scholarly journals A functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experience

2021 ◽  
Vol 11 (1) ◽  
pp. 1-23
Author(s):  
Cory J Evans ◽  
John M Olson ◽  
Bama Charan Mondal ◽  
Pratyush Kandimalla ◽  
Ariano Abbasi ◽  
...  
Keyword(s):  
Blood Cell ◽  
Functional Genomics ◽  
Undergraduate Students ◽  
Undergraduate Research ◽  
Cell Types ◽  
Bioinformatic Analysis ◽  
Research Experience ◽  
Loss Of Function ◽  
Fluorescent Reporter ◽  
Stem Retention

Abstract Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.

scholarly journals Fermentation revival in the classroom: investigating ancient human practices as CUREs for modern diseases

2020 ◽  
Vol 367 (21) ◽  
Author(s):  
Jennifer K Lyles ◽  
Monika Oli
Keyword(s):  
Undergraduate Research ◽  
Bioinformatic Analysis ◽  
Research Experience ◽  
Group Presentation ◽  
Student Knowledge ◽  
Laboratory Equipment ◽  
Lecture Material ◽  
Hands On ◽  
Human Practices ◽  
Survey Responses

ABSTRACT A course-based undergraduate research experience (CURE) was designed to integrate key microbiological principles and techniques into an authentic research experience in a classroom setting and was implemented in an undergraduate microbiology laboratory course. Students conducted a 6-week study in order to determine the identity and quantity of unique probiotic species from various types of kefir. This course module followed an inquiry-based pedagogical approach in which students use the scientific process to investigate an unknown question with no predetermined outcome. During each lab, relevant microbiological topics and laboratory concepts were presented. Students then performed various laboratory techniques, reinforcing the lecture material with hands-on experience. In addition, students participated in reflection through group presentation of their results, bioinformatic analysis and literature review. Based on data collected from pre- and post-study survey responses, both student knowledge and attitudes towards the topics covered improved due to participation in this CURE. Importantly, this CURE can be implemented at many levels of education, requiring only minimal resources and common laboratory equipment.

scholarly journals Early year undergraduate researchers’ reflections on the values and perceived costs of their research experience

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Gaye D. Ceyhan ◽  
John W. Tillotson
Keyword(s):  
Achievement Motivation ◽  
Undergraduate Students ◽  
Undergraduate Research ◽  
Intrinsic Value ◽  
Value Theory ◽  
Research Experience ◽  
Expectancy Value ◽  
Research Experiences ◽  
Research Findings ◽  
Future Work

Abstract Background Prior research reported that motivational beliefs that individuals attach to specific tasks predict continuing interest and persistence in the task. A motivational approach may be particularly useful for understanding undergraduate students’ engagement with research in their first and second years in college. The current study utilizes the expectancy-value theory of achievement motivation to qualitatively explore how much and in what ways early year undergraduate researchers value their research experience and what kinds of costs they associate with it. Results The results revealed that intrinsic value had the highest expression in participants’ motivation to engage in research. The second most expressed value type was the utility value of undergraduate research with regards to obtaining the desired outcomes, and attainment value played the least important role in participants’ motivation to engage in research. Findings also indicated that some of the participants associated a cost(s) to their research experience. The highest mentioned perceived cost was opportunity cost, where participants commented on losing other valued alternatives when engaging in research. Participants commented on the time, effort, or amount of work needed to engage in research, and a few participants commented on the emotional cost associated with their research experience in terms of the fear of failure. Conclusion As perceived cost is the least studied in the expectancy-value framework, this study contributes to cost values within college students, particularly about early year undergraduate researchers. The findings of this study can form the basis for future work on exploring ways to increase the values and decrease the costs students experience in their undergraduate research experiences.

Comparing Mentor and Mentee Perspectives in a Research-Based Undergraduate Mentoring Program

2012 ◽  
Author(s):  
Janet Y. Tsai ◽  
Daria Kotys-Schwartz ◽  
Beverly Louie ◽  
Virginia Ferguson ◽  
Alyssa Berg
Keyword(s):  
Graduate Students ◽  
Undergraduate Students ◽  
Undergraduate Research ◽  
Retention Rate ◽  
Mentoring Relationships ◽  
Mentoring Program ◽  
Research Experience ◽  
Engineering Research ◽  
Reflective Questions ◽  
Undergraduate Mentoring

At the University of Colorado Boulder (CU), a research-based undergraduate mentoring program is now in its second year of implementation. The program, Your Own Undergraduate Research Experience (YOU’RE@CU) has three main goals: improve the retention rate of diverse groups in undergraduate engineering, build undergraduate interest in engineering research, and prepare graduate students to take on leadership roles in either academia or industry-based research careers. In YOU’RE@CU, undergraduate students are paired with a graduate mentor and work in the graduate student’s lab several hours a week. Undergraduate mentees enroll in a one-credit seminar course focusing on research and graduate school opportunities, and are assessed via pre- and post-surveys to gauge their excitement and interest in engineering. The undergraduates also respond to biweekly qualitative reflective questions while participating in the program. Graduate mentors complete several reflective questions about their experiences and are required to complete pre- and post-assessments. Adopting a person-centered, case study approach, this paper focuses on two telling examples of research-based mentoring relationships in the YOU’RE@CU program. Given identical mentor training through YOU’RE@CU, two graduate students start the Spring 2012 semester by meeting with their mentees to launch a research project. By examining application, pre-survey, reflective questions, and post-survey responses from these four participants, the differences in the trajectory of the two paired mentoring relationships can be clearly seen over the course of one semester. This close examination of two disparate mentoring relationships is instructive in understanding the subtle details that create either a positive learning environment or an uncomfortable lab situation for young engineers, and assists program administrators in making improvements in subsequent years.

Undergraduate Research at a Liberal Arts College during a Time of Disruption

2020 ◽  
Vol 4 (1) ◽  
pp. 77-78
Author(s):  
Christopher Fuse ◽  
◽  
Ashley Cannaday ◽  
Whitney Coyle ◽  
◽  
...  
Keyword(s):  
Undergraduate Students ◽  
Liberal Arts ◽  
Undergraduate Research ◽  
Liberal Arts College ◽  
Computational Studies ◽  
Research Experience ◽  
Research Practices ◽  
New Techniques ◽  
Usual Research

Due to the COVID-19 pandemic, the authors, who have expertise in acoustics, optics, and astrophysics, decided to pivot from the experimental components of their research and focus instead on computational studies. Many of their usual research practices were adapted, creating new techniques to optimize the remote research experience for their undergraduate students.

scholarly journals MUREs - a new member of the URE-CURE family of research opportunities for undergrads

2021 ◽  
Author(s):  
Holly E. Bates ◽  
Shanna Lowes ◽  
Sarah L. West
Keyword(s):  
Undergraduate Students ◽  
Undergraduate Research ◽  
Small Scale ◽  
Research Experience ◽  
Research Experiences ◽  
Research Opportunities ◽  
Biology Students ◽  
Undergraduate Research Experiences ◽  
Stem Students ◽  
Experiential Research

Undergraduate research experiences are important for the development of scientific identity, appreciation of authentic research, and to improve persistence towards science careers. We identified a gap in experiential research opportunities for undergraduate Biology students who were seeking a formal yet small-scale research experience that was unique to their own interests and career aspirations. These opportunities may be especially worthwhile for STEM students aspiring to non-research scientific careers (i.e., medicine, dentistry, forensics, communication) and underrepresented STEM students. Here, we reflect on the use of small-scale, individualized undergraduate research experiences that are based on established methods (MURE). These experiences have helped to fill this gap and create problem-centred learning opportunities for undergraduate students that are as unique as the students themselves.

scholarly journals A Composite Textual Phenomenological Approach to CUREs versus Traditional Laboratory Experiences

2021 ◽  
Author(s):  
Amie Sommers ◽  
Dana Richter-Egger ◽  
Christine Cutucache
Keyword(s):  
Student Retention ◽  
Stem Education ◽  
Undergraduate Students ◽  
Time Management ◽  
Undergraduate Research ◽  
Phenomenological Approach ◽  
Research Experience ◽  
Research Questions ◽  
Effective Models ◽  
Laboratory Experiences

Here we present unique perspectives from undergraduate students (n=3) in STEM who have taken both a traditional laboratory iteration and a Course-based Undergraduate Research Experience (CURE) iteration of the same introductory chemistry course. CUREs can be effective models for integrating research in courses and fostering student learning gains. Via phenomenological interviews, we asked students to describe the differences in their perspectives, feelings, and experiences between a traditional lab guided by a lab manual and a CURE. We found that (i.) critical thinking/problem solving, (ii.) group work/collaboration, (iii.) student-led research questions and activities, and (iv.) time management are the top four emergent themes associated with the CURE course. Students also indicated that they learned more disciplinary content in the CURE, and, importantly, that they prefer it over the traditional lab. These findings add another dimension of success to CUREs in STEM education, particularly surrounding student retention.

scholarly journals Structures of three actinobacteriophage capsids: Roles of symmetry and accessory proteins

2020 ◽  
Author(s):  
Jennifer Podgorski ◽  
Joshua Calabrese ◽  
Lauren Alexandrescu ◽  
Deborah Jacobs-Sera ◽  
Welkin Pope ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Major Capsid Protein ◽  
Undergraduate Research ◽  
Multiple Drug Resistance ◽  
Structural Diversity ◽  
Bioinformatic Analysis ◽  
Multiple Drug ◽  
Accessory Proteins ◽  
Human Pathogens ◽  
Research Experience

AbstractMycobacterium tuberculosis and abscessus are major human pathogens that are part of the Actinobacteria phylum. Increasing multiple drug resistance in these bacteria has led to a renewed interest in using viruses that infect these bacteria for therapy. In order to understand these viruses, a course-based undergraduate research experience (CURE) program run by SEA-PHAGES at the University of Pittsburgh and HHMI has isolated, sequenced, and annotated over 3000 actinobacteriophages (viruses that infect Actinobacteria). Little work has been done to investigate the structural diversity of these phage, all of which are thought to use a common protein fold, the HK97-fold, in their major capsid protein. Here we describe the structure of three actinobacteriophage capsids isolated by students that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately 6 angstroms, which allowed confirmation that each phage uses the HK97-fold to form their capsid. One phage, Rosebush, has a novel variation of the HK97-fold. Four novel accessory proteins, that form the capsid head along with the major capsid protein, were identified that show limited or no homology to known proteins. The genes that encode the proteins were identified using SDS-PAGE and mass spectrometry. Bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.

scholarly journals A model for training undergraduate students in collaborative science

FACETS ◽  
2018 ◽  
Vol 3 (1) ◽  
pp. 818-829 ◽  
Author(s):  
Nora J. Casson ◽  
Colin J. Whitfield ◽  
Helen M. Baulch ◽  
Sheryl Mills ◽  
Rebecca L. North ◽  
...  
Keyword(s):  
Undergraduate Students ◽  
Graduate School ◽  
Early Stage ◽  
Undergraduate Research ◽  
Learning Objectives ◽  
Research Experience ◽  
Faculty Advisors ◽  
Scientific Disciplines ◽  
Wide Range ◽  
Collaborative Skills

Engagement of undergraduate students in research has been demonstrated to correlate with improved academic performance and retention. Research experience confers many benefits on participants, particularly foundational skills necessary for graduate school and careers in scientific disciplines. Undergraduate curricula often do not adequately develop collaborative skills that are becoming increasingly useful in many workplaces and research settings. Here, we describe a pilot program that engages undergraduates in research and incorporates learning objectives designed to develop and enhance collaborative techniques and skills in team science that are not typical outcomes of the undergraduate research experience. We conducted a collaborative science project that engaged faculty advisors and upper year undergraduates at four institutions and conducted a review to assess the program’s efficacy. Students developed a broad suite of competencies related to collaborative science, above and beyond the experience of completing individual projects. This model also affords distinct advantages to faculty advisors, including the capacity of the network to collect and synthesize data from different regions. The model for training students to conduct collaborative science at an early stage of their career is scalable and adaptable to a wide range of fields. We provide recommendations for refining and implementing this model in other contexts.

scholarly journals The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt Signaling

2020 ◽  
Vol 8 (1) ◽  
pp. 5
Author(s):  
Meagan Kurland ◽  
Bryn O’Meara ◽  
Dana K. Tucker ◽  
Brian D. Ackley
Keyword(s):  
Transcription Factors ◽  
Wnt Signaling ◽  
Ectopic Expression ◽  
Cell Types ◽  
Loss Of Function ◽  
Cell Specification ◽  
Fluorescent Reporter ◽  
Hox Gene ◽  
Amino Butyric Acid ◽  
Number Of Cells

Nervous systems are comprised of diverse cell types that differ functionally and morphologically. During development, extrinsic signals, e.g., growth factors, can activate intrinsic programs, usually orchestrated by networks of transcription factors. Within that network, transcription factors that drive the specification of features specific to a limited number of cells are often referred to as terminal selectors. While we still have an incomplete view of how individual neurons within organisms become specified, reporters limited to a subset of neurons in a nervous system can facilitate the discovery of cell specification programs. We have identified a fluorescent reporter that labels VD13, the most posterior of the 19 inhibitory GABA (γ-amino butyric acid)-ergic motorneurons, and two additional neurons, LUAL and LUAR. Loss of function in multiple Wnt signaling genes resulted in an incompletely penetrant loss of the marker, selectively in VD13, but not the LUAs, even though other aspects of GABAergic specification in VD13 were normal. The posterior Hox gene, egl-5, was necessary for expression of our marker in VD13, and ectopic expression of egl-5 in more anterior GABAergic neurons induced expression of the marker. These results suggest egl-5 is a terminal selector of VD13, subsequent to GABAergic specification.

scholarly journals A Comprehensive Faculty, Staff, and Student Training Program Enhances Student Perceptions of a Course-Based Research Experience at a Two-Year Institution

2014 ◽  
Vol 13 (4) ◽  
pp. 724-737 ◽  
Author(s):  
Thomas D. Wolkow ◽  
Lisa T. Durrenberger ◽  
Michael A. Maynard ◽  
Kylie K. Harrall ◽  
Lisa M. Hines
Keyword(s):  
Student Perceptions ◽  
Undergraduate Students ◽  
Staff Training ◽  
Undergraduate Research ◽  
Randomized Study ◽  
Geographic Region ◽  
Support Staff ◽  
Early Research ◽  
Research Experience ◽  
Research Experiences

Early research experiences must be made available to all undergraduate students, including those at 2-yr institutions who account for nearly half of America's college students. We report on barriers unique to 2-yr institutions that preclude the success of an early course-based undergraduate research experience (CURE). Using a randomized study design, we evaluated a CURE in equivalent introductory biology courses at a 4-yr institution and a 2-yr institution within the same geographic region. We found that these student populations developed dramatically different impressions of the experience. Students at the 4-yr institution enjoyed the CURE significantly more than the traditional labs. However, students at the 2-yr institution enjoyed the traditional labs significantly more, even though the CURE successfully produced targeted learning gains. On the basis of course evaluations, we enhanced instructor, student, and support staff training and reevaluated this CURE at a different campus of the same 2-yr institution. This time, the students reported that they enjoyed the research experience significantly more than the traditional labs. We conclude that early research experiences can succeed at 2-yr institutions, provided that a comprehensive implementation strategy targeting instructor, student, and support staff training is in place.

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