promote greater learning in undergraduate science courses.

Testing within the science classroom is commonly used for both formative and summative assessment purposes to let the student and the instructor gauge progress toward learning goals. Research within cognitive science suggests, however, that testing can also be a learning event. We present summaries of studies that suggest that repeated retrieval can enhance long-term learning in a laboratory setting; various testing formats can promote learning; feedback enhances the benefits of testing; testing can potentiate further study; and benefits of testing are not limited to rote memory. Most of these studies were performed in a laboratory environment, so we also present summaries of experiments suggesting that the benefits of testing can extend to the classroom. Finally, we suggest opportunities that these observations raise for the classroom and for further research.

The synthesis map is a multidimensional educational tool that provides insight into students' mental models and promotes students' synthetic knowledge generation.

Concept mapping was developed as a method of displaying and organizing hierarchical knowledge structures. Using the new, multidimensional presentation software Prezi, we have developed a new teaching technique designed to engage higher-level skills in the cognitive domain. This tool, synthesis mapping, is a natural evolution of concept mapping, which utilizes embedding to layer information within concepts. Prezi's zooming user interface lets the author of the presentation use both depth as well as distance to show connections between data, ideas, and concepts. Students in the class Biology of Cancer created synthesis maps to illustrate their knowledge of tumorigenesis. Students used multiple organizational schemes to build their maps. We present an analysis of student work, placing special emphasis on organization within student maps and how the organization of knowledge structures in student maps can reveal strengths and weaknesses in student understanding or instruction. We also provide a discussion of best practices for instructors who would like to implement synthesis mapping in their classrooms.

Molecular mechanics and dynamics characterization of an in silico mutated protein: a stand-alone lab module or support activity for in vivo and in vitro analyses of targeted proteins.

Over the past 20 years, the biological sciences have increasingly incorporated chemistry, physics, computer science, and mathematics to aid in the development and use of mathematical models. Such combined approaches have been used to address problems from protein structure-function relationships to the workings of complex biological systems. Computer simulations of molecular events can now be accomplished quickly and with standard computer technology. Also, simulation software is freely available for most computing platforms, and online support for the novice user is ample. We have therefore created a molecular dynamics laboratory module to enhance undergraduate student understanding of molecular events underlying organismal phenotype. This module builds on a previously described project in which students use site-directed mutagenesis to investigate functions of conserved sequence features in members of a eukaryotic protein kinase family. In this report, we detail the laboratory activities of a MD module that provide a complement to phenotypic outcomes by providing a hypothesis-driven and quantifiable measure of predicted structural changes caused by targeted mutations. We also present examples of analyses students may perform. These laboratory activities can be integrated with genetics or biochemistry experiments as described, but could also be used independently in any course that would benefit from a quantitative approach to protein structure-function relationships.

A molecular genetics laboratory course applying bioinformatics and cell biology in the context of original research.

Research based laboratory courses have been shown to stimulate student interest in science and to improve scientific skills. We describe here a project developed for a semester-long research-based laboratory course that accompanies a genetics lecture course. The project was designed to allow students to become familiar with the use of bioinformatics tools and molecular biology and genetic approaches while carrying out original research. Students were required to present their hypotheses, experiments, and results in a comprehensive lab report. The lab project concerned the yeast casein kinase 1 (CK1) protein kinase Yck2. CK1 protein kinases are present in all organisms and are well conserved in primary structure. These enzymes display sequence features that differ from other protein kinase subfamilies. Students identified such sequences within the CK1 subfamily, chose a sequence to analyze, used available structural data to determine possible functions for their sequences, and designed mutations within the sequences. After generating the mutant alleles, these were expressed in yeast and tested for function by using two growth assays. The student response to the project was positive, both in terms of knowledge and skills increases and interest in research, and several students are continuing the analysis of mutant alleles as summer projects.

Measurement of chronic oxidative and inflammatory stress by quantification of isoketal/levuglandin gamma-ketoaldehyde protein adducts using liquid chromatography tandem mass spectrometry.

Measurement of F(2)-isoprostanes (F(2)-IsoPs) has been independently verified as one of the most reliable approaches to assess oxidative stress in vivo. However, the rapid clearance of F(2)-IsoPs makes the timing of sample collection critical for short-lived oxidative insults. Isoketals (IsoKs) are gamma-ketoaldehydes formed via the IsoP pathway of lipid peroxidation that rapidly react with lysyl residues of proteins to form stable protein adducts. Oxidative stress can also activate cyclooxygenases to produce prostaglandin H(2), which can form two specific isomers of IsoK-levuglandin (LG) D(2) and E(2). Because adducted proteins are not rapidly cleared, IsoK/LG protein adduct levels can serve as a dosimeter of oxidative and inflammatory damage over prolonged periods of time as well as brief episodes of injury. Quantification of IsoK/LG protein adducts begins with liquid-phase extraction to separate proteins from lipid membranes, allowing measurement of both IsoK/LG protein adducts and F(2)-IsoP from the same sample if desired. IsoK/LG-lysyl-lactam adducts are measured by liquid chromatography tandem mass spectrometry after proteolytic digestion of extracted proteins, solid-phase extraction and preparative HPLC.

A mass spectrometry based method for distinguishing between symmetrically and asymmetrically dimethylated arginine residues.

The arginine methylation of proteins is involved in several important cellular activities, most notably transcriptional control. Arginine dimethylation can take two distinct forms, symmetric and asymmetric, catalyzed by different classes of enzymes. To establish a method for the mass spectrometric identification and characterization of this post-translational modification, we analyzed synthetic peptides with symmetrically or asymmetrically methylated arginine residues by electrospray ionization tandem mass spectrometry. We observed abundant characteristic ions at [M+nH-31](n+) and [M+nH-70](n+) in spectra of symmetrically methylated peptides and at [M+nH-45](n+) in spectra of asymmetrically methylated peptides. We speculate these ions arise from neutral loss of monomethylamine, dimethylcarbodiimide, and dimethylamine, respectively. These characteristic ions allowed the rapid identification of a symmetrically arginine-dimethylated peptide from myelin basic protein and a symmetrically arginine-dimethylated peptide from SmD3 co-immunoprecipitated with the methyltransferase-associated protein pICln, suggesting that this method may provide a rapid means to screen for and characterize dimethylarginine sites.

Modification of proteins by isoketal-containing oxidized phospholipids.

Oxidative stress frequently leads to altered function of membrane proteins. Isoketals are highly reactive products of the isoprostane pathway of free radical-induced lipid peroxidation that rapidly form covalent protein adducts and exhibit a remarkable proclivity to form protein cross links in vitro. Examination of isoketal adducts from an animal model of oxidative injury revealed that initial adducts were formed by isoketals esterified in phospholipids, representing a novel oxidative injury-associated modification of proteins by phospholipids. Maturation of adducts involved cleavage from phospholipids and conversion of adducts to a more stable chemical form that can be detected for extended periods. Because initial adducts were formed by phospholipid-esterified isoketals, the functional consequence of isoketal adduction was examined using a model membrane protein (a cardiac K(+) channel). These studies revealed that isoketal adduction profoundly altered protein function, inhibiting potassium current in a dose-dependent manner. These findings indicate that phospholipid-esterified isoketals rapidly adduct membrane proteins and that such modification can alter protein function, suggesting a generalized cellular mechanism for alteration of membrane function as a consequence of oxidative stress.

Tapasin is a facilitator, not an editor, of class I MHC peptide binding.

Tapasin has been proposed to function as a peptide editor to displace lower affinity peptides and/or to favor the binding of high affinity peptides. Consistent with this, cell surface HLA-B8 molecules in tapasin-deficient cells were less stable and the peptide repertoire was substantially altered. However, the binding affinities of peptides expressed in the absence of tapasin were unexpectedly higher, not lower. The peptide repertoire from cells expressing soluble tapasin was similar in both appearance and affinity to that presented in the presence of full-length tapasin, but the HLA-B8 molecules showed altered cell surface stability characteristics. Similarly, the binding affinities of HLA-A*0201-associated peptides from tapasin(+) and tapasin(-) cells were equivalent, although steady state HLA-A*0201 cell surface expression was decreased and the molecules demonstrated reduced cell surface stability on tapasin(-) cells. These data are inconsistent with a role for tapasin as a peptide editor. Instead, we propose that tapasin acts as a peptide facilitator. In this role, it stabilizes the peptide-free conformation of class I MHC molecules in the endoplasmic reticulum and thus increases the number and variety of peptides bound to class I MHC. Full-length tapasin then confers additional stability on class I MHC molecules that are already associated with peptides.