This CURE has been peer-reviewed as meeting CUREnet's review criteria.
HideIdentification of Telomere Regulating Genes in Drosophila melanogaster
Chun Zhou
Location: Mercy College-Main Campus
Abstract
Telomeres are the natural ends of linear chromosomes and contribute to the maintenance of chromosome stability. Without the capping effect of telomeres, broken chromosomes can undergo the breakage-fusion-bridge cycle which may cause cancer. In Drosophila melanogaster, telomeres are extended by telomere-specific non-LTR retrotransposons which serve as an alternative, yet similar approach to the telomerase. Previously, we described a genetic factor called Telomere elongation (Tel) on the third chromosome of fruit flies that can enhance telomere elongation. Another telomere-elongating gene was also identified in the similar chromosomal region in D. melanogaster. In the present study, we used a bioinformatic approach to identify the genes in this chromosomal region that have the potential to influence chromosomal stability in Drosophila. We hypothesized that the genes with the function of modulating chromosomal structure could have the potential to regulate telomere length or structure. We extracted genomic DNA from the fly strains in which one of these identified candidate genes had been mutated. Using real-time PCR, we are analyzing the telomere length among different mutant strains with the Oregon-R wild-type strain as the control. In addition, to probe whether or not the disruption of these candidate genes causes a structural defect of telomeres, we have performed polytene chromosome staining. The results will help identify the genes that play a role in regulating telomere length and/or structure. This original research project has been conducted in two biology courses, Genetics (BIOL 360) and Research in Biology I (BIOL 370) at Mercy College since the summer semester of 2018. BIOL 360 is a course for several majors, including biology and health science, and BIOL 370 is a higher level course for biology students. The students in the Research in Biology I class conducted the real-time PCR and polytene chromosome staining experiments as their main learning activities, while the students in the Genetics class conducted the bioinformatics and regular PCR experiments as their lab activities. Together, this original research project has been supporting the CURE activities in two biology courses.
Shared Student Goals
- Read primary research articles
- Design research studies with hypothesis, methods, and expected types of results
- Perform the experiments and troubleshoot experimental issues
- Communicate the research findings via lab meetings and in-class research presentations
- Produce a clear and reliable research notebook
BIOL 360-Specific Student Goals
- Master the experimental skills required in the BIOL360 Genetics course (model organism culture, phenotype observation, bioinformatic gene analysis, micropipetting, genomic DNA extraction, DNA concentration measurement, PCR, DNA gel electrophoresis, gel imaging, and image analysis)
BIOL 370-Specific Student Goals
- Design research experiments and develop experimental protocols
- Master the experimental skills required in the BIOL370 Research in Biology I course (model organism culture, phenotype observation, bioinformatic gene analysis, micropipetting, genomic DNA extraction, DNA concentration measurement, PCR, DNA gel electrophoresis, gel imaging, image analysis, real-time PCR, polytene chromosome staining, and immunofluorescent microscopy)
- Communicate the research findings to the public by making poster presentations in local and regional undergraduate research conferences, including the annual Westchester Undergraduate Research Conference in spring and the annual conference of the Metropolitan Association of College and University Biologists (MACUB) in fall
Research Goals
- Identify candidate genes that are involved in chromosome remodeling and detect telomere retrotransposons using PCR (BIOL360)
- Identify the genes that regulate telomere length using real-time PCR and/or telomere structure using polytene chromosome staining (BIOL370)
Context
This CURE was designed to be taken by junior and senior undergraduate students at Mercy College. There are about 20 students in the BIOL 360 Genetics class, and the students have majors of biology, health science, veterinary technology, and clinical laboratory science. The BIOL 360 course meets twice a week with one lecture class and one lab class. All the CURE activities are conducted in the lab classes (two hours and 50 minutes per class). There are about eight biology students in the BIOL 370 Research in Biology I class, which runs for about six hours per week. In both classes, the CURE activities run over an entire semester.
Target Audience: BIOL 360: Junior and senior students of Biology, Health Science, Veterinary Technology, and Clinical Laboratory Science; BIOL 370: Biology students
CURE Duration: A full semester
CURE Design
The overall rationale of conducting the same original research project in two biology courses is to gradually complete an authentic, original research in the field of molecular genetics in biology courses. During these CURE in-class activities, undergraduate students experience all major aspects of performing an original research while mastering modern molecular genetic techniques.
The maximal student number is eight in BIOL 370. The students in this class are of Biology major and more motivated in conducting the research as an important aspect of their career development. In addition, most students in this class have done certain level of biology research. Thus, the students in this class are required to conduct their individual research experiments to investigate telomere length and structure in the mutant fly strains in which their selected candidate genes are mutated. This design gives each student a completely independent research experience over an entire semester to study the candidate genes that she or he selected through the bioinformatics approach. Such course-based experience allows the students to conduct graduate school-like research work in a regular class that meets for about six hours per week for 15 weeks. Consequently, the students are able to develop experimental protocols, repeat their experiments, and troubleshoot experimental issues to move this research project forward. Finally, the students present their research work in local and regional research conferences: the annual Westchester Undergraduate Research Conference in spring and the annual MACUB Conference in fall.
The experimental protocols and methods that are developed by BIOL 370 then are utilized in a more general course, BIOL 360, which are taken by students of multiple majors. This guarantees the quality of students' study in BIOL 360 as the students in BIOL 360 are of various majors and lack previous research experience to develop a research. In BIOL 360, students work as randomly assigned research teams. They conduct the experiments that are tested in BIOL 370, thereby being able to focus on designing their experiments for their selected mutants, performing the experiments, practicing technical skills, repeating the experiments for valid data, and interpreting their data.
Together, the strategy of the present CURE project is able to give an authentic research experience in regularly scheduled biology courses over a semester. At the same time, the original research project itself has also been developed through the work of the undergraduate students in BIOL 360 and BIOL 370 over the past several semesters. Furthermore, this strategy scaffolds the research experience for motivated biology students. For example, some students became interested in the research project in BIOL 360 and took BIOL 370 for more advanced, independent research during the following semester. To these students, the CURE-based BIOL 360 and BIOL 370 offer an opportunity to complete a whole year of undergraduate research.
In both classes, the instructions are designed in a detailed manner so that students have a clear understanding on the assignments, expected outcomes, class policies, and relatively objective rubrics. In addition, timely communication opportunities are offered to students to clarify any unclear issues that may arise during the semester.
The present CURE project can be applied in undergraduate genetics courses and/or research courses. The course-coupled CURE strategy presented here can be applied to other undergraduate teaching subjects. One of the advantages of the course-coupled CURE strategy is to help the faculty members in teaching-focused colleges who often lack time to conduct their research due to heavy teaching load. This strategy would allow them to develop their own research project(s) by working with undergraduate students and having undergraduate students drive the research project forward toward original findings.
In both courses, upon completing the research activities, the students not only master the experimental techniques that are required by a regular non-CURE class, but also acquire additional experiment skills and scientific thinking skills.
Core Competencies: Analyzing and interpreting data, Asking questions (for science) and defining problems (for engineering), Constructing explanations (for science) and designing solutions (for engineering), Planning and carrying out investigations
Nature of Research: Basic research, Informatics/Computational research, Wet lab/Bench research
Tasks that Align Student and Research Goals
Student Goals ↓
Summarize the current knowledge about the telomere elongation mechanisms in fruit flies based on three student-identified reviews
Use PubMed
Generate an annotated bibliography
Use PubMed
Generate an annotated bibliography
Discuss the hypothesis, experimental methods, and expected types of results
Conduct the planned experiments
Repeat the experiments
Troubleshoot the experimental issues
Repeat the experiments
Troubleshoot the experimental issues
Report the team research progress in monthly lab meetings and present team findings at the end of the semester using PPT slides
Test and develop major experimental protocols including real-time PCR, polytene staining, and immunofluorescent microscopy
Instructional Materials
BIOL 360 research schedule:
- Week 1: Bioinformatics_Gene analysis_Part I (The NCBI genome database and FlyBase databse)
- Week 2: Bioinformatics_Gene analysis_Part II
- Week 3: Troubleshooting-1
- Week 4: Lab meeting-1
- Week 5: Drosophila phenotype observation
- Week 6: Isolation of genomic DNA
- Week 7: DNA measurement and electrophoresis
- Week 8: Troubleshooting-2
- Week 9: Lab meeting-2
- Week 10: PCR
- Week 11: PCR data analysis
- Week 12: PCR-Repeat
- Week 13: PCR data analysis-Repeat
- Week 14: Lab meeting-3
- Week 15: End-of-semester oral presentation
BIOL 370 research schedule:
- Individual experimental schedules (Students conduct their individual research experiments according to their own progress in all the classes except for the ones used for monthly lab meetings and fly passage.)
- Monthly lab meetings
- Fly passage every two weeks (All students passage their fly strains on the same two-week schedule.)
- One week for poster generation and one day for attending an undergraduate research conference
Assessment
BIOL 360 assessment: Total 100 points that are converted to 15 points toward the final grade
- Mastering experimental techniques (30 points). See example skill assessment (Microsoft Word 2007 (.docx) 17kB Oct31 19).
- Maintaining weekly lab notes in an electronic lab notebook (30 points)
- Annotated bibliography (16 points)
- Lab meeting presentations (15 points)
- End-of-semester in-class oral presentation (9 points)
BIOL 370 assessment: Total 100 points
- Mastering experimental techniques (30 points)
- Maintaining daily lab notes in an electronic lab notebook (30 points)
- Annotated bibliography (16 points)
- Lab meeting presentations (15 points)
- Poster presentation in the research conference (9 points). See example student poster (Acrobat (PDF) 606kB Oct31 19).
CURE assessment:
- The Undergraduate Research Student Self-Assessment (URSSA) is used to assess the learning gains of the students.
Instructional Staffing
This CURE project has been in the process of development since the summer of 2018. It is now close to be finalized. The author wishes that this CURE project can be implemented as a regular practice for future BIOL 360 and BIOL 370 courses by the author and other faculty members who teach these courses.
Author Experience
Chun Zhou, Mercy College-Main Campus
The author participated in the two-day COURSE-BASED UNDERGRADUATE RESEARCH EXPERIENCES (CURE) INSTITUTE at Mercy College in 2018. It was a great experience with which I learned how to design and conduct a CURE course. After that, I obtained the support from our Department of Natural Sciences to purchase the fly incubators for developing this CURE project. Since then, this CURE project has gone through four semesters (Summer and Fall of 2018; Spring and Fall of 2019). It is at the point that the synergy between BIOL 360 and BIOL 370 is evident. It is also noticeable that some students became more interested in research and decided to take BIOL 370 after completing BIOL 360. The author thanks all the support and believes that CURE is a high-impact practice that can improve students' overall quality, high-level learning skills, and course learning outcomes for both biology and non-biology students. More importantly, CURE can promote biology students to further develop their career.
Advice for Implementation
To implement CURE in a regular biology course, it is essential for the instructor to test the experimental protocols before the semester starts. The author was able to complete this task by conducting volunteer research work in summer together with volunteer undergraduate students. If possible, it would be ideal if one could get extra support from lab staff. Another way to address this issue is to have a higher level class, such as BIOL 370 here, to develop the experimental protocols and then use these protocols in a lower level class, such as BIOL 360 in the present CURE project.
It was also learned that undergraduate students may repeat an experiment several times to get valid data. Thus, in our designed schedule, certain classes are set aside for students to repeat their experiments.
Students benefit the most with proper technical demonstrations. Thus, the instructor of this CURE project made sure to be familiar with all the experimental protocols and identified various ways for clear demonstration. In addition, some undergraduate students who took BIO360 in the spring became interested in the research project itself and decided to volunteer to continue their research in the following summer and to take the BIOL 370 course in the fall semester during which they helped other students on experimental skills. This helped the implementation of BIO370 and motivated other students in BIOL 370.
To implement this original research project for the planned CURE courses, a significant cost on purchasing reagents is needed. Currently, the reagents are covered by the instructor's Faculty Development Grant and the Department of Natural Sciences. However, in the future, a mechanism to secure the funding for this CURE project would need to be developed.
Iteration
The students are actively engaging in troubleshooting and repeating the experiments in order to obtain valid data. We set aside certain classes for the students to discuss, troubleshoot and repeat their experiments.
Using CURE Data
The research data are maintained on an electronic notebook managing system and available to all the students. Students gain authorship in their poster presentations for the undergraduate research conferences. The URSSA data are used by Mercy College for developing CURE-based courses.
Resources
1. Casacuberta, E. (2017) Drosophila: Retrotransposons making up telomeres. Viruses. 9, 192.
2. Frydrychova, R. C., Biessmann, H., and Mason, J. M. (2008) Regulation of telomere length in Drosophila. Cytogenet Genome Res . 122, 356-364.
3. Melnikova, L., and Georgiev, P. (2002) Enhancer of terminal gene conversion, a new mutation in Drosophila melanogaster that induces telomere elongation by gene conversion. Genetics. 162, 1301-1312.
4. Siriaco, G. M., Cenci, G., Haoudi, A., Champion, L. E., Zhou, C., Gatti, M. and Mason, J. M. (2002). Telomere elongation (Tel), a new mutation in Drosophila melanogaster that produces long telomeres. Genetics, 160, 235-245.