Progress 10/01/20 to 09/30/21
Outputs
Target Audience:In addition to student trainees, this work was submitted to scientific journals for peer review. Additionally, the PI participated in a Q&A news article. Therefore, the audiences included students, other scientists, as well as the general public. Changes/Problems:Our lab relocated in the calendar year, which shifted our access to shared equipment. The department helped fund the purchase of some new equipment for our lab and some trades with other PIs allowed us to set up a sustainable lab space that is now much more product and research-active. We have a strict lab covid protocol to limit exposures among lab personnel so that our research can proceed despite the pandemic. What opportunities for training and professional development has the project provided?Training documents continue to be refined to facilitate the rapid onboarding of new undergraduates to the lab. This includes additional training videos of basic everyday tasks. This has substantially reduced the one-on-one training time required for the PI and graduate students. Additionally, in addition to a weekly lab meeting for everyone, the graduate students meet with teams of undergraduates on a weekly basis and the PI meets with the graduate students on a weekly basis. This provides many opportunities for challenges to be presented and managed on a regular basis. Additionally, most of the efforts this year were molecular and computational, which provided extensive training opportunities for my students. As we get closer to the endpoint of some of these projects, students have been able to get more exposure to the entire process start to finish on research more generally. How have the results been disseminated to communities of interest?All undergraduates and graduate students involved in research are required to write a paper and present it at our lab meeting. These students are now well versed in the experimental goals and outcomes to share with their communities as they graduate from Auburn and move on to their next career stage. Additionally, each graduate student presented a poster at a scientific research meeting. Due to the COVID-19 pandemic, both conferences were held virtually. Poster Presentation. Natalia Rivera-Rincon and Stevison LS. 2020. Changes in frequency of polymorphic inversions on natural populations of Drosophila robusta. Southeastern Population Ecology and Evolutionary Genetics. Virtual Conference. https://doi.org/10.6084/m9.figshare.13135970.v1 Poster Presentation. Altindag UH and Stevison LS. 2021. Recombination Rate Plasticity and Interchromosomal Effect in Drosophila pseudoobscura. 62nd Annual Drosophila Research Conference. Virtual Conference organized by Genetics Society of America. What do you plan to do during the next reporting period to accomplish the goals?Our primary goal this year is to finally publish our manuscript. We have submitted it to a different journal and received reviews in a rapid time frame as compared to the previous journal. Additionally, we are hoping to overcome the segregation issues of mutant stocks by switching species. This project was included in a proposal to NIH that we hope to hear back on by May 2022. Finally, we will do a preliminary analysis of our genome sequencing pilot 768 individuals with the goal of sequencing 2500 more over the summer.
Impacts
What was accomplished under these goals?
In Fall 2020, our lab relocated from CASIC to the main campus. Manuscript: As noted in last year's report, following peer review, the editors and reviewers suggested that we combine the two manuscripts form 2020 into a single manuscript. We have successfully done this and resubmitted it for further peer review. Unfortunately, review delays due to the pandemic have delayed a decision for several months. Ongoing Project 1: Following the move of our lab from CASIC to Rouse Life Sciences, we were able to set up a private molecular space that could be better managed by the PI. Not being part of a larger shared space with senior PIs made for a much more productive year. In spring 2021, DNA was isolated and quantified from a subset of samples. Specifically, we selected 768 samples (eight 96-well plates). We did this using Zymo kits to extract the DNA and shared equipment in Rouse. We then quantified the DNA using various protocols and a plate reader. We then use the SeqWell PlexWell 84 kits to generate 8 pooled libraries of each 96-well plate. This was then validated further using qubit, qPCR, and gel electrophoresis. In summer 2021, we sent these samples out for sequencing with the company Novogene. They further did independent QC using a Bioanalyzer. They returned >800 million 150 bp PE reads. This resulted in an estimated average coverage per sample of 0.72X (fewer than 10 were under 0.3X). This was ~20% higher than estimated by the company. Greater than 96% of reads were successfully demultiplexed into individually dual barcoded samples. These raw data of ~80GB have been backed up and the downloads verified. Ongoing Project 2: As described in the 2019 report as Project #3, this project was set to complete in April 2020. However, due to the COVID-19 pandemic, this experiment was terminated and the genetic crosses were discarded. Without undergraduates to help with the data collection, it was decided to postpone the experiment. Towards the end of Summer 2020, it was restarted, and following a few setbacks in getting back into the lab, data collection was completed on November 23, 2020. However, in the process of peer review on our other project, we discovered that the mutant markers we were using had significant segregation bias that made these results unreliable. Therefore, we are in the process of rethinking this project substantially, likely opting to use a different species altogether. Ongoing Project #3: This has expanded significantly based on an AAES-Seed grant. We submitted a year 1 project update report on those findings elsewhere.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2021
Citation:
Altindag UH, HN Taylor, C Shoben, KA Pownall, and LS Stevison. In Revision. Putative condition-dependent viability selection in wild type stocks of Drosophila pseudoobscura. Pre-print on BioRxiv: DOI: 10.1101/2020.04.10.036129v3.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
News Article: Buzz kill: Auburn researcher offers advice for ridding homes of pesky fruit flies. Expert Answers . July 1, 2021. http://ocm.auburn.edu/experts/2021/07/011124-stevison-fruit-flies-expert-answers.php
" First published in Auburn News 7/2/2021
" Published in Alabama NewsCenter 7/4/2021
o https://www.alabamanewscenter.com/2021/07/04/buzz-kill-auburn-university-researcher-offers-advice-for-ridding-homes-of-pesky-fruit-flies/
" Published in COSAM Today Newsletter 7/6/2021
o http://www.auburn.edu/cosam/news/cosam_today/2021/07/july-06-2021.htm
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Datasets and code: Altindag UHg and LS Stevison. 2020. Peak Plasticity Project. Github Repository v2: DOI: 10.5281/zenodo.4477672.
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Progress 10/01/19 to 09/30/20
Outputs
Target Audience:In addition to the undergraduate and graduate student trainees, this work was submitted as pre-prints to the Biorxiv server. Therefore, it reached several scientisits doing similar work in this field. Changes/Problems:The COVID-19 pandemic was a huge setback to our research goals. With the shutdown of the university to undergraduates, we discarded a large experiment in March 2020, effectively transitioning the lab into maintenance mode with no research being conducted. This also took an emotional toll on students and for several months (including summer which is typically our most productive) we had no access to undergraduate researchers. While we restarted in the Fall of 2020, we were forced to stagger our visits to the lab and continue our lab meetings virtually. This had the unintended consequence of losing cohesion as a lab group, which we are still working to rebuild. What opportunities for training and professional development has the project provided?Training documents continue to be refined to facilitate rapid onboarding of new undergraduates to the lab. This includes additional training videos of basic everyday tasks. This has substantially reduced the one-on-one training time required for the PI and graduate students. Additionally, in addition to a weekly lab meeting for everyone, the graduate students meet with teams of undergraduates on a weekly basis and the PI meets with the graduate students on a weekly basis. This provides many opportunities for challenges to be presented and managed on a regular basis. How have the results been disseminated to communities of interest?All undergraduates and graduate students involved in research are required to write a paper and present at our lab meeting. These students are now well versed in the experimental goals and outcomes to share with their communities as they graduate from Auburn and move on to their next career stage. Additionally, the graduate student presented two posters and the PI one poster during the annual period on this research. Due to the COVID-19 pandemic, both of these events were held virtually. Poster Presentation. Altindag UH and Stevison LS. 2020. "Recombination Rate Plasticity and Interchromosomal Effect in Drosophila pseudoobscura". AU Student Research Symposium, Auburn University. Poster Presentation. Altindag UH and Stevison LS. 2020. "Recombination Rate Plasticity and Interchromosomal Effect in Drosophila pseudoobscura". The Allied Genetics Conference (TAGC) 2020. Online. doi.org/10.6084/m9.figshare.12148419.v1 Poster Presentation. Stevison LS, Altindag UH, Taylor TN, Shoeben C, and Pownall KA. 2020. "Recombination rate plasticity in Drosophila pseudoobscura". The Allied Genetics Conference (TAGC) 2020. Online. doi.org/10.6084/m9.figshare.12142638.v1 What do you plan to do during the next reporting period to accomplish the goals?The ultimate goal of this research is to examine recombination rate plasticity genome wide. Although our NSF grant gave us the funds to do this, the pandemic dramatically setback those plans. We are now relocated to a new location on Auburn's campus and are in the process of beginning a pilot sequencing project which includes 768 progeny from the temperature experiment conducted last year. Once we isolated DNA, we will prepare next generation sequencing libraries and send them out for sequencing (by May 2021). We will then analyze the resulting sequence data with the hope that we can complete the originally proposed 3000 libraries by the end of summer 2021. This would provide the crucial data necessary to address our research questions.
Impacts
What was accomplished under these goals?
In Fall 2019, we continued three major experiments which wrapped up early in the reporting year. The remainder of the year was spent conducting data entry, data analysis, and writing up each project for publication. Manuscript #1: The culmination of several experiments were completed in November 2019. Once the fly husbandry was completed, a draft manuscript was submitted to the pre-print server biorixiv in April 2020. It was also submitted to a the journal Heredity for publication. Despite receiving critical peer reviews, it was rejected by the journal. We incorporated the suggested changes and revised the manuscript. A new version was then uploaded to the pre-print server in July 2020 and submitted to the journal G3. It went through peer review and we are currently revising it with the hope that it will be accepted. Manuscript #2: In addition to our prior experiments on temperature and recombination rate, we also were investigating maternal age. These experiments were completed just prior to the reporting period. While efforts to concurrently write this manuscript and #1 above were underway, the pandemic diluted these efforts delaying a final draft until July 2020. This manuscript was archived in the pre-print server biorxiv and submitted to the journal G3 as a companion to the revised manuscript #1. However, following peer review, the editors and reviewers suggested that we combine the two manuscripts into a single manuscript. We are currently editing these with the hope that a final version of this combined manuscript will be accepted in the following reporting year. Ongoing Project 1: With the peak timing of plasticity identified as day 9 in our prior experiments, we conducted a large scale genetic cross using wild type flies with the ultimate goal of sequencing these flies using whole genome sequencing. As with our most recent experiments, progeny were partitioned into 24 hour increments and stored in 96-well plates. The fly husbandry of this project completed on February 15, 2020. Our goal was to immediately start DNA isolation and genome library preparation. However, these efforts were delayed due to the COVID-19 pandemic (see below). Ongoing Project 2: As described in last year's report as Project #3, this project was set to complete in April 2020. However, due to the COVID-19 pandemic, this experiment was terminated and the genetic crosses discarded. Without undergraduates to help with the data collection, it was decided to postpone the experiment. Towards the end of Summer 2020, it was restarted and following a few setbacks in getting back into the lab, data collection completed on November 23, 2020. Our goal is to complete data analysis and write-up this project in the upcoming reporting year. Ongoing Project #3: In May 2020, we secured an AAES-Seed grant related to this work that involved a new project investigation flies in the wild native to Alabama, Drosophila robusta. We began collecting at Chewacla State Park in Auburn and were able to establish two living stocks in the lab. We also refined the protocol for larval salivary chromosome preps.
Publications
- Type:
Other
Status:
Under Review
Year Published:
2020
Citation:
Altindag UHg, C Shoben, and LS Stevison. 2020. Refining the timing of recombination rate plasticity in response to temperature in Drosophila pseudoobscura. Pre-print on BioRxiv: DOI: 10.1101/2020.04.10.036129.
- Type:
Other
Status:
Under Review
Year Published:
2020
Citation:
Pownall K, HN Taylor, UH Altindag, and LS Stevison. 2020. Maternal age alters recombination rate in Drosophila pseudoobscura. Pre-print on BioRxiv: DOI: 10.1101/2020.07.20.212548.
- Type:
Other
Status:
Accepted
Year Published:
2020
Citation:
AAES AgR-SEED Grant Funded. Drosophila as a model to study how climate change alters genome integrity. Started October 1, 2020.
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Progress 07/01/19 to 09/30/19
Outputs
Target Audience:This project is in the early stages and has mostly reached undergraduate and graduate student trainees. In the process of being involved in this research, these students have also been exposed to primary scientific research and gained valuable experience in a research lab. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training documents have been refined to facilitate rapid onboarding of new undergraduates to the lab. This includes a comprehensive manual for the fly lab and a video of how to prepare fly food media. This has substantially reduced the one-on-one training time required for the PI and graduate students. How have the results been disseminated to communities of interest?All undergraduates and graduate students involved in research are required to write a paper and present at our lab meeting. These students are now well versed in the experimental goals and outcomes to share with their communities as they graduate from Auburn and move on to their next career stage. Additionally, our lab participated in the Destination STEM program organized by COSAM Outreach Office. We highlighted the importance of the fruit fly as a model for genetics research. This event reached ~1,100 students from 18 local schools across the Southeast, as far reaching as Texas. What do you plan to do during the next reporting period to accomplish the goals?Part of this work has recently been funded by the NSF. Therefore, we are setting up crosses to collect progeny in the 9-day post-mating peak identified through recent experimentation. These progeny will be grinded up and sent out for sequencing to generate the the fine-scale genome wide recombination map. Though that work is only funded for the temperature treatment, we plan to continue other stresses with the mutant stocks as well.
Impacts
What was accomplished under these goals?
This year, we conducted several experiments to refine the timing of recombination plasticity in Drosophila pseudoobscura. We also have been working to determine how age influences plasticity. Finally, we have been investigating the interaction between recombination rate plasticity and interchromosomal effect (ICE). For each project, we used X-linked phenotypic mutants cut, scalloped, yellow, and sepia in Drosophila pseudoobscura to facilitate rapid screening of recombinant flies. Our experimental approach used a backcross design, crossing to wildtype to avoid fitness effects of the mutant markers. Control females were aged 7 days to sexual maturity and reared at 21°C. Recombination rate measurements targeted the first 12 days after females were mated, with females transferred every 72 hours and limited to a single mating event to avoid additional stress from male harassment. Project 1: To identify the peak timing of plasticity due to temperature stress (26°C) during development. As a result of our treatment, we observed a significant effect on overall fecundity (p=0.00144) indicative of a fitness effect. We first identified a peak of plasticity 7-9 days post-mating. Using subsequent 24 hour transfers for only 6-10 days post-mating, we narrowed this peak to 9 days post-mating (p=0.00824). This timepoint had an average of 14.54% difference in recombination rate across the three intervals (N21=3424; N26=2082). This result is critical for further experimentation in this system, which is ongoing. Interestingly, we observe plasticity in intervals that are <50cM (y-sd; sd-ct), as well as intervals >50cM apart (y-se), suggesting that plasticity can be detected across large portions of the chromosome. Finally, our results show a large variance in recombination rates among replicates in both control and treatment, but especially in the treatment. This variance bolsters the support for necessary replication in experimental designs studying recombination rate variation more broadly across systems. Project 2: We investigated the impact of female age on meiotic recombination rate in this system. First, a survivorship assay was used to determine an appropriate age for observing age-related plasticity. We selected the age of 35 days, which corresponds to senescence across 32.6% of replicates. As a result of age, we observed a significant effect on overall fecundity (p= 0.00115) indicative of a fitness effect. We also found an average of 15.73% difference in recombination rate due to age over multiple intervals and timepoints (N7=6217; N35=4506). This result suggests that age permanently alters recombination in a manner distinctly different from temperature stress. Project 3: In addition to projects 1-2, we conducted the same experiments in a series of crosses where the 3rd chromosome of the strain of flies had a different chromosomal arrangement. This allowed us to compare those results to the experimental results in Projects 1-2 to see how interchromosomal effect is influenced by environmental plasticity. Our results are quite different for age and temperature, again suggesting very different mechanisms for these two processes.
Publications
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