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The preparation of future scientists, the technical workforce, and informed citizens will require continued transformation to the ways we approach STEM teaching and learning. Undergraduate STEM education is rapidly emerging as a focus of faculty scholarship, but new models for reform need to be developed and tested to accelerate changes in teaching practices. This paper describes a flexible, participant-driven, multi-phase, collaborative approach to developing open educational resources (OERs) that leverages linked communities of practice (CoPs). Equally valuable, our framework for development, adaptation, dissemination, and validation of OERs provides a platform for faculty professional development and sustained support through cooperative mentoring. The three linked CoPs in the framework include incubators for the creation of initial OERs, Faculty Mentoring Networks (FMNs) for the implementation and adaptation of OERs for classroom use, and Education Research Communities to assess the effectiveness of the OERs. The CoPs create numerous benefits for participating faculty, including the ability to collaborate in the Scholarship of Teaching and Learning (SoTL) through scholarly publication of OERs and their assessment; ongoing mentorship in implementation of OERs in the classroom; and development of educational leadership skills and experience. Thus, the three CoPs synergize with one another to build and sustain capacity through providing vetted, up-to-date educational resources, as well as ongoing training and support for faculty. While we developed this approach for the rapidly changing field of bioinformatics, the linked CoP framework will have utility for STEM education reform more broadly and disciplines beyond STEM.

The COVID-19 pandemic has led to an urgent need for engaging computational alternatives to traditional laboratory exercises. Here we introduce a customizable and flexible workflow, designed with the SARS CoV-2 virus that causes COVID-19 in mind, as a means of reinforcing fundamental biology concepts using bioinformatics approaches. This workflow is accessible to a wide range of students in life science majors regardless of their prior bioinformatics knowledge, and all software is freely available, thus eliminating potential cost barriers. Using the workflow can thus provide a diverse group of students the opportunity to conduct inquiry-driven research. Here we demonstrate the utility of this workflow and outline the logical steps involved in the identification of therapeutic or vaccine targets against SARS CoV-2. We also provide an example of how the workflow may be adapted to other infectious microbes. Overall, our workflow anchors student understanding of viral biology and genomics and allows students to develop valuable bioinformatics expertise as well as to hone critical thinking and problem-solving skills, while also creating an opportunity to better understand emerging information surrounding the COVID-19 pandemic.

While it is essential for life science students to be trained in modern techniques and approaches, rapidly developing, interdisciplinary fields such as bioinformatics present distinct challenges to undergraduate educators. In particular, many educators lack training in new fields, and high-quality teaching and learning materials may be sparse. To address this challenge with respect to bioinformatics, the Network for the Integration of Bioinformatics into Life Science Education (NIBLSE), in partnership with Quantitative Undergraduate Biology Education and Synthesis (QUBES), developed incubators, a novel collaborative process for the development of open educational resources (OER). Incubators are short-term, online communities that refine unpublished teaching lessons into more polished and widely usable learning resources. The resulting products are published and made freely available in the NIBLSE Resource Collection, providing recognition of scholarly work by incubator participants. In addition to producing accessible, high-quality resources, incubators also provide opportunities for faculty development. Because participants are intentionally chosen to represent a range of expertise in bioinformatics and pedagogy, incubators also build professional connections among educators with diverse backgrounds and perspectives and promote the discussion of practical issues involved in deploying a resource in the classroom. Here we describe the incubator process and provide examples of beneficial outcomes. Our experience indicates that incubators are a low cost, short-term, flexible method for the development of OERs and professional community that could be adapted to a variety of disciplinary and pedagogical contexts.

As high-throughput methods become more common, training undergraduates to analyze data must include having them generate informative summaries of large datasets. This flexible case study provides an opportunity for undergraduate students to become familiar with the capabilities of R programming in the context of high-throughput evolutionary data collected using macroarrays. The story line introduces a recent graduate hired at a biotech firm and tasked with analysis and visualization of changes in gene expression from 20,000 generations of the Lenski Lab's Long-Term Evolution Experiment (LTEE). Our main character is not familiar with R and is guided by a coworker to learn about this platform. Initially this involves a step-by-step analysis of the small Iris dataset built into R which includes sepal and petal length of three species of irises. Practice calculating summary statistics and correlations, and making histograms and scatter plots, prepares the protagonist to perform similar analyses with the LTEE dataset. In the LTEE module, students analyze gene expression data from the long-term evolutionary experiments, developing their skills in manipulating and interpreting large scientific datasets through visualizations and statistical analysis. Prerequisite knowledge is basic statistics, the Central Dogma, and basic evolutionary principles. The Iris module provides hands-on experience using R programming to explore and visualize a simple dataset; it can be used independently as an introduction to R for biological data or skipped if students already have some experience with R. Both modules emphasize understanding the utility of R, rather than creation of original code. Pilot testing showed the case study was well-received by students and faculty, who described it as a clear introduction to R and appreciated the value of R for visualizing and analyzing large datasets. [ABSTRACT FROM AUTHOR]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.07.019 Byline: Christopher T. Burket (a), Christina E. Higgins (a), Lynn C. Hull (a), Patricia M. Berninsone (b), Elizabeth F. Ryder (a) Keywords: Adhesion; Fasciculation; Neuron; Development; Immunoglobulin superfamily; Migration; Proteoglycan; Caenorhabditis elegans Abstract: The adhesion of growing neurites into appropriate bundles or fascicles is important for the development of correct synaptic connectivity in the nervous system. We describe fasciculation defects of animals with mutations in the C. elegans gene dig-1 and show that dig-1 encodes a giant molecule (13,100 amino acids) of the immunoglobulin superfamily. Five new alleles of dig-1 were isolated in a screen for mutations affecting the morphology or function of several classes of head sensory neurons. Mutants showed process defasciculation of several classes of neurons. Analysis of a temperature-sensitive allele revealed that dig-1 is required during embryogenesis for normal process fasciculation of one class of head sensory neuron. Partial sequencing of two alleles, RNA interference (RNAi) and rescuing experiments showed that dig-1 encodes a giant molecule of the immunoglobulin superfamily. DIG-1 protein contains many domains associated with adhesion, is likely secreted, and has some features of proteoglycans. dig-1 mutants were originally isolated due to their displaced gonads [Thomas, J.H., Stern, M.J., Horvitz, H.R., 1990. Cell interactions coordinate the development of the C. elegans egg-laying system. Cell 62, 1041-52]; thus, dig-1 alleles were also characterized for their effects on gonad placement. Mutant phenotypes suggest that DIG-1 may mediate cell movement as well as process fasciculation and that different regions of the protein may mediate these functions. Author Affiliation: (a) Worcester Polytechnic Institute, Department of Biology and Biotechnology, 100 Institute Road, Worcester, MA 01609, USA (b) Boston University Goldman School of Dental Medicine, Department of Molecular and Cell Biology, Boston Medical Center, 715 Albany Street Evans-437, Boston, MA 02118, USA Article History: Received 13 March 2006; Revised 17 July 2006; Accepted 18 July 2006

Clonal analysis after infecting retinal progenitor cells with retroviral vectors that code for beta galactosidase, human placental alkaline phosphatase or a viral core protein from 2.5 to 7.0 embryonic days helps study the growth of chicken retina. Several cell types are present in the clones, indicating the multipotency of the growing retinal progenitor cells. Closely formed cell arrays and scattered independent cells constitute the clones arising from early infections. Peripheral retina exhibits greater tangential dispersion and clonal complexity, which reduce with the duration of the infection.

C. Walsh and C. L. Cepko (1) recently reported that clonally related neurons are found in widely dispersed areas of rat cerebral cortex. They used a 'cocktail' of 100 identifiable [...]