Malate dehydrogenase: a story of diverse evolutionary radiation.

Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.

Developing Science Literacy in Students and Society: Theory, Research, and Practice.

The subject of scientific literacy has never been more critical to the scientific community as well as society in general. As opportunities to spread misinformation increase with the rise of new technologies, it is critical for society to have at its disposal the means for ensuring that its citizens possess the basic scientific literacy necessary to make critical decisions on topics like climate change, biotechnology, and other science-based issues. As the Guest Editors of this themed issue of the Journal of Microbiology and Biology Education, we present a wide array of techniques that the scientific community is using to promote scientific literacy in both academic and nonacademic settings. The diversity of the techniques presented here give us confidence that the scientific community will rise to the challenge of ensuring that our society will be prepared to make fact-based and wise decisions that will preserve and improve our quality of life.

Using personas and the ADKAR framework to evaluate a network designed to facilitate sustained change toward active learning in the undergraduate classroom.

One promising practice for increasing active learning in undergraduate science education is the use of a mentoring network. The Promoting Active Learning and Mentoring (PALM) Network was launched with practitioners from several professional societies and disciplines to make changes in their teaching based on evidence-based practices and to encourage the members to reflect deeply on their teaching experiences. Members of the Network interviewed seven previous Fellows, 1 to 6 years after completing their fellowship, to better understand the value of the Network and how these interactions impacted their ability to sustain change toward more active teaching practices. The interviews resulted in the creation of three personas that reflect the kinds of educators who engaged with the Network: Neil the Novice, Issa the Isolated, and Etta the Expert. Key themes emerged from the interviews about how interactions with the PALM Network sustained change toward evidence-based teaching practices allowing the members to readily adapt to the online learning environment during the COVID-19 pandemic. Understanding how the personas intersect with the ADKAR model contributes to a better understanding of how mentoring networks facilitate transformative change toward active learning and can inform additional professional development programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s44217-022-00023-w.

Preprint articles as a tool for teaching data analysis and scientific communication.

The skill of analyzing and interpreting research data is central to the scientific process, yet it is one of the hardest skills for students to master. While instructors can coach students through the analysis of data that they have either generated themselves or obtained from published articles, the burgeoning availability of preprint articles provides a new potential pedagogical tool. We developed a new method in which students use a cognitive apprenticeship model to uncover how experts analyzed a paper and compare the professional's cognitive approach to their own. Specifically, students first critique research data themselves and then identify changes between the preprint and final versions of the paper that were likely the results of peer review. From this activity, students reported diverse insights into the processes of data presentation, peer review, and scientific publishing. Analysis of preprint articles is therefore a valuable new tool to strengthen students' information literacy and understanding of the process of science.

COVID-360: A Collaborative Effort to Develop a Multidisciplinary Set of Online Resources for Engaging Teaching on the COVID-19 Pandemic.

The COVID-19 pandemic has challenged undergraduate instructors and students in an unprecedented manner. Each has needed to find creative ways to continue the engaged teaching and learning process in an environment defined by physical separation and emotional anxiety and uncertainty. As a potential tool to meet this challenge, we developed a set of curricular materials that combined our respective life science teaching interests with the real-time scientific problem of the COVID-19 pandemic in progress. Discrete modules were designed that are engaging to students, implement active learning-based coursework in a variety of institutional and learning settings, and can be used either in person or remotely. The resulting interdisciplinary curriculum, dubbed "COVID-360," enables instructors to select from a menu of curricular options that best fit their course content, desired activities, and mode of class delivery. Here we describe how we devised the COVID-360 curriculum and how it represents our efforts to creatively and effectively respond to the instructional needs of diverse students in the face of an ongoing instructional crisis.

Facilitating Long-Term Mentoring To Effectively Implement Active Learning Instruction: Formation of the Promoting Active Learning and Mentoring (PALM) Network.

A large body of data suggests that implementing active learning practices in a STEM classroom contributes to increased success in both achievement of student learning outcomes and retention of students. Despite these findings, significant barriers exist for instructors implementing active learning strategies in their undergraduate classrooms. These barriers can be effectively addressed by providing sustained support to instructors and postdoctoral trainees interested in implementing active learning strategies in their teaching practice. The Promoting Active Learning and Mentoring (PALM) network attains this objective by connecting instructors interested in learning more about active learning (Fellows) with individuals who have extensive expertise related to this practice (mentors). These facilitated connections occur in the form of active mentorship for a year or more, virtual journal clubs, and biannual gatherings of PALM Fellows and mentors. Here, we describe the foundation on which PALM was built and explain how a successful mentorship program can pave the way for educators to adapt and implement evidence-based practices like active learning in a college classroom.

Undergraduates Phenotyping Arabidopsis Knockouts in a Course-Based Undergraduate Research Experience: Exploring Plant Fitness and Vigor Using Quantitative Phenotyping Methods.

We present a curriculum description, an initial student outcome investigation, and sample scientific results for a representative Course-Based Undergraduate Research Experience (CURE) that is part of the "Undergraduates Phenotyping Arabidopsis Knockouts" (unPAK) network. CUREs in the unPAK network characterize quantitative phenotypes of the model plant Arabidopsis from across environments to uncover connections between genotype and phenotype. Students in unPAK CUREs grow plants in a replicated block design and make quantitative measurements throughout the semester. This CURE enables students to answer plant science questions that draw from fields such as environmental science, genetics, ecology, and evolution. Findings indicate that this experience provides students with opportunities to make relevant scientific discoveries. Eighty percent of student datasets produced from the CURE met criteria for inclusion in the project database, indicative of student learning in data collection and analysis of quantitative plant traits. Student datasets uncovered novel effects of mutation on plant form. In addition, students' science self-efficacy increased as a result of course participation, and faculty feedback on course implementation was positive. We present unPAK as a new network that supports CUREs and research experiences focused on collecting biological data made publicly available to the scientific community. The unPAK CUREs can be tailored to address instructor interests or pedagogical needs while involving students in research investigating quantitative plant phenotypes.

An Undergraduate Research Project Utilizing CRISPR-Cas9 Gene Editing Technology to Study Gene Function in Arabidopsis thaliana.

The CRISPR-Cas9 system functions in microbial viral pathogen recognition pathways by identifying and targeting foreign DNA for degradation. Recently, biotechnological advances have allowed scientists to use CRISPR-Cas9-based elements as a molecular tool to selectively modify DNA in a wide variety of other living systems. Given the emerging need to bring engaging CRISPR-Cas9 laboratory experiences to an undergraduate audience, we incorporated a CRISPR-based research project into our Genetics class laboratories, emphasizing its use in plants. Our genetic manipulations were designed for Arabidopsis thaliana, which despite serving as a plant research model, has traditionally been difficult to use in a classroom setting. For this project, students transformed plasmid DNA containing the essential CRISPR-Cas9 gene editing elements into A. thaliana. Expression of these elements in the plant genome was expected to create a deletion at one of six targeted genes. The genes we chose had a known seedling and/or juvenile loss-of-function phenotype, which made genetic analysis by students with a limited background possible. It also allowed the project to reach completion in a typical undergraduate semester timeframe. Assessment efforts demonstrated several learning gains, including students' understanding of CRISPR-Cas9 content, their ability to apply CRISPR-Cas9 gene editing tools using bioinformatics and genetics, their ability to employ elements of experimental design, and improved science communication skills. They also felt a stronger connection to their scientific education and were more likely to continue on a STEM career path. Overall, this project can be used to introduce CRISPR-Cas9 technology to undergraduates using plants in a single-semester laboratory course.

Distributed phenomics with the unPAK project reveals the effects of mutations.

Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.

Integrating CRISPR-Cas9 Technology into Undergraduate Courses: Perspectives from a National Science Foundation (NSF) Workshop for Undergraduate Faculty, June 2018.

As CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 technology becomes more mainstream in life science research, it becomes critical for undergraduate instructors to devise engaging ways to bring the technology into their classrooms. To help meet this challenge, the National Science Foundation sponsored a workshop for undergraduate instructors in June 2018 at The Ohio State University in conjunction with the annual Association of Biology Laboratory Educators meeting based on a workflow developed by the workshop's facilitators. Over the course of two and a half days, participants worked through a modular workflow for the use of CRISPR-Cas9 in a course-based (undergraduate) research experience (CURE) setting while discussing the barriers each of their institutions had to implementing such work, and how such barriers could be overcome. The result of the workshop was a team with newfound energy and confidence to implement CRISPR-Cas9 technology in their courses and the development of a community of undergraduate educators dedicated to supporting each other in the implementation of the workflow either in a CURE or modular format. In this article, we review the activities and discussions from the workshop that helped each participant devise their own tailored approaches of how best to bring this exciting new technology into their classes.

Release of transcriptional repression through the HCR promoter region confers uniform expression of HWP1 on surfaces of Candida albicans germ tubes.

The mechanisms that fungi use to co-regulate subsets of genes specifically associated with morphogenic states represent a basic unsolved problem in fungal biology. Candida albicans is an important model of fungal differentiation both for rapid interconversion between yeast and hyphal growth forms and for white/opaque switching mechanisms. The Sundstrom lab is interested in mechanisms regulating hypha-specific expression of adhesin genes that are critical for C. albicans hyphal growth phenotypes and pathogenicity. Early studies on hypha-specific genes such as HWP1 and ALS3 reported 5' intergenic regions that are larger than those typically found in an average promoter and are associated with hypha-specific expression. In the case of HWP1, activation and repression involves a 368 bp region, denoted the HWP1 control region (HCR), located 1410 bp upstream of its transcription start site. In previous work we showed that HCR confers developmental regulation to a heterologous ENO1 promoter, indicating that HCR by itself contains sufficient information to couple gene expression to morphology. Here we show that the activation and repression mediated by HCR are localized to distinct HCR regions that are targeted by the transcription factors Nrg1p and Efg1p. The finding that Efg1p mediates both repression via HCR under yeast morphological conditions and activation conditions positions Efg1p as playing a central role in coupling HWP1 expression to morphogenesis through the HCR region. These localization studies revealed that the 120 terminal base pairs of HCR confer Efg1p-dependent repressive activity in addition to the Nrg1p repressive activity mediated by DNA upstream of this subregion. The 120 terminal base pair subregion of HCR also contained an initiation site for an HWP1 transcript that is specific to yeast growth conditions (HCR-Y) and may function in the repression of downstream DNA. The detection of an HWP1 mRNA isoform specific to hyphal growth conditions (HWP1-H) showed that morphology-specific mRNA isoforms occur under both yeast and hyphal growth conditions. Similar results were found at the ALS3 locus. Taken together, these results, suggest that the long 5' intergenic regions upstream of hypha-specific genes function in generating mRNA isoforms that are important for morphology-specific gene expression. Additional complexity in the HWP1 promoter involving HCR-independent activation was discovered by creating a strain lacking HCR that exhibited variable HWP1 expression during hyphal growth conditions. These results show that while HCR is important for ensuring uniform HWP1 expression in cell populations, HCR independent expression also exists. Overall, these results elucidate HCR-dependent mechanisms for coupling HWP1-dependent gene expression to morphology uniformly in cell populations and prompt the hypothesis that mRNA isoforms may play a role in coupling gene expression to morphology in C. albicans.

Improving medical students' knowledge of genetic disease: a review of current and emerging pedagogical practices.

Genetics is an essential subject to be mastered by health professional students of all types. However, technological advances in genomics and recent pedagogical research have changed the way in which many medical training programs teach genetics to their students. These advances favor a more experience-based education focused primarily on developing student's critical thinking skills. In this review, we examine the current state of genetics education at both the preclinical and clinical levels and the ways in which medical and pedagogical research have guided reforms to current and emerging teaching practices in genetics. We discover exciting trends taking place in which genetics is integrated with other scientific disciplines both horizontally and vertically across medical curricula to emphasize training in scientific critical thinking skills among students via the evaluation of clinical evidence and consultation of online databases. These trends will produce future health professionals with the skills and confidence necessary to embrace the new tools of medical practice that have emerged from scientific advances in genetics, genomics, and bioinformatics.

A course-based research experience: how benefits change with increased investment in instructional time.

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Improved student linkage of Mendelian and molecular genetic concepts through a yeast-based laboratory module.

A study of modern genetics requires students to successfully unite the principles of Mendelian genetics with the functions of DNA. Traditional means of teaching genetics are often successful in teaching Mendelian and molecular ideas but not in allowing students to see how the two subjects relate. The laboratory module presented here attempts to present classical and molecular genetic concepts together as an inquiry-based exploration appropriate for high school or introductory undergraduate students. Using the non-essential APQ12 gene in the budding yeast Saccharomyces cerevisiae, students perform PCR, selective growth, and sporulation experiments to establish the ploidy and APQ12 zygosity of a series of unknown strains. Each experiment contributes data to characterize the unknown strains, but complete characterization is not possible without assimilating the data from all of the experiments. The module allows students to consider concepts normally introduced and emphasized in Mendelian genetics and explore them using molecular and experimental tools. Comparison of pre-module and post-module assessment surveys show an increase in student ability to link Mendelian concepts to experimental procedures relying on DNA analysis. The development of modules such as these provides students of all backgrounds with the tools to engage the complexities and issues that constitute modern principles of inheritance.

Extensive phenotypic variation among allelic T-DNA inserts in Arabidopsis thaliana.

T-DNA insertion mutants are a tool used widely in Arabidopsis thaliana to disrupt gene function. We phenotyped multiple homozygous T-DNA A. thaliana mutants at each of two loci (AT1G11060 and AT4G00210). We measured life history traits, including germination, size at reproduction and fruit production. Allelic T-DNA lines differed for most traits at AT1G11060 but not at AT4G00210. However, insertions in exons differed from other insertion positions in AT4G00210 but not in AT1G11060. We found evidence for additional insertions in approximately half of the lines, but found few phenotypic consequences. In general, our results suggest that a cautious interpretation of T-DNA phenotypes is warranted.

Integral membrane proteins Brr6 and Apq12 link assembly of the nuclear pore complex to lipid homeostasis in the endoplasmic reticulum.

Cells of Saccharomyces cerevisiae lacking Apq12, a nuclear envelope (NE)-endoplasmic reticulum (ER) integral membrane protein, are defective in assembly of nuclear pore complexes (NPCs), possibly because of defects in regulating membrane fluidity. We identified BRR6, which encodes an essential integral membrane protein of the NE-ER, as a dosage suppressor of apq12 Delta. Cells carrying the temperature-sensitive brr6-1 allele have been shown to have defects in nucleoporin localization, mRNA metabolism and nuclear transport. Electron microscopy revealed that brr6-1 cells have gross NE abnormalities and proliferation of the ER. brr6-1 cells were hypersensitive to compounds that affect membrane biophysical properties and to inhibitors of lipid biosynthetic pathways, and displayed strong genetic interactions with genes encoding non-essential lipid biosynthetic enzymes. Strikingly, brr6-1 cells accumulated, in or near the NE, elevated levels of the two classes of neutral lipids, steryl esters and triacylglycerols, and over-accumulated sterols when they were provided exogenously. Although neutral lipid synthesis is dispensable in wild-type cells, viability of brr6-1 cells was fully dependent on neutral lipid production. These data indicate that Brr6 has an essential function in regulating lipid homeostasis in the NE-ER, thereby impacting NPC formation and nucleocytoplasmic transport.

Harnessing genomics to explore the processes and evolution of mRNA export.

The export of quality-controlled mRNAs across the nuclear membrane for translation is mediated by a set of core proteins that are conserved throughout eukaryotes and have been best-characterized in Saccharomyces cerevisiae. The increased genomic complexity that arose during metazoan evolution, however, has resulted in increased systematic complexity that is reflected in the presence of additional metazoan mRNA export factors. In some cases, metazoans encode families of closely-related factors whereas in fungi, a single homolog is present. An exciting new study examines metazoan mRNA export from a global perspective through the use of a genome-wide RNA interference screen in Drosophila melanogaster. This screen identified several novel factors that contribute to mRNA export while reaffirming the strong evolutionary conservation that exists between Drosophila and yeast homologs that are essential for mRNA export. The study also showed that several factors were specifically required for the export of an intron-containing transcript but not for one lacking an intron. Taken together, this study underscores the value of genomic approaches for understanding complex biological processes.

Role of actin cytoskeletal dynamics in activation of the cyclic AMP pathway and HWP1 gene expression in Candida albicans.

Changes in gene expression during reversible bud-hypha transitions of the opportunistic fungal pathogen Candida albicans permit adaptation to environmental conditions that are critical for proliferation in host tissues. Our previous work has shown that the hypha-specific adhesin gene HWP1 is up-regulated by the cyclic AMP (cAMP) signaling pathway. However, little is known about the potential influences of determinants of cell morphology on HWP1 gene expression. We found that blocking hypha formation with cytochalasin A, which destabilizes actin filaments, and with latrunculin A, which sequesters actin monomers, led to a loss of HWP1 gene expression. In contrast, high levels of HWP1 gene expression were observed when the F-actin stabilizer jasplakinolide was used to block hypha formation, suggesting that HWP1 expression could be regulated by actin structures. Mutants defective in formin-mediated nucleation of F-actin were reduced in HWP1 gene expression, providing genetic support for the importance of actin structures. Kinetic experiments with wild-type and actin-deficient cells revealed two distinct phases of HWP1 gene expression, with a slow, actin-independent phase preceding a fast, actin-dependent phase. Low levels of HWP1 gene expression that appeared to be independent of stabilized actin and cAMP signaling were detected using indirect immunofluorescence. A connection between actin structures and the cAMP signaling pathway was shown using hyper- and hypomorphic cAMP mutants, providing a possible mechanism for up-regulation of HWP1 gene expression by stabilized actin. The results reveal a new role for F-actin as a regulatory agent of hypha-specific gene expression at the bud-hypha transition.