Welcome to CourseSource, an open-access journal of peer-reviewed teaching resources for undergraduate biology and physics

We publish articles that are organized around courses in both biological and physics disciplines, and aligned with learning goals established by professional societies representing those disciplines. Please let us know what you think as you explore the articles and other information in the journal. We welcome your comments, questions, and/or suggestions. You can also follow us @CourseSource on Twitter to receive notifications about newly published articles and announcements!

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Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson

Leigh Ann Samsa*, Melissa Eslinger, Adam Kleinschmit, Amanda Solem, Carlos C. Goller*

Version: 1.0

Published on 09.2021

There is a growing need for integration of “Big Data” into undergraduate biology curricula. Transcriptomics is one venue to examine biology from an informatics perspective. RNA sequencing has largely replaced the use of microarrays for whole genome gene expression studies. Recently, single cell RNA sequencing (scRNAseq) has unmasked population heterogeneity, offering unprecedented views into the inner workings of individual cells. scRNAseq is transforming our understanding of development, cellular identity, cell function, and disease. As a ‘Big Data,’ scRNAseq can be intimidating for students to conceptualize and analyze, yet it plays an increasingly important role in modern biology. To address these challenges, we created an engaging case study that guides students through an exploration of scRNAseq technologies. Students work in groups to explore external resources, manipulate authentic data and experience how single cell RNA transcriptomics can be used for personalized cancer treatment. This five-part case study is intended for upper-level life science majors and graduate students in genetics, bioinformatics, molecular biology, cell biology, biochemistry, biology, and medical genomics courses. The case modules can be completed sequentially, or individual parts can be separately adapted. The first module can also be used as a stand-alone exercise in an introductory biology course. Students need an intermediate mastery of Microsoft Excel but do not need programming skills. Assessment includes both students’ self-assessment of their learning as answers to previous questions are used to progress through the case study and instructor assessment of final answers. This case provides a practical exercise in the use of high-throughput data analysis to explore the molecular basis of cancer at the level of single cells.

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bioinformatics, cancer, transcriptomics, high-throughput, Data wrangling, Single cell RNA sequencingq
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Design Your Own Flow Cytometry Experiment: A Four-Week Inquiry Laboratory

Joseph J. Dolence

Version: 1.0

Published on 09.2021

Due to its importance to the field, flow cytometry should be one of the hallmark methods a student learns in the lab portion of an undergraduate immunology course. Flow cytometry is a classic lab technique utilized within immunology and molecular biology research, as well as clinical laboratories to isolate cell populations from harvested tissue stained with a combination of antibodies to cell-specific markers. Despite its importance, instructions on how to complete lab exercises involving flow cytometry largely remain in primary literature articles without the level of detail necessary to teach the lab with ease, especially for those instructors without prior advanced flow cytometry knowledge. In this regard, this Lesson aims to provide clear, easy to follow instructions for how to successfully bring flow cytometry experiments to an undergraduate immunology, cell, or molecular biology teaching lab. In this Lesson, I describe a four-week lab module I teach in my upper-level undergraduate immunology course each fall. Students design and conduct their own experiment to address an immunological question of their choice using flow cytometry. Through this experience, they develop a greater understanding of the cellular makeup of the immune tissues they stain and analyze as the students work to answer a testable hypothesis and communicate their findings by writing a lab report and giving an oral presentation. Overall, this lab allows students to increase their knowledge of flow cytometry and what is necessary to conduct a realistic research experience to answer biological questions within immunology.

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Immunology, experimental design, Flow cytometry, Mice

CourseSource Blog - view more

Two postdoc positions in biology education research

September 1, 2021

We are excited to share the below advertisements for two biology education research postdoc positions.  These postdocs will join our research team to explore how Open Educational Resources (OERs) have helped the biology community enact Vision and Change principles.  

One postdoc will work at the University of Nebraska-Lincoln and one postdoc will work at Cornell University.  Applicants wishing to be considered for both positions should apply to both.  Applicants wishing to be considered for only one location should apply just to that position.  

More information and directions for application submission can be found below.  Applicants may wish to read news stories about the project from Nebraska, Cornell, and UMaine.  We welcome applicants from diverse backgrounds and look forward to bringing new ideas, perspectives, and expertise to our team.

Sincerely,

Michelle Smith, Cornell University

Brian Couch, University of Nebraska-Lincoln

Erin Vinson, University of Maine

 

News articles about the project:

https://news.unl.edu/newsrooms/today/article/nsf-funded-husker-led-project-to-evaluate-open-access-educational-resources/

https://news.cornell.edu/stories/2021/08/2m-grant-fund-assessment-biology-education

https://umaine.edu/news/blog/2021/08/13/researchers-assess-whether-open-educational-resources-improved-biology-instruction/

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Cornell University

College of Arts and Sciences

 

Postdoctoral Associate: Evaluating how open educational resources facilitate implementation of Vision and Change principles across diverse institutions

Applications are invited for a full time postdoctoral researcher in the Department of Ecology and Evolutionary Biology (EEB) at Cornell University. The successful candidate will advance undergraduate biology education by examining how Vision and Change (V&C) principles are being enacted in biology courses across a variety of undergraduate institutions. This project is part of a collaboration that includes Dr. Brian Couch (University of Nebraska-Lincoln) and Erin Vinson (University of Maine).

This project will focus on the use of open educational resources (OERs), which are educational materials that are available in the public domain. The research will involve conducting a scoping review of OER article content from a variety of journals (e.g., CourseSource), surveying authors and users to determine their engagement with OERs, developing student assessments, and observing instructors teaching with OERs in a variety of classrooms. The primary duties and responsibilities include leading the scoping review, developing and deploying surveys, designing protocols to observe instructors teaching with OERs, and analyzing student and instructor data. There will be opportunities to engage with instructors in professional development activities. The successful candidate will disseminate the results through publications and presentations at meetings.

Discipline-based education research is an important area of study at Cornell, with collaborators (faculty, postdocs, and graduate and undergraduate students) in physics, biology, and other STEM fields. The successful candidate will have an opportunity to mentor and work with many individuals and participate in weekly education journal clubs and research meetings with the larger EEB and Cornell community.

Qualifications:

The Postdoctoral Associate will be appointed for a one-year period with the possibility of extension for additional years based on satisfactory performance.

To apply: Applicants should submit their cover letter, CV, a 1-2 page research statement including relevant background and experiences, and a diversity statement, as well as the names and email or phone contacts of three professional references to:  https://academicjobsonline.org/ajo/jobs/19170.

Review of applications will begin on October 1, 2021.

Please contact Dr. Smith (mks274@cornell.edu) with any questions.

Diversity and Inclusion are a part of Cornell University's heritage. We are a recognized employer and educator valuing AA/EEO, Protected Veterans, and Individuals with Disabilities. We also recognize a lawful preference in employment practices for Native Americans living on or near Indian reservations.

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University of Nebraska-Lincoln

School of Biological Sciences

 

Postdoctoral Associate: Evaluating how open educational resources facilitate implementation of Vision and Change principles across diverse institutions

Applications are invited for a full time postdoctoral researcher in the School of Biological Sciences at the University of Nebraska-Lincoln (UNL). The successful candidate will advance undergraduate biology education by examining how Vision and Change (V&C) principles are being enacted in biology courses across a variety of undergraduate institutions. This project is part of a collaboration that includes Dr. Michelle Smith (Cornell University) and Erin Vinson (University of Maine).

This project will focus on the use of open educational resources (OERs), which are educational materials that are available in the public domain. The research will involve conducting a scoping review of OER article content from a variety of journals (e.g., CourseSource), surveying authors and users to determine their engagement with OERs, developing student assessments, and observing instructors teaching with OERs in a variety of classrooms. The primary duties and responsibilities include developing and deploying surveys, optimizing assessment instruments, contributing to the scoping review, designing protocols to observe instructors teaching with OERs, and analyzing student and instructor data. There will be opportunities to engage with instructors in professional development activities. The successful candidate will disseminate the results through publications and presentations at meetings.

Discipline-based education research (DBER) is an important area of study at UNL, with collaborators (faculty, postdocs, and graduate and undergraduate students) across STEM disciplines. The successful candidate will have an opportunity to mentor and work with many individuals and participate in weekly education journal clubs and research meetings with the larger DBER community.

Qualifications:

The Postdoctoral Associate will be appointed for a one-year period with the possibility of extension for additional years based on satisfactory performance.

To apply: Applicants should submit their cover letter, CV, a 1-2 page research statement including relevant background and experiences, and a diversity statement, as well as the names and email or phone contacts of three professional references to Dr. Brian Couch (bcouch2@unl.edu).

Review of applications will begin on October 1, 2021.

Please contact Dr. Couch with any questions.

The University of Nebraska-Lincoln (UNL) seeks to achieve a working and learning environment that is open to all people. Diversity is the hallmark of great institutions of learning and has long been one of the strengths of our society. Dignity and respect for all in the UNL community is the responsibility of each individual member of the community. The realization of that responsibility across the campus is critical to UNL's success. For UNL's non-discrimination information, see http://www.unl.edu/equity/notice-nondiscrimination.

As an EO/AA employer, qualified applicants are considered for employment without regard to race, color, ethnicity, national origin, sex, pregnancy, sexual orientation, gender identity, religion, disability, age, genetic information, veteran status, marital status, and/or political affiliation. See http://www.unl.edu/equity/notice-nondiscrimination.

July 2021 Online Writing Studio a Success!
July 2021 Online Writing Studio a Success!

July 22, 2021

The next Online CourseSource Writing Studio will take place in August focused on writing lessons for online classes. This coming fall, we will host semester-long Faculty Mentoring Networks focused on writing lesson articles (in collaboration with QUBES). Applications for Fall 2021 FMN participants will be open soon. If you are interested in applying, keep an eye out for announcements on the website (https://www.coursesource.org/), on Twitter (https://twitter.com/CourseSource), through the Society for the Advancement of Biology Education Research (SABER) listserv, and other biology professional society listservs.