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The Pipeline CURE: An Iterative Approach to Introduce All Students to Research Throughout a Biology Curriculum

Participation in research provides personal and professional benefits for undergraduates. However, some students face institutional barriers that prevent their entry into research, particularly those from underrepresented groups who may stand to gain the most from research experiences. Course-based undergraduate research experiences (CUREs) effectively scale research availability, but many only last for a single semester, which is rarely enough time for a novice to develop proficiency. To address these challenges, we present the Pipeline CURE, a framework that integrates a single research question throughout a biology curriculum. Students are introduced to the research system - in this implementation, C. elegans epigenetics research - with their first course in the major. After revisiting the research system in several subsequent courses, students can choose to participate in an upper-level research experience. In the Pipeline, students build resilience via repeated exposure to the same research system. Its iterative, curriculum-embedded approach is flexible enough to be implemented at a range of institutions using a variety of research questions. By uniting evidence-based teaching methods with ongoing scientific research, the Pipeline CURE provides a new model for overcoming barriers to participation in undergraduate research.

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Katie M. Sandlin onto Bioinformatics

DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College.

Advances in high-throughput techniques have resulted in a rising demand for scientists with basic bioinformatics skills as well as workshops and curricula that teach students bioinformatics concepts. DNA Detective is a workshop we designed to introduce students to big data and bioinformatics using CyVerse and the Dolan DNA Learning Center's online DNA Subway platform. DNA Subway is a user-friendly workspace for genome analysis and uses the metaphor of a network of subway lines to familiarize users with the steps involved in annotating and comparing DNA sequences. For DNA Detective, we use the DNA Subway Red Line to guide students through analyzing a "mystery" DNA sequence to distinguish its gene structure and name. During the workshop, students are assigned a unique Arabidopsis thaliana DNA sequence. Students "travel" the Red Line to computationally find and remove sequence repeats, use gene prediction software to identify structural elements of the sequence, search databases of known genes to determine the identity of their mystery sequence, and synthesize these results into a model of their gene. Next, students use The Arabidopsis Information Resource (TAIR) to identify their gene's function so they can hypothesize what a mutant plant lacking that gene might look like (its phenotype). Then, from a group of plants in the room, students select the plant they think is most likely defective for their gene. Through this workshop, students are acquainted to the flow of genetic information from genotype to phenotype and tackle complex genomics analyses in hopes of inspiring and empowering them towards continued science education.

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Katie M. Sandlin onto Bioinformatics

A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21st century STEM workforce. Recent evidence however demonstrates that there are significant barriers to teaching these skills at the undergraduate level including lack of faculty training, lack of student interest in bioinformatics, lack of vetted teaching materials, and overly full curricula. To this end, the James Madison University, Center for Genome & Metagenome Studies (JMU CGEMS) and other PUI collaborators are devoted to developing and disseminating engaging bioinformatics teaching materials specifically designed for streamlined integration into general undergraduate biology curriculum. Here, we have developed and integrated a fun introductory level lesson to command line next generation sequencing (NGS) analysis into a large enrollment core biology course. This one-off activity takes a crucial but mundane aspect of NGS quality control (QC) analysis and incorporates the use of Emoji data outputs using the software FASTQE to pique student interest. This amusing command line analysis is subsequently paired with a more rigorous research-grade software package called FASTP in which students complete sequence QC and filtering using a few simple commands. Collectively, this short lesson provides novice-level faculty and students an engaging entry point to learning basic genomics command line programming skills as a gateway to more complex and elaborated applications of computational bioinformatics analyses.

Primary image: Undergraduate students learn the basics of command line NGS quality analysis using the FASTQE and FASTP programs.

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Katie M. Sandlin onto Bioinformatics

Using Bioinformatics and Molecular Visualization to Develop Student Hypotheses in a Malate Dehydrogenase Oriented CURE

Developing student creativity and ability to develop a testable hypothesis represents a significant challenge in most laboratory courses. This lesson demonstrates how students use facets of molecular evolution and bioinformatics approaches involving protein sequence alignments (Clustal Omega, Uniprot) and 3D structure visualization (Pymol, JMol, Chimera), along with an analysis of pertinent background literature, to construct a novel hypothesis and develop a research proposal to explore their hypothesis. We have used this approach in a variety of institutional contexts (community college, research intensive university and primarily undergraduate institutions, PUIs ) as the first component in a protein-centric course-embedded undergraduate research experience (CURE) sequence. Built around the enzyme malate dehydrogenase, the sequence illustrates a variety of foundational concepts from the learning framework for Biochemistry and Molecular Biology. The lesson has three specific learning goals: i) find, use and present relevant primary literature, protein sequences, structures, and analyses resulting from the use of bioinformatics tools, ii) understand the various roles that non-covalent interactions may play in the structure and function of an enzyme. and iii) create/develop a testable and falsifiable hypothesis and propose appropriate experiments to interrogate the hypothesis. For each learning goal, we have developed specific assessment rubrics. Depending on the needs of the course, this approach builds to an in-class student presentation and/or a written research proposal. The module can be extended over several lecture and lab periods. Furthermore, the module lends itself to additional assessments including oral presentation, research proposal writing and the validated pre-post Experimental Design Ability Test (EDAT). Although presented in the context of course-based research on malate dehydrogenase, the approach and materials presented are readily adaptable to any protein of interest.

Primary image: Mind map of the hypothesis development.

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Katie M. Sandlin onto Bioinformatics

Hands-On, Hands-Off: The Community College Genomics (ComGen) Course-Based Undergraduate Research Experience

Science is a process of discovery where failure is inherent and iteration is necessary, yet instructors often teach the scientific process as if it is a controlled, highly supervised, confirmatory practice of following directions to get a known answer. We believe this mismatch occurs because instructors often struggle to feel comfortable in facilitating open-ended inquiry and giving students the trust and autonomy to experience an authentic scientific process. In this quarter-long lab curriculum, we bring the scientific process into the classroom in the form of an authentic course-based undergraduate research experience (CURE). We present a pedagogy, which is hands-on for students and hands-off for instructors, that incorporates and celebrates the learning that occurs from failing safely and often. The research project presented in this article is a genomics-based CURE where students sequence and analyze DNA genome segments. Throughout the lesson, we present core instructional structures and techniques that are transferable to any project and help scaffold and support the learning impact of the CURE. In the following curriculum, we outline this pedagogy, applied to a model CURE focused on sequencing a bacterium, and suggest ways that both the pedagogy and the core components of our CURE (i.e., journal club, posters, lab notebook, and self-assessments) transfer to other courses, and other research projects.

Primary Image: Gita Bangera guiding Bellevue College students through the ComGen research process in a cellular biology course.

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Katie M. Sandlin onto Bioinformatics

Day 1 Slides (Includes Project Red Bus Logic Map)

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Patrick Freeland onto Sensing the Earth Summit

National Ecological Observatory Network (NEON) - Resources

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Katherine Jones onto Sensing the Earth Summit

Introduction to Carpentries Presentation

Presentation presented by Alycia Crall on 18 November.

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Alycia Crall onto Sensing the Earth Summit

Climate Literacy and Energy Awareness Network (CLEAN) Resources for Educators Presentation

See the slides which describe the CLEAN network, resources for educators, and more

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Patrick Freeland onto Sensing the Earth Summit

TCU NEON Map

See the map which situates TCUs in NEON Ecoregions and near sensors

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Patrick Freeland onto Sensing the Earth Summit

Notes from the Sensing The Earth June Meeting

See the notes from the Sensing The Earth Meeting

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Patrick Freeland onto Sensing the Earth Summit

Menu of Services

This file describes services and training opportunities for TCU Faculty

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Patrick Freeland onto Sensing the Earth Summit

Quad Chart Analysis

Folder that includes the Quad Chart Analysis from the June Sensing The Earth Summit

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Patrick Freeland onto Sensing the Earth Summit

Visualizing Global CO2 Emissions

CO2 emissions modeling exercise

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Anne Cross onto Ecology Class

Ecological Forecasting Initiative

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Katherine Jones onto Sensing the Earth Summit

Making bioinformatics tools classroom-friendly

Poster on using Cyverse resources to make classroom that make using bioinformatics in the classroom a more manageable experience presented at the 2020 BIOME Institute: Cultivating Scientific Curiosity

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Katie M. Sandlin onto Bioinformatics

Macrosystems EDDIE Links

Overview of Macrosystems EDDIE 

Web pages for Macrosystems EDDIE ecological forecasting teaching modules (which include links to the R Shiny app webpage for each module as well as other teaching materials): 

Module 5: Introduction to Ecological Forecasting 

Module 6: Understanding Uncertainty in Ecological Forecasts 

Module 7: Using Data to Improve Ecological Forecasts 

Module 8: Using Ecological Forecasts to Guide Decision Making 

 

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Katherine Jones onto Sensing the Earth Summit

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

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Katie M. Sandlin onto Bioinformatics

Running Carpentries Workshops Without Internet Access

Carpentries Offline is a project that aims to bring Carpentries workshops to areas where there is limited or no Internet access. In this video (4:21), we aim to show how we are addressing the challenge.

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Alycia Crall onto Sensing the Earth Summit

From Dirt to <em>Streptomyces</em> DNA

The purpose of this semester-long Lesson is to give students an authentic, course-based undergraduate research experience during which they learn basic and advanced microbiological and molecular biology techniques. This project begins with the isolation of a suspected Streptomyces bacterium from a soil sample and concludes with its identification. Students collect data, regarding colony and cell morphology, biochemical characteristics, the production of secondary metabolites, and employs the PCR using custom-designed primers to the Streptomyces 16s rRNA gene. The project culminates with the identification of their soil isolate using the National Center for Biotechnology Information (NCBI) web site to perform nucleotide blasts. The blastn program provides the final piece of evidence used to confirm, or not, the identification of their isolate as a Streptomyces from 16s rRNA gene sequence data, hence the title “From Dirt to Streptomyces DNA. In addition, the Lesson focuses on the Streptomyces bacteria to address several ASM aligned goals and objectives. These include prokaryotic growth phases and ways in which interactions of microorganisms among themselves and with their environment is determined by their metabolic abilities.  In addition, this Lesson illustrates how microbial metabolism is important to a relevant societal issue, the need for new antibiotic discovery particularly given the rise of antibiotic resistance strains of clinically relevant bacteria. It also illustrates the microbial diversity of soil and the developmental/physiological strategies employed in such a competitive environment. This Lesson hopes to impart both the thrill and challenges associated with scientific discovery.

Primary image: Photomicrograph of Streptomyces colonies growing on ISP 2 agar. The Streptomyces are student isolates showing stages of morphological development. Photomicrograph by Marc A. Brodkin.

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Aga Gałązka onto Microbiology

The Carpentries Toolkit of IDEAS

The Toolkit of IDEAS (Inclusion, Diversity, Equity and Accessibility Strategies) is a practical resource for Carpentries’ Instructors, helpers, and workshop hosts. We know that many people care about inclusion, diversity, equity and accessibility but are not sure how it connects to teaching foundational coding and data science skills. This toolkit aims to bridge this gap. 

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Alycia Crall onto Sensing the Earth Summit

Molecular CaseNet Biweekly meeting related (Nov. 11, 2022)

Case presentations

  • Aeisha Thomas (Streptokinase - Bacteria Sourced Drug For Cardiovascular Disease)
  • Swati Agrawal (A Case study of Drug Resistance in Leishmania)
  • Alexander Escobar (Running Out of Time)

We actually ran out of time. We will hear about more case outlines in the next meeting.

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Shuchismita Dutta onto Meeting Recordings

Life in Urban Environments: The Impact of Urbanization on Life-History Traits in Amphibian Species

This lesson focuses on urbanization and its negative effects on species, specifically amphibians. The lesson will also provide hands-on statistical analyses and critical thinking questions to promote a better understanding of this ecological problem.

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Katie Weglarz onto ForEBio

Coyote Habituation and a Scientist Spotlight on Dr. Christopher Schell

Dr. Christopher Schell is an ecologist who uses a variety of techniques to study mammalian carnivores in urban areas. This scientist spotlight uses graphs from his study on parental habituation to human disturbance in coyotes.

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Profile picture of Katie Weglarz

Katie Weglarz onto ForEBio