Progress 10/01/12 to 09/30/15
Outputs
Target Audience:This grant is a student training grant and supported a graduate student during his PhD studies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Chris attended the EuPathDB workshop in Georgia, which has been critical to developing his skills in identifying gene families involved in parasitism. How have the results been disseminated to communities of interest?Chris gave a talk at the EuPathDB workshop as well as a local meeting focused on protists. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Graduate student, Chris Paight, was financially supported during this proposal in his training in evolutionary genomic methods. He has made substantial progress in his studies and is well versed in a variety of bioinformatic methods. Chris is currently working on two papers, which will be submited this summer.
Publications
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Progress 10/01/13 to 09/30/14
Outputs
Target Audience: Oomycete infections of crop plants and ornamentals cause blights, wilts, cankers, rusts, lesions and/or (root) rots whereas infestations in shellfish and finfish facilities can result in the loss of over 50% of high value brood stocks. As a lineage, oomycetes are a significant threat to U.S. National food security and cost agriculture and aquaculture industries billions in losses on an annual basis. This project will fund graduate students to perform a comparative genomic analysis of related free living and pathogenic oomycetes to identify genomic changes related to becoming pathogenic. Understanding the evolution of pathogenicity factors is an important step in developing treatment strategies for oomycete infections. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Supported graduate student Paight will be attending the EUpath workshop in George in the final reporting period to expand his methodological toolbox. Supported graduate student Salomaki attended the Bioinformatics workshop at the Roscoff Marine Station, Roscoff, France, during this reporting period. How have the results been disseminated to communities of interest? Both students Paight and Salomaki have attended national and international meetings, presenting at both. In the final reporting period they will do the same and add new publications to the dissemination. What do you plan to do during the next reporting period to accomplish the goals? The final genome analysis for our two oomycetes are underway and should be published in the final reporting period. Supported students will continue to expand their bioinformatic skills in both formal and informal settings.
Impacts
What was accomplished under these goals?
A program was developed using evolutionary gene networks and published during this reporting period (Misner et al 2013). Students trained with NIFA support continue to identify novel uses for this method, which will be published in the final reporting period. Supported students have continued to make progress in both their training and research. Two additional papers have already been published in the final reporting period that will be cited in the final report. At least three more are anticipated, including the full genomes of our two oomycetes of interest.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Misner*, I., C. Bicep, P. Lopez, S. Halary, E. Bapteste & C. E. Lane 2013. Sequence Comparative Analysis using Netowrks (SCAN): software for evaluating de novo transcript assembly from next generation sequencing. Molecular Biology and Evolution. 30(8):19751986.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
OBrien, M, I. Misner, C. E. Lane 2013. Mitochondrial genome sequences and
comparative genomics of Achlya hypogyna and Thraustotheca clavata. Journal of
Eukaryotic Microbiology 61: 146-154.
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Progress 10/01/12 to 09/30/13
Outputs
Target Audience: This support is for the salary and tuition for a graduate student. The student in question has been hired and has completed the expected requirements during this reporting period. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? The student has taken class in the computer science department and a new class in the CMB department to improve their analytical skills. How have the results been disseminated to communities of interest? Preliminary analysis of these data will be presented at the International Society for Evolutionary Protistology, in Banff, Alberta in August 2014. What do you plan to do during the next reporting period to accomplish the goals? The genome of the parasite will be sequenced and comparatively analyzed by the supported graduate student for his dissertation research. We anticipate writing a manuscript in the late part of 2014.
Impacts
What was accomplished under these goals?
The hired graduate student is in the process ofanalyzingnewly created sequence data that was produced during this reporting period. Currently we are analyzing the host genome and the parasite genome is being isolated for sequencing. The student has made significant progress in his programming and Unix command line skills in order to take on this challenging task.
Publications
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