Next Generation Sequencing (NGS) has become an important tool in the biological sciences and has a growing number of applications across medical fields. Currently, few undergraduate programs provide training in the design and implementation of NGS applications. Here, we describe an inquiry‐based laboratory exercise for a college‐level molecular biology laboratory course that uses real‐time MinION deep sequencing and bioinformatics to investigate characteristic genetic variants found in cancer cell‐lines. The overall goal for students was to identify non‐small cell lung cancer (NSCLC) cell‐lines based on their unique genomic profiles. The units described in this laboratory highlight core principles in multiplex PCR primer design, real‐time deep sequencing, and bioinformatics analysis for genetic variants. We found that the MinION device is an appropriate, feasible tool that provides a comprehensive, hands‐on NGS experience for undergraduates. Student evaluations demonstrated increased confidence in using molecular techniques and enhanced understanding of NGS concepts. Overall, this exercise provides a pedagogical tool for incorporating NGS approaches in the teaching laboratory as way of enhancing students' comprehension of genomic sequence analysis. Further, this NGS lab module can easily be added to a variety of lab‐based courses to help undergraduate students learn current DNA sequencing methods with limited effort and cost.
Physiologists turned Geneticists: Identifying transcripts and genes for neuronal function in the Marbled Crayfish, Procambarus virginalis
The number of undergraduate researchers interested in pursuing neurophysiological research exceeds the research laboratory positions and hands-on course experiences available because these types of experiments often require extensive experience or expensive equipment. In contrast, genetic and molecular tools can more easily incorporate undergraduates with less time or training. With the explosion of newly sequenced genomes and transcriptomes, there is a large pool of untapped molecular and genetic information which would greatly inform neurophysiological processes. Classically trained neurophysiologists often struggle to make use of newly available genetic information for themselves and their trainees, despite the clear advantage of combining genetic and physiological techniques. This is particularly prevalent among researchers working with organisms that historically had no or only few genetic tools available. Combining these two fields will expose undergraduates to a greater variety of research approaches, concepts, and hands-on experiences. The goal of this manuscript is to provide an easily understandable and reproducible workflow that can be applied in both lab and classroom settings to identify genes involved in neuronal function. We outline clear learning objectives that can be acquired by following our workflow and assessed by peer-evaluation. Using our workflow, we identify and validate the sequence of two new Gamma Aminobutyric Acid A (GABAA) receptor subunit homologs in the recently published genome and transcriptome of the marbled crayfish, Procambarus virginalis. Altogether, this allows undergraduate students to apply their knowledge of the processes of gene expression to functional neuronal outcomes. It also provides them with opportunities to contribute significantly to physiological research, thereby exposing them to interdisciplinary approaches.
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- Award ID(s):
- 1755098
- NSF-PAR ID:
- 10278978
- Date Published:
- Journal Name:
- Journal of undergraduate neuroscience education
- Volume:
- 19
- Issue:
- 1
- ISSN:
- 1544-2896
- Page Range / eLocation ID:
- A36-A51
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract -
In this proposal, we will share some initial findings about how teacher and student engagement in cogenerative dialogues influenced the development of the Culturally Relevant Pedagogical Guidelines for Computational Thinking and Computer Science (CRPG-CSCT). The CRPG-CSCT’s purpose is to provide computer science teachers with tools to enhance their instruction by accurately reflecting students’ diverse cultural resources in the classroom. Additionally, the CRPG-CSCT will provide guidance to non-computer science teachers on how to facilitate the integration of computational thinking skills to a broad spectrum of classes in the arts, humanities, sciences, social sciences, and mathematics. Our initial findings shared here are part of a larger NSF-funded research project (Award No. 2122367) which aims to better understand the barriers to entry and challenges for success faced by underrepresented secondary school students in computer science, through direct engagement with the students themselves. Throughout the 2022-23 academic year, the researchers have been working with a small team of secondary school teachers, students, and instructional designers, as well as university faculty in computer science, secondary education, and sociology to develop the CRPG-CSCT. The CRPG-CSCT is rooted in the tenets of culturally relevant pedagogy (Ladson-Billings, 1995) and borrows from Muhammad’s (2020) work in Cultivating Genius: An Equity Framework for Culturally and Historically Responsive Literacy. The CRPG-CCT is being developed over six day-long workshops held throughout the academic year. At the time of this submission, five of the six workshops had been completed. Each workshop utilized cogenerative dialogues (cogens) as the primary tool for organizing and sustaining participants’ engagement. Through cogens, participants more deeply learn about students’ cultural capital and the value of utilizing that capital within the classroom (Roth, Lawless, & Tobin, 2000). The success of cogens relies on following specific protocols (Emdin, 2016), such as listening attentively, ensuring there are equal opportunities for all participants to share, and affirming the experiences of other participants. The goal of a cogen is to reach a collective decision, based on the dialogue, that will positively impact students by explicitly addressing barriers to their engagement in the classroom. During each workshop, one member of the research team and one undergraduate research assistant observed the interactions among cogen participants and documented these in the form of ethnographic field notes. Another undergraduate research assistant took detailed notes during the workshop to record the content of small and large group discussions, presentations, and questions/responses throughout the workshops. A grounded theory approach was used to analyze the field notes. Additionally, at the conclusion of each workshop, participants completed a Cogen Feedback Survey (CFS) to gather additional information. The CFS were analyzed through open thematic coding, memos, and code frequencies. Our preliminary results demonstrate high levels of engagement from teacher and student participants during the workshops. Students identified that the cogen structure allowed them to participate comfortably, openly, and honestly. Further, students described feeling valued and heard. Students’ ideas and experiences were frequently affirmed, which served as an important step toward dismantling traditional teacher-student boundaries that might otherwise prevent them from sharing freely. Another result from the use of cogens was the shared experience of participants comprehending views from the other group’s perspective in the classroom. Students appreciated the opportunity to learn from teachers about their struggles in keeping students engaged. Teachers appreciated the opportunity to better understand students’ schooling experiences and how these may affirm or deny aspects of their identity. Finally, all participants shared meaningful suggestions and strategies for future workshops and for the collective betterment of the group. Initial findings shared here are important for several reasons. First, our findings suggest that cogens are an effective approach for fostering participants’ commitment to creating the conditions for students’ success in the classroom. Within the context of the workshops, cogens provided teachers, students, and faculty with opportunities to engage in authentic conversations for addressing the recruitment and retention problems in computer science for underrepresented students. These conversations often resulted in the development of tangible pedagogical approaches, examples, metaphors, and other strategies to directly address the recruitment and retention of underrepresented students in computer science. Finally, while we are still developing the CRPG-CSCT, cogens provided us with the opportunity to ensure the voices of teachers and students are well represented in and central to the document.more » « less
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ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.
IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.
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In this Great Ideas for Teaching Students (GIFTS) paper, we offer learning outcomes that we are beginning to recognize from our eight-week research experience for undergraduates (REU). There are four characteristics that have been found to be essential to success in Science, Technology, Engineering, and Mathematics (STEM) fields: a strong sense of STEM identity, scientific self-efficacy, a sense of belonging, and a psychological sense of community. This is especially true for first-year and transfer students pursuing STEM undergraduate degrees. A variety of studies have been published that go into detail about why these characteristics in particular have such a significant effect on student performance and retention. This paper will present Critical Self-Reflection as a practical way to integrate development of these characteristics into student research experiences to foster experiential learning that goes beyond increasing technical skills. STEM students are not often trained to critically self-reflect on their experiences in classroom and research settings. An inability for undergraduates to reflect intentionally on their experiences creates greater risk for attrition from STEM disciplines. Curated reflective experiences in collaborative learning settings can offer professional development opportunities to enhance students’ social and technical communication skills. There are four phases within the scaffolded Critical Self-Reflection framework: Learning to Reflect, Reflection for Action, Reflection in Action, and Reflection on Action. When applying the evidence-based practice, STEM undergraduate researchers describe their perceptions via three activities: creating a legacy statement, participating in facilitated dialogue sessions, and writing curated reflection journal entries within an REU. Through critical self-reflection exercises, we are beginning to find growth of first-year and transfer STEM undergraduates in the following areas: understanding of their role in the lab; confidence in their researcher identity; expression of agency; observation and communication skills; and intentionality for action. Participating in this self-reflection allows students to make meaning of their experience enabling them to hone the aforementioned characteristics that creates a pathway from their undergraduate experience to undergraduate degree completion, graduate degree attainment, and to the STEM workforce.more » « less
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Accepted Manuscript1.0
- Journal Article:
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