Progress 02/15/18 to 02/14/19
Outputs
Target Audience:The target audience of my training/career development plan are minority students and technical staff at the USDA-APHIS CPHST Lab in Edinburg, TX. While collecting and preparing samples from the Mexican Fruit Fly Mass-rearing Facility at their center, the Project Director Sheina Sim and Project Primary Advisor Scott Geib held a CRISPR/microinjection workshop which began with a seminar describing the process of making heritable mutations using the CRISPR/Cas9 system and continued with a practical laboratory session in which we injected live embryo with guide RNA and Cas9 protein targeting several gene targets in Anastrepha ludens. The target audience of my project plan are state departments of agriculture as well as the USDA-APHIS who would be utilizing the the products of my research to protect American agrilculture by suppressing and eradicating invasive Mexican Fruit Fly. Changes/Problems:The major hurdle of this project was the difficulty in generating a complete, contiguous, and accurate genome assembly for this species. This pushed the timeline for the data analysis. I also decided to hold a microinjection workshop instead of a bioinformatic workshop because it would be more beneficial to the community as the students and technicians at the location we held the microinjection workshop had limited access to these techniques and expertise. What opportunities for training and professional development has the project provided?This project and my Primary Advisor Scott Geib provided me the opportunity to attend a workshop held at UC Berkeley where I learned the programming language python which has immenseley aided me in the analysis, format manipulation, and visual representation of my data. This grant and project also contributed to my hiring as a Category 1 USDA-ARS Scientist. How have the results been disseminated to communities of interest?The methods we developed for CRISPR microinjections in Tephritidae have been disseminated to communities of interest through a microinjection workshop we held at a collaborating USDA-APHIS laboratory which had an employee base made largely of minority individuals, and this product was also disseminated in the form of a scientific publication. The foundational genomic tools developed throughout the course of this project will be made publicly available through various data repositories. What do you plan to do during the next reporting period to accomplish the goals?To accomplish these goals, I will contribute to do this work as part of my base-funded research. I will employ new techniques as they become available to characterize the translocations in Genetic Sexing Strains of A. ludens and identify the gene causing black pupae. Using the data collected during this project, I will also attempt to create a new Genetic Sexing Strain of A. ludens that incorporates a conditional lethal trait which facilitates the mass-rearing of a male-only line.
Impacts
What was accomplished under these goals?
Of the goals of this project, I have accomplished the development, genotyping, and data analysis of mapping populations of A. ludens for the purpose of generating a linkage map and identifying the loci and contig most tightly linked to the black pupae trait. I have also developed as a teacher and a mentor through my initiating and instructing a microinjection workshop at a collaborating USDA-APHIS facility. I have also developed as a teacher and a mentor in my current employment as a Category 1 USDA-ARS Scientist where I now supervise one permanent technician and three undergraduate research scientist assistants.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
The ABCs of CRISPR in Tephritidae: developing methods for inducing heritable mutations in the genera Anastrepha, Bactrocera, and Ceratitis.
Sheina B. Sim, Angela N. Kauwe, Rocio E.Y. Ruano, Pedro Rendon, and Scott M. Geib
Insect Molecular Biology (2019) January 10, 2017 vol. 28 no. 2 277-289; doi: 10.1111/imb.12550
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Transpacific coalescent pathways of coconut rhinoceros beetle biotypes: resistance to biological control catalyzes resurgance of an old pest.
J. Bradley Reil, Camile Doorenweerd, Michael San Jose, Sheina B. Sim, Scott M. Geib, and Daniel Z. Rubinoff
Molecular Ecology 2018; doi:10.1111/mec.14879
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Genome Annotation Generator: A simple tool for generating and correcting WGS annotation tables for NCBI submission.
Scott M. Geib, Brian Hall, Theodore Derego, Forest T. Bremer, Kyle Cannoles, and Sheina B. Sim.
GigaScience 2018; 10.1093/gigascience/giy018
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Molecular characterization of interspecific competition of Diachasmimorpha longicaudata (Ashmead) and Fopius arisanus (Sonan) parasitizing the oriental fruit fly, Bactrocera dorsalis (Hendel).
Guang Hong Liang, Lie Qing Fu, Jun Xian Zheng, Hao Yu Lin, Jian Hui Lin, Sheina B. Sim, Eric B. Jang, Wade P. Heller, and Scott M. Geib
Biological Control 2018 vol. 118(10-15); https://doi.org/10.1016/j.biocontrol.2017.11.012
|
Progress 02/15/17 to 02/14/19
Outputs
Target Audience:The target audience of my training/career development plan are minority students and technical staff at the USDA-APHISCPHST Lab in Edinburg, TX. While collecting and preparing samples from the Mexican Fruit Fly Mass-rearing Facility at their center, the Project Director Sheina Sim and Project Primary Advisor Scott Geib held a CRISPR/microinjection workshop which began with a seminar describing the process of making heritable mutations using the CRISPR/Cas9 system andcontinued with a practical laboratory session in which we injected live embryo with guide RNA and Cas9 protein targetingseveral gene targets in Anastrepha ludens. The target audience of my project plan are state departments of agriculture as well as the USDA-APHIS who would be utilizing the the products of my research to protect American agrilculture by suppressing and eradicating invasive MexicanFruit Fly. American farmers will also benefit from this research as their crops would be free of fruit fly infestation and will not encounter barriers to export because of fruit flies. Changes/Problems:The biggest challenge of this project was generating an adequate genome assembly of my species of interest. This took longer than expected and ultimately limited the amount of data analysis I could accomplish. What opportunities for training and professional development has the project provided?The most impactful way this project has allowed me to develop professionally was that gave me the experience to be competitive for research scientist positions. In the last few months that I was funded by this grant, I was interviewed for three permanent positions and was offered all of them. I am now a Category 1 Research Biologist with the USDA-ARS and can continue to do work relavent to this project. How have the results been disseminated to communities of interest?My results have been disseminated in the form of peer-reviewed journal publications, presentations at meetings and symposiums, and as a training workshop at a collaborating USDA-APHIS facility. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Of these goals, I was able to identify SNP loci linked to the black pupae mutation in A. ludens through the creation of mapping populations and generating a high-quality draft genome assembly. The results of this research will be submitted for publication in this and the following fiscal year. In addition to the research accomplished in this and the previous reporting period, I was also able to contribute to the community and develop as a teacher and mentor by holding a CRISPR and microinjection workshop at a remote USDA-APHIS facility in Edinburg, TX. At this facility, a majority of the technical staff belong to a minority and underserved group, and due to its geographic location, there are few opportunities to gain this training and expertise. This grant as also led to my improvement as a scientist and a manager. Because of my independent funding, I had full control of my experiments and budget. This experience helped me gain confidence as a scientist and convinced me that I have the skills and knowledge necessary to do this work. Lastly, this grant also gave me the freedom to author and co-author 11 manuscripts over the two reporting periods of this grant.
Publications
|
Progress 02/15/17 to 02/14/18
Outputs
Target Audience:The target audience of my training/career development plan are the students of the University of Hawaii at Hilo and the University of Hawaii at Manoa. These two institutions are both minority serving institutions serving Alaska Native and Native Hawaiian and Asian Americans and Native American Pacific Islander students. At both the University of Hawaii at Hilo and the University of Hawaii at Manoa, the student body is largely composed of students who identify as female (60.7% and 67% repectively), students who fall into a minority group (76% and 75% respectively), and of those in a minority group, a large proportion are of Native Hawaiian descent (35.5% and 25% respectively). The target audience of my project plan are farmers who are affected by my study system, Anastrepha ludens, and the regulatory agency the USDA-APHIS whose charge it is to eradicate A. ludens from affected areas and maintain that the United States is free of certain fruit fly species. Changes/Problems:The biggest challenge of this project is developing a high-quality genome for the Anastrepha ludens genome as it is larger than previous genomes I have assembled in the past and thus may have more repetitive regions that are difficult to assemble, resulting in a less contiguous genome assembly than anticipated. What opportunities for training and professional development has the project provided?This project has provided me with training to perform microinjections and design experiments which utilize insect trangenic and targeted mutagenesis techniques. Additionally, I have been selected into a competitive program to receive peer-review training from editors at the Genetic Society of America (GSA) for the GSA journals Genetics and G3 for the purpose of developing my scientific writing and scientific peer-review skills. Lasty, I received training in the computing language Python which significantly improved my ability to do bioinformatic analysis of the genomic data generated in this project. How have the results been disseminated to communities of interest?The results of this project have been disseminated as journal articles in peer-reviewed journals such as G3, the Journal of Economic Entomology, Molecular Ecology Resources, and Biological Invasions. In addition, the results of this project have been presented at invited symposia at several conferences such as the Entomological Society of America annual meeting, at the annual Sequencing, Finishing, and Analysis in the Future meeting, at the phylogenetics course held at the University of Hawaii, Manoa, at the entomology course held at the University of Hawaii, Hilo, and the Third FAO-IAEA International Conference on Area-wide Management of Insect Pests: Integrating the Sterile Insect and Related Nuclear and Other Techniques. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, I will make the data generated from this project available at public data repositories, and I will continue to publish the results of the project in peer-reviewed journals and present the data in national and international conferences. Additionally, I will attend NIFA-sponsored Project Directors and Beneficiaries Meeting.
Impacts
What was accomplished under these goals?
To achieve the first goal of this project: Identify the causative mutation for black pupae in Anastrepha ludens, I have developed and genotyped mapping populations for Anastrepha ludens and generated a linkage map for A. ludens To achieve the second goal of this project: Characterize the translocation conferring sex-linkage of black pupae, I have performed linked-read sequencing of one A. ludens strains (Family-10 male) and generated a de novo assembly for this strain. To achieve the fourth goal of this project: develop as a teacher and mentor, I have performed guest lectures at two minority serving institutions, the University of Hawaii at Manoa and the University of Hawaii at Hilo, I have accepted applicants for undergraduate research, and I have mentored 6 undergraduate students from the University of Hawaii at Hilo, To achieve the fifth goal of this project: improve as a scientist and manager, I have Attended the insect genetic techniques training workshop through the Insect Genetic Techniques-Research CoordinationNetwork funded by the National Science Foundation, composed and submitted manuscripts describing findings for publication, attended and presenting my findings at the annual Entomological Society of America meeting in 2017, had my performance evaluated quarterly by Dr. Geib, and have held several meetings to communicate project findings and accomplishments.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
A New Diagnostic Resource for Ceratitis capitata Strain Identification Based on QTL Mapping
Sheina B. Sim, Raul Ruiz-Arce, Norman B. Barr and Scott M. Geib
G3: Genes, Genomes, Genetics November 1, 2017 vol. 7 no. 11 3637-3647; https://doi.org/10.1534/g3.117.300169
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae
Sheina B. Sim and Scott M. Geib
G3: Genes|Genomes|Genetics June 2017 7: 1927-1940; https://doi.org/10.1534/g3.117.040170
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Population genomics and comparisons of selective signatures in two invasions of melon fly, Bactrocera cucurbitae (Diptera: Tephritidae)
Julian R. Dupuis, Sheina B. Sim, Michael San Jose, Luc Leblanc, M. Aftab Hoassain, Daniel Rubinoff, Scott M. Geib
Biological Invasions November 2017 1-18; https://doi.org/10.1007/s10530-017-1621-z
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
mvmapper: Interactive spatial mapping of genetic structures
Dupuis JR, Bremer FT, Jombart T, Sim SB, Geib SM.
Mol Ecol Resour. 2017;00:16. https://doi.org/10.1111/1755-0998.12724
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Genetic Evidence for the Introduction of Rhagoletis pomonella (Diptera: Tephritidae) into the Northwestern United States
Sheina B Sim, Meredith M Doellman, Glen R Hood, Wee L Yee, Thomas H Q Powell, Dietmar Schwarz, Robert B Goughnour, Scott P Egan, Gilbert St Jean, James J Smith, Tracy E Arcella, Jason D K Dzurisin, and Jeffrey L Feder
|
|