Progress 04/01/19 to 03/31/23
Outputs
Target Audience:The primary target audience are undergraduate students who participate the research and education experience. Specifically, we wish to recruit students with interests in the biological sciences with a focus on agriculture, genetics and plant science. We aim to recruit a diverse cohort of students representing different types of undergraduate institutions, as well as including members of groups underrepresented in the biological, agricultural, and plant sciences. An additional target audience are the faculty mentors associated with the students, who can continue projects developed during the summer research period. Changes/Problems:The only major change in the last year of the REEU was a return to an in-person experience. Students once again came to the College of Charleston for their research experience, including living as a cohort in the dormitories. What opportunities for training and professional development has the project provided?As described above, the program trained 6 undergraduate participants in the REEU. Students were trained in statistical analysis in the R statistical framework, in bioinformatics, in plant phenotyping, and in agricultural genomics and its applications. Students generally learned research techniques, and were taught scientific ethics and strategies for pursuing careers in the agricultural and life sciences. Further details of student experiences are described under accomplishments. In addition, the project manager, April Bisner, developed additional skills in project management and coordination of data management. How have the results been disseminated to communities of interest?We have utilized the unPAK network of educational institutions to recruit students from diverse backgrounds. unPAK institutions include research universities, primarily undergraduate institutions, community colleges, and historically-Black or Latino-serving institutions. Our REEU students have been drawn from all of these types of institutions. Participating students have included members of minority groups underrepresented in the agricultural sciences, as well as first-time college students. In addition to manuscripts published on the REEU experience in previous periods, a manuscript is in preparation for PeerJ that includes REEU associated research. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
We conducted a summer research experience during the summer of 2022. The College of Charleston had allowed a return to full in-person learning, and so we transitioned back from a remote online research experience to an in-person experience for the summer of 2022. To recruit students, we reached out to faculty from the other 18 unPAK network institutions to ask for nominations of students who showed promise in and interest in the plant sciences. Students were asked to submit CVs and nominating faculty submitted a letter of support. From the nominated students we identified 6 students to participate in the 2022 REEU. Our student group included two students from minority groups, three female students, one student from an historically black college, one student from a community college. All students were from primarily undergraduate institutions. The summer program ran from June 12, 2022 through July 16, 2022. The program began by introducing students to the basics of Arabidopsis thaliana biology, of plant phenotyping, and of working with large datasets. Students were introduced to statistical analysis techniques in the R statistical framework. The program began by introducing students to the basics of plant phenotyping. Before the program began, we had grown a series of Arabidopsis thaliana plant lines, each containing a single mutation at a gene known to affect leaf shape or structure. Our intent was to study the phenotypes of these lines to determine if the mutations affecting leaf shape or structure also affected attributes of growth, plant architecture or reproductive potential. The students phenotyped the plants for growth and life history characters during the first two weeks of the REEU. They worked on this project as a joint exercise. After completing data collection, we worked collectively to develop a plan for statistical analysis. As discussed below, students were introduced to statistical analysis techniques in the R statistical framework. During the remainder of the program, students conducted analyses on the data they collected at the beginning of the program. During the program, we conducted workshops on utilizing the R statistical framework, working with bioinformatic data, using the unPAK database to extract phenotypic data, methods for collecting phenotypic data, strategies for data management, ethical behavior in the sciences, laboratory safety protocols, and on strategies for finding and interpreting the primary literature in the sciences. Each student also worked on 1-2 individual projects during the REEU. Topics of individual projects included: testing for effects of genotype on temperature on plant responses to a root fungal endophyte, repurposing determining how to use retired PCR machines for temperature based germination assays, testing the consequences of adding microplastic fibers to agar in which plants were growing, evaluating the effect of trichome density and neighbor identity on responses to simulated herbivory, evaluating the effects on root length of exposure of plants to a root fungal endophyte at varying nutrient and salt levels. During the REEU the faculty and students also participated in a number of field trips and team building experiences. For example, we visited the USDA Vegetable Laboratory in Charleston to understand how genetic methods are applied to breeding broccoli and other crops. Two faculty members from other unPAK institutions gave seminars about biology and plant genetics. We had a career panel that included unPAK affiliates, including alums of the REEU program, and discussed a variety of career paths that involve plant biology. We also took a field trip to Stono Preserve, a 1000-acre nature preserve that is part of the College of Charleston, to discuss the history of land use and agriculture in the Lowcountry of South Carolina. The students all stayed together in one dormitory, thus building camaraderie among the cohort. The program was evaluated by an external evaluator (Dr. Danielle Jensen-Ryan) who surveyed students and faculty before and after participating in the REEU. Participants were asked about expectations before the program and reflected on these expectations after the conclusion of the program. Students reported the program exceeded their expectations.
Publications
|
Progress 04/01/21 to 03/31/22
Outputs
Target Audience:The primary target audience are undergraduate students who participate the research and education experience. Specifically, we recruit students with interests in the biological sciences with a focus on agriculture, genetics and plant science. We recruit a diverse cohort of students representing different types of undergraduate institutions, as well as including members of groups underrepresented in the biological, agricultural, and plant sciences. An additional target audience are the faculty mentors associated with the students, who can continue projects developed during the summer research period. In the reporting period, we reached out to our 18 partnerinstitutions in the unPAK program (undergraduates Phenotyping Arabidopsis Knockouts) which includes RI, PUI, HBCU, Hispanic-serving and community colleges. Changes/Problems:For the 2022REEU, we are returning to an in-person experience (as we had in 2019). Our institution is allowing more in-person activities, while maintaining some COVID-19 mitigation protocols. We plan to include the number of students we can have in the laboratory with safe social distancing protocols. What opportunities for training and professional development has the project provided?As described above, the program trained 11 undergraduate participants in the REEU. Students were trained in statistical analysis in the R statistical framework, in bioinformatics, in plant phenotyping, and in agricultural genomics and its applications. Students generally learned research techniques, and were taught scientific ethics and strategies for pursuing careers in the agricultural and life sciences. Further details of student experiences are described under accomplishments. In addition, the project manager, April Bisner, developed additional skills in team management, coordination of data management and production of video (YouTube) instructions to teach protocols associated with growing plants with the at-home phenotyping kits.. How have the results been disseminated to communities of interest?We have utilized the unPAK network of educational institutions to recruit students from diverse backgrounds. unPAK institutions include research universities, primarily undergraduate institutions, community colleges, and historically-Black or Latino-serving institutions. Our REEU students have been drawn from all of these types of institutions, and we continued to recruit from these institutions for the 2021online REEU and 2022 in-person REEU. Participating students have included members of minority groups underrepresented in the agricultural sciences, as well as first-time college students. In 2021 we published an article in the Journal of Microbiology and Biology Education describing our methodologies and evaluation outcomes from transitioning from an in-person REEU to an online REEU due to the COVID-19 pandemic, and an additional article was published describing research findingsin the journal Genetica and included a REEU undergraduate participant co-author. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will return to an in-person experience as our institution shifts its management of the COVID-19 pandemic. Students will again be recruited from participating unPAK institutions, and we will recruit a number of students that can safely social distance in the laboratory. We will return to an increased focus on growing and phenotyping plants, while maintaing some of our enhanced methods for communicating data science.In addition, we will complete an analysis of the evaluation from the summer 2021REEU to refine our practices during the 2022REEU.
Impacts
What was accomplished under these goals?
While the genomic era has been a revolution in crop science, there remains a critical gap in application of DNA sequence data to crop improvement. Furthermore, there is a lack of scientists trained to work with both genetic data and measurements of plant characteristics. unPAK (undergraduates Phenotyping Arabidopsis Knockouts) addresses this challenge through large scale phenotyping-- measuring plant characters--of single gene mutants in the model plant Arabidopsis thaliana. The REEU trained a cohort of undergraduate students from diverse backgroundsin data science, plant phenotyping, genomics, and computational biology-- helping to produce the next generation of researchers capable of using big data and genetics to understand plant biology and improve crop species. Objective I: Provide asummer research experience totrain students in conceptual knowledge, scientific process, research skills, and data sciencethrough acohort experimentfocusing on key concepts of genetically based plant vigor and yield,faculty-mentored student-directed inquiry projects,data analyses, andweekly activitiesexposing students the varied aspects of agricultural science will inspire the next generation in the diverse agricultural sector. Accomplishments: We conducted a summer research experience during the summer of 2021.The summer program ran just over 5 weeks from mid-June2021through mid-July 2021. For the 2021REEU, the COVID-19 pandemic prevented physical gathering at the College of Charleston campus. We requested, and were granted by USDA, a change in scope to allow an online research experience program.The entire program was conducted online. Details of training and activities are given in the corresponding objectives below. Objective II. Provide research experiencesgroups of 10 students for each of 4 summers Accomplishments: We trained 11 undergraduate students in the summer of 2021. Objective III: Recruit students from diverse backgrounds and institutions Accomplishments: To recruit students, we reached out to faculty from the other 18 unPAK network institutions to ask for nominations of students who showed promise in and interest in the plant sciences. Students were asked to submit CVs and nominating faculty submitted a letter of support. From the nominated students we identified 11 students to participate in the 2021REEU, the same number as in the 2020 REEU. Our student group included 3students from underrepresented minority groups, seven female students, seven students from primarily undergraduate institutions (including two students from Historically Black Colleges), and twostudents from community colleges. Objective IV. Complete a joint experiment for each cohort with an objective of a cohort publication Accomplishments: The program began by introducing students to data analysis in the R statistical framework and to working with genomic data. In the in-person cohort of 2019, we had grown a series of Arabidopsis thaliana plant lines, each containing a single mutation at a different position on chromosome 4. Our intent was to study the phenotypes of these lines to determine if the positon of the gene on the chromosome could be used to make predictions about the effects of mutation on phenotype. The 2019 students phenotyped the plants for growth and life history characters. While we began analyses in 2019, we opted to conduct more thorough analyses in 2021 as we could dedicate the entire program time to statistical analysis. We also developed a joint paper outline and began writing a manuscript as a group. In addition, as in 2020 we mailed kits to all students that included seeds and growing materials. Each student grew a collection of 12 natural accessions of Arabidopsis thaliana in their own homes, recorded phenotypic data on the germination rate, growth, and timing of reproduction in these plants. Environmental data were collected with a HOBO datalogger. At the end of the program, phenotypic data was analyzed as a second joint cohort exercise. Objective V. Conduct individual experiments with faculty mentors Accomplishments Each student also worked on 1-2 indvidual projects during the REEU. Topics of invidual projects included, describing patterns of variation in gene effect depending on epigenetic state, building a gene tree of the WRKY transcription factory gene family in Black Raspberry and Arabidopsis, assessing the degree to which growth environments influenced phenotypic diversity across a set of mutants. Objective VI. Train students in phenotyping, data visualization, statistical analysis, bioinformatic analysis, and molecular genetics. All training will be in a plant biology framework. Accomplishments: The above activities led to all participating students working for weeks in all of the topics above, with the exception of hands-on molecular genetics in the laboratory as a consequence of the shift to an online experience. However, we were able to provide a greader emphasis on data visualization, statistical analysis, and bioinformatic analysis. Objective VII. Maintain network cohesion through joint activities and continued communication after participation Accomplishments: During the REEU the faculty and students also participated in a number of additional joint activities. We attended seminars from plant biologists (such as on the history of broccoli breeding and the effects of light saturation on plant coloration). We held workshops on a number of topics: utliizing the R statistical framework, working with bioinformatic data, using the unPAK database to extract phenotypic data, methods for collecting phenotypic data, and strategies for data management. We had a career panel with researchers at a variety of career stages (graduate students, career agricultural scientists, tenured faculty). We have continued communication post-program by maintaining a Slack networking environment to facilitate continued discussion of manuscript writing and data analysis. The program was evaluated by an external evaluator (Dr. Danielle Jensen-Ryan) who surveyed students and faculty before and after participating in the REEU. Participants were asked about expectations before the program, and reflected on these expectations after the conclusion of the program. Students reported the program exceeded their expectations. A paper relating to research from our REEU program was published in the journal Genetica and included a REEU undergraduate participant co-author..
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Lee, J., Murren, C.J. Macroscopic variation in Arabidopsis mutants despite stomatal uniformity across soil nutrient environments. Genetica 149, 253266 (2021). https://doi.org/10.1007/s10709-021-00133-7
|
Progress 04/01/20 to 03/31/21
Outputs
Target Audience:The primary target audience are undergraduate students who participate the research and education experience. Specifically, we wish to recruit students with interests in the biological sciences with a focus on agriculture, genetics and plant science. We aim to recruit a diverse cohort of students representing different types of undergraduate institutions, as well as including members of groups underrepresented in the biological, agricultural, and plant sciences. An additional target audience are the faculty mentors associated with the students, who can continue projects developed during the summer research period. Changes/Problems:For the 2021 REEU, the COVID-19 pandemic continued to prevent physical gathering at the College of Charleston campus. We requested in 2020, and were granted by USDA, a change in scope to allow an online research experience program. When the pandemic is reduced sufficiently to allow in-person REEU activities again, we will return to an in-person experience. One result from our evaluation of our 2020 cohort was that students wanted more information about the details of scheduling of the REEU experience, and we will provide that during the 2021 REEU. What opportunities for training and professional development has the project provided?As described above, the program trained 11 undergraduate participants in the REEU. Students were trained in statistical analysis in the R statistical framework, in bioinformatics, in plant phenotyping, and in agricultural genomics and its applications. Students generally learned research techniques, and were taught scientific ethics and strategies for pursuing careers in the agricultural and life sciences. Further details of student experiences are described under accomplishments. In addition, the project manager, April Bisner, developed additional skills in team management and coordination of data management. How have the results been disseminated to communities of interest?We have utilized the unPAK network of educational institutions to recruit students from diverse backgrounds. unPAK institutions include research universities, primarily undergraduate institutions, community colleges, and historically-Black or Latino-serving institutions. Our REEU students have been drawn from all of these types of institutions, and we continued to recruit from these institutions for the 2020 online REEU and 2022 in-person REEU. Participating students have included members of minority groups underrepresented in the agricultural sciences, as well as first-time college students. In 2021 we published an article in the Journal of Microbiology and Biology Education describing our methodologies and evaluation outcomes from transitioning from an in-person REEU to an online REEU due to the COVID-19 pandemic. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we continued to apply the change of scope associated with the COVID-19 pandemic. The 2021 unPAK REEU will be an online experience. Students will again be recruited from participating unPAK institutions and we will aim to recruit 10 or more students. We will focus on data analysis using an existing unanalyzed dataset. In addition, we will send plants to the participants so they can participate in and learn phenomic techniques wherever they are during the pandemic. In addition, we will complete an analysis of the evaluation from the summer 2020 REEU to refine our practices during the 2021 and other future REEUs.
Impacts
What was accomplished under these goals?
We conducted a summer research experience during the summer of 2020. For the 2020 REEU, the COVID-19 pandemic prevented physical gathering at the College of Charleston campus. We requested, and were granted by USDA, a change in scope to allow an online research experience program. To recruit students, we reached out to faculty from the other 18 unPAK network institutions to ask for nominations of students who showed promise in and interest in the plant sciences. Students were asked to submit CVs and nominating faculty submitted a letter of support. From the nominated students we identified 11 students to participate in the 2020 REEU, an increase from the 9 participants in the 2019 REEU. Our student group included two students from underrepresented minority groups, four female students, 8 students from primarily undergraduate institutions, and three students from community colleges. The summer program ran from June 15 2020 through July 17 2020. The entire program was conducted online. The program began by introducing students to the basics of Arabidopsis thaliana biology, of plant phenotyping, and of working with large datasets. Students were introduced to statistical analysis techniques in the R statistical framework. As a joint exercise, we conducted data analysis on a large phenotyping study conducted by the unPAK group that had not yet been analyzed. The experiment included phenotypic data from mutant lines, natural accessions, and wild-type plants grown across four environmental conditions that varied in temperature and nutrient availability. In addition, we mailed kits to all students that included seeds and growing materials. Each student grew a collection of 12 natural accessions of Arabidopsis thaliana in their own homes, recorded phenotypic data on the germination rate, growth, and timing of reproduction in these plants. Environmental data were collected with a HOBO datalogger. At the end of the program, phenotypic data was analyzed as a second joint cohort exercise. Each student also worked on 1-2 indvidual projects during the REEU. Topics of invidual projects included: cataloging crop species with genes homologous to those found in Arabidopsis thaliana, describing patterns of variation in gene structure across natural populations of Arabidopsis thaliana, evaluating the potential for cocultivation with a fungus to improve plant performance, describing the contribution of members of the WRKY trancription factor gene family to plant growth and reproduction, and identifying mutations that contributed to extreme plant size . During the REEU the faculty and students also participated in a number of additional activities. We attended seminars from plant biologists (such as on the history of broccoli breeding and the effects of light saturation on plant coloration). We held workshops on a number of topics: utliizing the R statistical framework, working with bioinformatic data, using the unPAK database to extract phenotypic data, methods for collecting phenotypic data, strategies for data management, One of the participating students will be attending a PhD program in plant biology in fall 2021, and another will be in a master's program in genetic counseling. Another student is working at UC Davis on coding an automated plant phenotyping system for plant images. One student graduated and now works in plant biology. The remaining students are still in undergraduate programs pursuing their degrees. The program was evaluated by an external evaluator (Dr. Danielle Jensen-Ryan) who surveyed students and faculty before and after participating in the REEU. Participants were asked about expectations before the program, and reflected on these expectations after the conclusion of the program. Students reported the program exceeded their expectations. We used the results of the evaluation to write a paper of recommendations for conducting undergraduate research experiences in remote or online circumstances and the paper was published in the Journal of Microbiology and Biology Education.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Jensen-Ryan, D., Murren, C.J., Bisner, A., Rutter, M.T. and Strand, A., 2021. Engaging Undergraduates in Research Experiences at a Distance: Insights and Recommendations for Remote UREs. Journal of microbiology & biology education, 22(1), pp.ev22i1-2375.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Jensen-Ryan, D., Murren, C.J., Rutter, M.T. and Thompson, J.J., 2020. Advancing science while training undergraduates: recommendations from a collaborative biology research network. CBELife Sciences Education, 19(4), p.es13.
|
Progress 04/01/19 to 03/31/20
Outputs
Target Audience:The primary target audience are undergraduate students who participate the the research and education experience. An additional target audience are the faculty mentors associated with the students, who can continue projects developed during the summer research period. Changes/Problems:For the 2020 REEU, the COVID-19 pandemic prevented physical gathering at the College of Charleston campus. We requested, and were granted by USDA, a change in scope to allow an online research experience program. When the pandemic is reduced sufficiently to allow in-person REEU activities again, we will return to an in-person experience. One result from our evaluation of our 2019 cohort was that students wanted to learn more about the USDA and about the REEU program in particular. We will incorporate a mini-lesson about the goals of USDA, NIFA and the REEU program. We will also discuss the diverse array of REEU experiences. What opportunities for training and professional development has the project provided?As described above, the program trained 7 undergraduate participants in the REEU. Students were trained in statistical analysis in the R statistical framework, in bioinformatics, in plant phenotyping, and in agricultural genomics and its applications. Students generally learned research techniques, and were taught lab safety, scientific ethics, and strategies for pursuing careers in the agricultural and life sciences. Further details of student experiences are described under accomplishments. In addition, the project manager, April Bisner, developed additional skills in team managment and coordination of data managment. How have the results been disseminated to communities of interest?We have utilizedthe unPAK network of educational institutions to recruit students from diverse backgrounds. unPAK institutions include research universities, primarily undergraduate institutions, community colleges, and historically-Black or Latino-serving institutions. Our REEU students have been drawn from all of these types of institutions, and we continued to recruit from these institutions for the 2020 online REEU we are currently running. Participating students have included members of minority groups underrepresented in the agricultural sciences, as well as first-time college students. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we applied forand received permission for a change of scope. The 2020 unPAK REEU will be an online experience. Students will again be recruited from participating unPAK institutions and we will aim to recruit 10 or more students. We will focus on data analysis using an exisiting unanalyzed dataset. In addition, we will send plants to the participants so they can participate in and learn phenomic techniques whereever they are during the pandemic. In addition, we will complete an analysis of the evaluation from the summer 2019 REEU to refine our practices during the 2020 and other future REEUs.
Impacts
What was accomplished under these goals?
We conducted a summer research experience during the summer of 2019. The government shutdown of the spring of 2019 delayed award implementation, and our recruiting began later than expected. Consequently, we ran a slightly smaller program than initially planned, with 9students. Our student group included two students from underrepresented minority groups, five female students, 7 students from primarily undergraduate institutions, and one student from a community college. We reached out to faculty from the other 18 unPAK network institutions to ask for nominations of students who showed promise in and interest in the plant sciences. Students were asked to submit CVs and nominating faculty submitted a letter of support. From the nominated students we identified 7 students to participate in the 2019 REEU. The summer program ran from June 12 2019 through July 24 2019. Participating students resided in Charleston SC and activities were primarily conducted on the campus of the College of Charleston. The program began by introducing students to the basics of plant phenotyping. Before the program began, we had grown a series of Arabidopsis thaliana plantlines, each containing a single mutation at a different position on chromosome 4. Our intent was to study the phenotypes of these lines to determine if the positon of the gene on the chromosome could be used to make predictions about the effects of mutation on phenotype. The students phenotyped the plants for growth and life history characters during the first two weeks of the REEU. They worked on this project as a joint exercise. After completing data collection, we worked collectively to develop a plan for statistical analysis. As discussed below, students were introduced to statistical analysis techniques in the R statistical framework. During the remainder of the program, students conducted analyses on the data they collected at the beginning of the program. During the program, we conducted workshops on utliizing the R statistical framework, working with bioinformatic data, using the unPAK database to extract phenotypic data, methods for collecting phenotypic data, strategies for data management, ethical behavior in the sciences, laboratory safety protocols, and on strategies for finding and interpreting the primary literature in the sciences. Each student also worked on 1-2 indvidual projects during the REEU. Topics of invidual projects included: evaluating the potential for cocultivation with a fungus to improve plant performance, describing the contribution of members of the WRKY trancription factor gene family to plant growth and reproduction, assessing the effects of spatial positioning within a growth chamber on plant traits, descrribing transgenerational effects on plant growth, evaluating acid phosphatase activity in mutant lines, and measuring the variance in traits among clonal plants. During the REEU the faculty and students also participated in a number of field trips and team building experiences. For example, we visitied the USDA Vegetable Laboratory in Charleston to understand how genetic methods are applied to breeding broccoli and other crops. We also particpated in joint activity with a local NSF REU program--a trawl of the Charleston Harbor to learn about the species of fish and invertebrates living there. Some students chose to continue their research after the end of the REEU program. Two students continued their indpendent projects are arepreparing manuscripts for publication. One of those students is now headed to medical school in the next academic year. Another student continued their experiment, bringing plants back to their home institution, presenting results at a poster session, and is now heading to a PhD program in plant biology, ecology and genetics. Finally, another student is continuing with their project as a senior thesis for their senior year of undergraduate. The program was evaluated by an external evaluator (Dr. Danielle Jensen-Ryan) who surveyed students and faculty before and after participating in the REEU. Participants were asked about expectations before the program, and reflected on these expectations after the conclusion of the program. Students reported the program exceeded their expectations. Students learned to work in a lab and conduct research, and connected with program materials and activities. Examples of ways the students planned to apply the information they learned was to finish their research and writing, go into plant research, go to graduate school / pursue a PhD, and present their findings as a poster or publication.
Publications
|
|