The Professional Identity of STEM Faculty as Instructors of Course-based Research Experiences.

The professional identity of scientists has historically been cultivated to value research over teaching, which can undermine initiatives that aim to reform science education. Course-Based Research Experiences (CRE) and the inclusive Research and Education Communities (iREC) are two successful and impactful reform efforts that integrate research and teaching. The aim of this study is to explicate the professional identity of instructors who implement a CRE within an established iREC and to explore how this identity contributes to the success of these programs.

Drug-Induced Differential Gene Expression Analysis on Nanoliter Droplet Microarrays: Enabling Tool for Functional Precision Oncology.

Drug-induced differential gene expression analysis (DGEA) is essential for uncovering the molecular basis of cell phenotypic changes and understanding individual tumor responses to anticancer drugs. Performing high throughput DGEA is challenging due to the high cost and labor-intensive multi-step sample preparation protocols. In particular, performing drug-induced DGEA on cancer cells derived from patient biopsies is even more challenging due to the scarcity of available cells.

Farnesol remodels the peritoneal cavity immune environment influencing pathogenesis during intra-abdominal infection.

c is a lifelong member of the mycobiome causing mucosal candidiasis and life-threatening, systemic, and intra-abdominal disease in immunocompromised and transplant patients. Despite the clinical importance of intra-abdominal candidiasis with mortality rates between 40% and 70%, the contribution of fungal virulence factors and host immune responses to disease has not been extensively studied. Secretion of the quorum-sensing molecule, farnesol, acts as a virulence factor for during systemic infection, while inducing local, protective innate immune responses in oral models of infection.

Spelling monosyllabic English words.

We conducted a megastudy to examine the spelling of American English monosyllables with typewritten responses. We related both sublexical and lexical/semantic factors to spelling accuracy and reaction time (RT) for the first keypress and response duration for spelling 1,856 monophonic monosyllables. We found that (a) each of 13 predictor variables was significantly related to performance for at least one measure, (b) orthographic length was unrelated to the first key RT, but did relate to accuracy and response duration, (c) sound-spelling and spelling-sound consistency was related to performance, and in particular, onset consistency related to accuracy and first key RT, but was unrelated to response duration, (d) contextual diversity was consistently related to performance across all measures, and (e) age of acquisition (AoA) was related to all measures, but was related more to the first key RT than response duration.

Models of Classroom Assessment for Course-Based Research Experiences.

Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessment - 1) Assessing Laboratory Work and Scientific Thinking; 2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; 3) Appraising Forms of Scientific Communication; and 4) Metacognition of Learning - along with a set of practices for each aim.

The PULSE Diversity Equity and Inclusion (DEI) Rubric: a Tool To Help Assess Departmental DEI Efforts.

In an attempt to redesign science, technology, engineering, and mathematics (STEM) departments to be more inclusive of all student populations, institutions of higher learning are reviewing their programs, policies, and the ways they engage students. The Partnership for Undergraduate Life Sciences Education (PULSE) has been working with STEM departments over the past 10 years to improve the student experience by incorporating evidence-based teaching practices and creating curricula with a deeper focus on conceptual understanding of scientific principles, competencies, and the process of science. PULSE created the PULSE rubrics, a set of five rubrics designed to assist life sciences departments in assessing their implementation of the recommendations of the American Association for the Advancement of Science Vision and Change report in the areas of curriculum, assessment, faculty practice and faculty support, infrastructure, and climate for change.

Genome Sequences of Gordonia Phages GrootJr and NovumRegina.

Two bacteriophages, GrootJr and NovumRegina, were discovered, sequenced, and annotated. These phages were isolated from distinct soil and water samples, respectively, on Gordonia terrae 3612. These phages belong to the CR2 subcluster and are similar in genome size and gene content.

Experience with Scientific Teaching in Face-to-Face Settings Promoted Usage of Evidence-Based Practices during Emergency Remote Teaching.

During the Spring of 2020, instructors across the nation scrambled to transition their face-to-face courses to remote/online modalities. Necessarily, teaching practices adapted. This study investigated how the usage of evidence-based practices as defined by scientific teaching (ST) was impacted during this rapid transition.

Minor Cannabinoids: Biosynthesis, Molecular Pharmacology and Potential Therapeutic Uses.

The medicinal use of can be traced back thousands of years to ancient China and Egypt. While marijuana has recently shown promise in managing chronic pain and nausea, scientific investigation of cannabis has been restricted due its classification as a schedule 1 controlled substance. A major breakthrough in understanding the pharmacology of cannabis came with the isolation and characterization of the phytocannabinoids -Δ-tetrahydrocannabinol (Δ-THC) and cannabidiol (CBD).

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace.

Planetary Health, Climate Change, and Lifestyle Medicine: Threats and Opportunities.

Global environmental degradation and climate change threaten the foundation of human health and well-being. In a confluence of crises, the accelerating pace of climate change and other environmental disruptions pose an additional, preventable danger to a global population that is both aging and carrying a growing burden of noncommunicable diseases (NCDs). Climate change and environmental disruption function as "threat multipliers," especially for those with NCDs, worsening the potential health impacts on those with suboptimal health.

Temporal rarity is a better predictor of local extinction risk than spatial rarity.

Spatial rarity is often used to predict extinction risk, but rarity can also occur temporally. Perhaps more relevant in the context of global change is whether a species is core to a community (persistent) or transient (intermittently present), with transient species often susceptible to human activities that reduce niche space. Using 5-12 yr of data on 1,447 plant species from 49 grasslands on five continents, we show that local abundance and species persistence under ambient conditions are both effective predictors of local extinction risk following experimental exclusion of grazers or addition of nutrients; persistence was a more powerful predictor than local abundance.

Digital imaging and vision analysis in science project improves the self-efficacy and skill of undergraduate students in computational work.

In many areas of science, the ability to use computers to process, analyze, and visualize large data sets has become essential. The mismatch between the ability to generate large data sets and the computing skill to analyze them is arguably the most striking within the life sciences. The Digital Image and Vision Applications in Science (DIVAS) project describes a scaffolded series of interventions implemented over the span of a year to build the coding and computing skill of undergraduate students majoring primarily in the natural sciences.

Teaching Metabolism in Upper-Division Undergraduate Biochemistry Courses using Online Computational Systems and Dynamical Models Improves Student Performance.

Understanding metabolic function requires knowledge of the dynamics, interdependence, and regulation of metabolic networks. However, multiple professional societies have recognized that most undergraduate biochemistry students acquire only a surface-level understanding of metabolism. We hypothesized that guiding students through interactive computer simulations of metabolic systems would increase their ability to recognize how individual interactions between components affect the behavior of a system under different conditions.

USP11 mediates repair of DNA-protein cross-links by deubiquitinating SPRTN metalloprotease.

DNA-protein cross-links (DPCs) are toxic DNA lesions that interfere with DNA metabolic processes such as replication, transcription, and recombination. USP11 deubiquitinase participates in DNA repair, but the role of USP11 in DPC repair is not known. SPRTN is a replication-coupled DNA-dependent metalloprotease that cleaves proteins cross-linked to DNA to promote DPC repair.

Increasing effects of chronic nutrient enrichment on plant diversity loss and ecosystem productivity over time.

Human activities are enriching many of Earth's ecosystems with biologically limiting mineral nutrients such as nitrogen (N) and phosphorus (P). In grasslands, this enrichment generally reduces plant diversity and increases productivity. The widely demonstrated positive effect of diversity on productivity suggests a potential negative feedback, whereby nutrient-induced declines in diversity reduce the initial gains in productivity arising from nutrient enrichment.

Benefits of a College STEM Faculty Development Initiative: Instructors Report Increased and Sustained Implementation of Research-Based Instructional Strategies.

The Summer Institutes on Scientific Teaching (SI) is a faculty development workshop in which science, technology, engineering, and mathematics (STEM) instructors, particularly from biology, are trained in the Scientific Teaching (ST) pedagogy. While participants have generally reported positive experiences, we aimed to assess how the SI affected participants' teaching practices. Building on a previously developed taxonomy of ST practices, we surveyed SI participants from the 2004-2014 SI classes regarding specific ST practices.

Sequencing and Annotation of Duggie and Hocus, Two Subcluster B1 Mycobacteriophages.

Two mycobacteriophage genomes were newly sequenced and annotated. Duggie and Hocus were discovered, enriched, and isolated from soil using mc155. The bacteriophages are lytic Siphoviridae and belong to the B1 subcluster.

Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships.

Ensuring undergraduate students become proficient in relating protein structure to biological function has important implications. With current two-dimensional (2D) methods of teaching, students frequently develop misconceptions, including that proteins contain a lot of empty space, that bond angles for different amino acids can rotate equally, and that product inhibition is equivalent to allostery. To help students translate 2D images to 3D molecules and assign biochemical meaning to physical structures, we designed three 3D learning modules consisting of interactive activities with 3D printed models for amino acids, proteins, and allosteric regulation with coordinating pre- and post-assessments.

Microbial processing of plant remains is co-limited by multiple nutrients in global grasslands.

Microbial processing of aggregate-unprotected organic matter inputs is key for soil fertility, long-term ecosystem carbon and nutrient sequestration and sustainable agriculture. We investigated the effects of adding multiple nutrients (nitrogen, phosphorus and potassium plus nine essential macro- and micro-nutrients) on decomposition and biochemical transformation of standard plant materials buried in 21 grasslands from four continents. Addition of multiple nutrients weakly but consistently increased decomposition and biochemical transformation of plant remains during the peak-season, concurrent with changes in microbial exoenzymatic activity.

Facilitating an International Research Experience Focused on Applied Nanotechnology and Surface Chemistry for American Undergraduate Students Collaborating with Mentors at a German Educational and Research Institution.

The "International Research Experience for Students (IRES)" at Doane University (DU) located in Crete, Nebraska, exposed undergraduate science, technology, engineering, and mathematics (STEM) students to international research at the Karlsruhe Institute of Technology (KIT) in Germany. The international collaboration team included three undergraduate researchers per year from DU, one faculty member and one postdoctoral fellow from DU, two faculty mentors at KIT, and several graduate, post-doctoral, and technical staff at KIT. Prior to departure to Germany, the students received extensive research training, as well as culture and language preparation from the mentors at DU.

Automated image analysis with ImageJ of yeast colony forming units from cannabis flowers.

Currently, in the state of Colorado and all other states within the United States of America with legalized marijuana programs, testing is required for bacteria, yeast, and mold on marijuana products. The Code of Colorado Regulations, 1 CCR 212-1, considers a passing result when a 1 g sample contains <10 colony forming units (CFU) for the total yeast and mold count (TYMC). These measurements are usually obtained by manually counting colonies on petri-dishes or 3 M™ Petrifilms™, which is a time consuming and user subjective process.

Genome Sequences of Three Cluster C Mycobacteriophages, Bipolarisk, Bread, and FudgeTart.

Three mycobacteriophages, Bipolarisk, Bread, and FudgeTart, were isolated from enriched soil samples found in Crete, NE. All three phages are lytic, belong to subcluster C1, and infect mc155. The structures of the three genomes are similar, with slight variations in gene number and content.

A qualitative analysis to identify the elements that support department level change in the life sciences: The PULSE Vision & Change Recognition Program.

The 2011 report, Vision and Change in Undergraduate Biology Education: A Call to Action, provided the impetus to mobilize the undergraduate life sciences education community to affect change in order to enhance the educational experiences of life sciences majors. The work of the appointed Partnership for Undergraduate Life Sciences Education (PULSE) Vision and Change (V&C) Leadership Fellows has focused on the development of programs and resources to support departmental change. In this report, we present a qualitative assessment of several documents generated from the PULSE V&C Leadership Fellow Recognition Team.