Progress 01/01/08 to 12/31/12
Outputs
OUTPUTS: Two of the three Ph.D. fellows have graduated and held postdoctoral positions, one at Towson University, working in plant bioinformatics with USDA-ARS and KAUST in Saudi Arabia, and the other at the Woods Hole Oceanographic Institution, working on harmful algal blooms. The other student, which didn't have a Masters when enrolled in the DIMO program, continues in the program. Fellows received extensive academic and research training in the area of diseases of marine organisms through existing and newly developed (i.e. Research Ethics and Communication, Techniques in Sequencing, Marine Molecular Ecology) coursework that took advantage of the diverse set of expertise of the faculty and participation in specialized workshops such as the Virginia Bioinformatics Training Workshop and AquaVet II, a workshop that provides training in aquatic pathology. In order to supply fellows with a culturally diverse environment providing the foundation to succeed in a career addressing complex issues in sciences, we established collaborations with institutions in the United States, as well as with international groups in South Korea, Mexico, Philippines, and France. One of our laboratories hosted two visiting international graduate students for short stays to learn some of the techniques we have developed. Two of the fellows performed short stays in international labs, one in South Korea (through an NNF-sponsored International Research Travel Award) and another in France (funded by the Rhode Island Agricultural Experiment Station). Dissemination activities included news articles, several presentations at national and international meetings, and presentations at open houses. A research article published by one of our fellows received extensive news coverage, including MSNBC, Yahoo News, Scientific American, National Public Radio, The Living Ocean, and many others (even The Himalayan Times!). The 3 students received many awards, including several travel and outstanding presentation awards. One of the students was an invited speaker at the Society for General Microbiology (2011) and at the Phycological Society of America Advanced Genomics Workshop (2011). Fellows also interacted with stakeholders (i.e. shellfish and finfish industry, non-governmental organizations, state and federal managers) through annual socials and outreach symposiums like the SeaGrant Baird Symposium in Lobster Shell Disease. The students were also active participants in the university and scientific communities, with service contributions from participation in open houses to active duties in the URI Graduate Student Association and professional societies. Products of the program included: a) creation of new curriculum and international research experiences; b) building up international collaborations, as well as those with faculty at URI and at neighboring institutions; c) participation of fellows in national and international workshops and meetings; and d) development of a well attended workshop in Evolutionary Networks Analysis and Visualization that provided training in the novel bioinformatics analysis software developed by our program. PARTICIPANTS: The PI, Marta Gomez-Chiarri managed the project and directed the graduate program, coordinating recruitment and selection of students with the co-PIs, coordinating curriculum development and activities, and organizing social activities. She is also the major advisor of one of the NNF fellows. She contributed her expertise in shellfish pathology and comparative immunology, as well as growing expertise in genomics. The Co-PIs, David Rowley (Pharmacy/Natural Products, Proteomics), Bethany Jenkins (Microbiology/Ecology, Evolution, Genomics), and Tatiana Rynearson (Oceanography/Ecology, Genomics), were instrumental in recruitment and selection of fellows and new curriculum development (i.e. Techniques in Sequencing, Bioinformatics, Marine Molecular Ecology). Two newly recruited members in the program, Chris Lane (Biology/Evolution, Genomics) and Susanne Menden-Deuer (Oceanography/Ecology), were instrumental in the program by being major advisors of 2 of the DIMO fellows and contributing to curriculum development and training experiences (i.e. Research Ethics and Communication). Other faculty participating in the program included David Nelson (Microbiology/Microbial Genetics, Director of the Genomics and Sequencing Center), Dan Udwary (Pharmacy/Bioinformatics, Natural Products), and Mercedes Rivero-Hudec (Chemical Engineering/Modeling). Participants also included the 3 NNF DIMO fellows, Elizabeth Harvey, Ian Misner, and Pilar Nelson (nee Gibson), as well as a team of postdoctoral fellows (3) and graduate students (>10) in the participant laboratories. National collaborators outside URI included Erin Bromage (U Mass Dartmouth, Fish Immunology, coadvisor of Pilar Nelson). International collaborators included the laboratories of Eric Bapteste (Protistan Genomics, Bioinformatics, U. Marie Curie, Paris, France, use of networks for the genomic analysis of protest evolution), Hae Jin Jeong (Harmful Algal Blooms, Seoul National U, South Korea), and Ricardo Vazquez (Aquatic Pathology, Genomics, Bioinformatics, CIBNOR, La Paz, Mexico). TARGET AUDIENCES: The target audiences of the NNF DIMO graduate program are wide and varied, a reflection of the diversity of research interests of the NNF fellows and faculty. The program targets the following audiences: 1) graduate students interested in training in the area of Diseases of Marine Organisms; 2) researchers interested in the use of novel genomics and bioinformatics tools (network analysis and visualization) in their research; 3) researchers in the areas of aquatic pathology, comparative immunology, microbial genetics, ecology and evolution of marine protistans, harmful algal blooms, eutrophication and marine biogeochemistry, predator/prey interactions, natural products, probiotics, vaccines, etc); 3) the aquaculture and fishing industries; 4) local, state, regional, and national regulatory agencies responsible for the health of coastal communities and the marine environment; 5) non-governmental organizations concerned about the marine environment; and 4) the general public. Efforts to reach those audiences include: a) development of courses and workshops; b) establishment of national and international collaborations; c) attendance of fellows and PIs to national and international meetings; d) active participation of fellows in professional societies; e) participation of representatives from stakeholder groups in DIMO social activities and presentations; and f) participation of DIMO fellows in networking activities with stakeholder groups and the public (i.e. the SeaGrant Baird Symposium on Lobster Shell Disease, open houses, Discover@URI) PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Disease is one of the biggest challenges for aquaculture, the fastest growing sector of world agriculture. This program generated experts capable to addressing the complex scientific, social, and economical issues related to the management of infectious diseases in a rapidly growing aquaculture industry and that can apply the tools of genomics and bioinformatics to solving research problems in the area of diseases of marine organisms. The successful training of the fellows that graduated is demonstrated by their current employment in the areas of interest relevant to the National Needs Fellows program (plant genomics/bioinformatics, harmful algal blooms), as well as numerous awards, presentations at national and international meetings, and publications. Assessment of the program through exit interviews demonstrated that the two fellows that have graduated achieved the targets established at the initiation of the program, rating the confidence on their skills in their target specialization areas (genomics/evolution, ecology/oceanography) as excellent. The fellows also felt confident about the breadth of knowledge in areas outside their expertise and the ability to succeed in a career in research and/or academia. The two graduated fellows rated the program as excellent, and highly valued the diversity of activities offered as part of the program, in particular the International Research experience and the social activities. The fellows valued the diversity of the disciplines and approaches in the program (from genes to ecosystems). Suggestions for improvement related to further developing strategies geared to increasing cohesiveness in the program, and included requiring fellows to meet more often and develop one collaborative project during the program. The NNF-DIMO graduate program has helped in the recruitment of new faculty, led to the development of specialized new courses in the area of marine genomics, increased the exposure of URI in the area of marine genomics, and led to a surge in interest and applications to the various graduate programs involved. The NNF DIMO program has also significantly contributed and benefited from the newly funded Rhode Island NSF EPSCoR program, which has a research focus on the effects of climate change on marine communities, including effects on diseases or marine organisms. The NNF DIMO program has also contributed to the revision and strengthening of graduate programs in Biological and Environmental Sciences at URI, providing a model for specialized training, leading to the creation of new curriculum that emphasizes communication, and capitalizing on the cohort approach and the sharing of technical resources and common approaches.
Publications
- Misner I, Sommer K, Bailey JC, Lane CE. 2010. Evidence for a vestigial plastid in Saprolegnian Oomycetes. 18th Meeting of the International Society for Evolutionary Protistology, Kanazawa Japan. Travel award.
- Misner I, Lindsey H, Bailey JC, Lane C. 2010. Core photosynthetic genes in Saprolegnian oomycetes: evidence for a plastid Evolution 2010, Portland, Oregon.
- Nelson PJ, Grizzote M, Gomez-Chiarri M, Bromage E. 2013. Leukocyte recruitment to the peritoneum of cultured summer flounder (Paralichthys dentatus) during bacterial infection. (in preparation).
- Innis C, Davis D, Mandelman J, Gibson PJ, Charron K, Schumacher I, Murphy W, Weber ES. 2010. Hematologic Values of Captive Acadian Redfish (Sebastes fasciatus) Journal of Zoo and Wildlife Medicine 41(3):432-437.
- Nelson* PJ, Grizotte M, Bromage E. 2011. A Practical Tool for Characterizing Immunity in a Flatfish: Summer Flounder (Paralichthys dentatus) Immunoglobulin Monoclonal Antibody. Poster presented at the 2nd Annual Discovery@URI, Kingston, RI. *Pilar Gibson is now married; her new name is Pilar Nelson.
- Nelson* PJ, Grizotte M, Bromage E. 2011. A Practical Tool for Characterizing Immunity in a Flatfish: Summer Flounder (Paralichthys dentatus) Immunoglobulin Monoclonal Antibody. Presented at the 36th Annual Eastern Fish Health Workshop, Mt. Pleasant, SC.
- Harvey, E. L., S. Menden-Deuer, T. Rynearson. 2013. Intra-specific genetic and behavioral diversity in the toxic raphidophyte, Heterosigma akashiwo (in prep)
- Harvey, E.L., H. Jeong, S. Menden-Deuer. 2013. Chemical cues drive shifts in movement behaviors and influences the grazing interactions between heterotrophic protest predators and a HAB alga (in review, Limnology & Oceanography)
- Strom, S. L., E. L. Harvey, K. A. Fredrickson, S. Menden-Deuer. 2013. Broad halo-tolerance as a refuge from predation in the harmful raphidophyte alga, Heterosigma akashiwo. J. Phycol. 49: 20-31
- Harvey, E.L. and S. Menden-Deuer. 2012. Phytoplankton fleeing from predators: a new mechanism for harmful algal bloom formation PLoS ONE 7(9): e46438.
- Harvey EL. 2012. The Impact of Predator-Prey Relationships on the Formation of Harmful Algal Blooms in Heterosigma Akashiwo. Ph.D. Thesis, University of Rhode Island.
- Harvey, E. L. and S. Menden-Deuer. 2011. Avoidance, movement, and mortality: the interactions between a protistan grazer and Heterosigma akashiwo, a harmful algal bloom species. Limnol. & Oceanogr. 56(1): 371-378
- Harvey, E. L. and S. Menden-Deuer. 2012. Predator-prey interactions and salinity tolerance can impact harmful algal bloom formation in Heterosigma akashiwo. ASLO Ocean Sciences Meeting, Salt Lake, UT. Outstanding Student Presentation Award.
- Harvey, E.L. and S. Menden-Deuer. 2011. Bloom formation in Heterosigma akashiwo: role of predation and physiology. 6th USA HAB Meeting, Austin, TX
- Harvey, E.L. and S. Menden-Deuer. 2011. Understanding harmful algal blooms in the ocean: the impact of predator/prey interactions. Environmental Protection Agency - Northeast Division, Narragansett, RI (invited)
- Harvey, E. L. and S. Menden-Deuer. 2011. Understanding harmful algal blooms in the ocean: the impact of predator/prey interactions. Discovery@URI Graduate Student Conference, Kingston, RI
- Menden-Deuer S. and Harvey E. L. 2011. Linking microscopic plankton behaviors to large-scale ecological patterns and processes. ASLO Aquatic Sciences Meeting, San Juan.
- Menden-Deuer S., Harvey E. L., Day W., and J. Graff. 2011. Deciphering predator prey interactions in the plankton. Bio-Physical Meeting, Aspen, CO
- Harvey, E. L. and S. Menden-Deuer. 2010. Anti-predator defense mechanisms of the toxic raphidophyte alga, Heterosigma akashiwo against potential heterotrophic protist predators. 14th International HAB Meeting, Crete, Greece
- Harvey, E. L. and S. Menden-Deuer. 2010. The role of halo-tolerance in providing a refuge for the toxic raphidophyte alga, Heterosigma akashiwo from heterotrophic protists and enhancing bloom formation. Gordon Conference (Marine Microbes), Tilton, NH
- Menden-Deuer, S and E. L. Harvey. 2010. Avoidance, movement, and mortality: the role of predator-prey interactions in harmful algal bloom dynamics. Eastern Pacific Ocean Conference, Mt. Hood, OR
- Harvey, E.L., S. Strom, S. Menden-Deuer. 2010. Can the halo-tolerance of the toxic raphidophyte alga, Heterosigma akashiwo provide a refuge from microzooplankton predation ASLO Ocean Sciences Meeting, Portland, OR.
- Menden-Deuer, S., E. Harvey, K. Fredrickson, S. Graham, S. Strom. 2009. Predator impacts on the vertical distribution and population dynamics of the toxic raphidophyte, Heterosigma akashiwo. 5th USA HAB Meeting, Ocean Shores, WA
- Harvey, E. L. and S. Menden-Deuer. 2009. Distribution and swimming behaviors of heterotrophic protist predators in response to the toxic raphidophyte algal, Heterosigma akashiwo. ASLO Aquatic Sciences Meeting, Nice, France.
- Misner I, E Bapteste, S Halary, P Lopez, JC Bailey, C Lane. 2013. Genomes of saprophytic Thraustotheca clavata and parasitic Achlya hypogyna shed light on the pathogenicity of oomycetes. In prep.
- VanAlstyne K.L., E.L. Harvey, M. Cataldo, A. Salas, S. Gifford, A. Nicely, A. Gehman, L. Chomiczewski. 2009. The release of dopamine by Ulvaria obscura and its allelopathic effects on algae and invertebrate larvae. Plant Biology Meeting, Honolulu, HI
- Harvey E.L. 2008. Effects of the toxic alga Heterosigma akashiwo on the distribution of single-celled planktonic grazers. New England Estuarine Research Society, Block Island, RI.
- Misner I, Bicep, C, Lane C. 2013. Sequence Comparative Analysis using Networks (SCAN): software for evaluating de novo transcript assembly from next generation sequencing. Mol Bio Evol (in review).
- Misner I, L Haus, JC Bailey, C Lane. 2013. Novel HGT events in the oomycetes support green algal origin of chromalveolate plastid. In prep.
- Misner I, G Lenard, T Richards, C Lane. 2013. Characterizing the conserved secretome of oomycetes. In prep.
- Misner I. 2012. The Genome Sequences of Achlya Hypogyna and Thraustotheca Clavata: Insights on Oomycete Parasite Evolution. Ph.D. Thesis, University of Rhode Island.
- Misner I, P Lopez, E Bapteste, JC Bailey, C Lane. 2011. Using evolutionary gene networks to uncover HGT in pathogenic oomycetes. Society for General Microbiology August 2011. Invited Speaker.
- Misner I. Visualizing transcriptome data using networks. 2011. Phycological Society of America Advanced Genomics Workshop. July 2011. Invited Speaker.
- Misner I, P Lopez, E Bapteste, JC Bailey, C Lane. 2011. Utilizing Evolutionary Gene Networks to Uncover Genomic Consequences of Adopting a Parasitic Lifestyle. Phycological Society of America Meeting. July 2011. Hoshaw Travel Award.
- Misner I, P Lopez, E Bapteste, JC Bailey, C Lane. 2011. Understanding oomycete gene evolution using evolutionary gene networks. Oomycete Molecular Genetics Network March 2011.
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: The three Ph.D. fellows in the DIMO program, including one minority fellow, show consistent progress and continue to showcase the strengths of the DIMO training program through high quality presentations at meetings, awards received, and publications in preparation. Two students have successfully passed the comprehensive examination and are graduating in 2012, resulting in a completion time for a doctoral degree of 4 years. The other student, which didn't have a Masters when enrolled in the DIMO program, has finished with the required coursework and shows solid progress in her research. In year 4 of the NNF DIMO program, fellows focused on their research and in completing training through participation in national and international workshops and international research travel experiences. One of our fellows continued to improve his skills in analysis of next generation sequencing data, receiving a trainee travel award to attend the Virginia Bioinformatics Training Workshop in May 2011 and participating in the development of a new tool to analyze genomic data using novel networks. A second fellow participated in an oceanographic research cruise. The third fellow received specialized training in the Comparative Pathology of Aquatic Animals through participation in the prestigious program AquaVet II in May 2011. In order to supply DIMO Fellows with a culturally diverse and supportive environment that provides the foundation to succeed in a career addressing complex issues in the area of diseases of marine organisms (objective 3), we continued our collaborations with international groups in South Korea, Mexico, Philippines, and France. One of our laboratories hosted two visiting international graduate students for short stays, one from Mexico and another from the Philippines, to learn some of the aquatic pathology, immunology, and genomics analysis techniques we have developed. One of the DIMO fellows performed a NNF-sponsored IRTA in South Korea during the summer of 2011. Dissemination activities include the DIMO website, several presentations at national and international meetings, and presentations at two open houses. The 3 students were encouraged to apply for travel and other awards, receiving a total of 5 awards in 2011, including a NNF International Research Travel Award. One of the students was an invited speaker at the Society for General Microbiology meeting in August 2011 and at the Phycological Society of America Advanced Genomics Workshop in July 2011. The students were also active participants in the university community, with service contributions from participation in open houses to active duties in the URI Graduate Student Association and professional societies. Products of the program in 2011 include: a) creation of new curriculum and international research experiences; b) building up international collaborations, as well as those with faculty at URI and at neighboring institutions, like the Center for Computer Science at Brown University and the Rhode Island School for Design; c) participation of fellows in national and international workshops and meetings in Aquatic Pathology and Evolutionary Genomics. PARTICIPANTS: The PI, Marta Gomez-Chiarri managed the project and directed the graduate program, coordinating recruitment and selection of students with the co-PIs, coordinating curriculum development and activities, and organizing social activities. She is also the major advisor of one of the NNF fellows. She contributed her expertise in shellfish pathology and comparative immunology, as well as growing expertise in genomics. The Co-PIs, David Rowley (Pharmacy/Natural Products, Proteomics), Bethany Jenkins (Microbiology/Ecology, Evolution, Genomics), and Tatiana Rynearson (Oceanography/Ecology, Genomics), were instrumental in selection of fellows and new curriculum development (i.e. Techniques in Sequencing, Bioinformatics, Molecular Ecology). Two newly recruited members in the program, Chris Lane (Biology/Evolution, Genomics) and Susanne Menden-Deuer (Oceanography/Ecology), were instrumental in the program by being major advisors of 2 of the DIMO fellows and contributing to curriculum development and training experiences (i.e. Research Ethics and Communication). Other faculty participating in the program included David Nelson (Microbiology/Microbial Genetics, Director of the Genomics and Sequencing Center), Dan Udwary (Pharmacy/Bioinformatics, Natural Products), and Mercedes Rivero-Hudec (Chemical Engineering/Modeling). Participants also included the 3 NNF DIMO fellows, Liz Harvey, Ian Misner, and Pilar Nelson, as well as a team of postdoctoral fellows (3) and graduate students (>10) in the participant laboratories. National collaborators outside URI included Erin Bromage (U Mass Dartmouth, Fish Immunology, coadvisor of Pilar Nelson). International collaborators included the laboratories of Eric Bapteste (Protistan Genomics, Bioinformatics, U. Marie Curie, Paris, France, use of networks for the genomic analysis of protest evolution), Hae Jin Jeong (Harmful Algal Blooms, Seoul National U, South Korea), and Ricardo Vazquez (Aquatic Pathology, Genomics, Bioinformatics, CIBNOR, La Paz, Mexico). TARGET AUDIENCES: The target audiences of the NNF DIMO graduate program are wide and varied, a reflection of the diversity of research interests of the NNF fellows and faculty. The program targets the following audiences: 1) graduate students interested in training in the area of Diseases of Marine Organisms; 2) researchers interested in the use of novel genomics and bioinformatics tools (network analysis and visualization) in their research; 3) researchers in the areas of aquatic pathology, comparative immunology, microbial genetics, ecology and evolution of marine protistans, harmful algal blooms, eutrophication and marine biogeochemistry, predator/prey interactions, natural products, probiotics, vaccines, etc); 3) the aquaculture and fishing industries; 4) local, state, regional, and national regulatory agencies responsible for the health of coastal communities and the marine environment; 5) non-governmental organizations concerned about the marine environment; and 4) the general public. Efforts to reach those audiences include: a) development of courses and workshops; b) establishment of national and international collaborations; c) attendance of fellows and PIs to national and international meetings; d) active participation of fellows in professional societies; e) participation of representatives from stakeholder groups in DIMO social activities and presentations; and f) participation of DIMO fellows in networking activities with stakeholder groups and the public (i.e. the SeaGrant Baird Symposium on Lobster Shell Disease, open houses, Discover@URI) PROJECT MODIFICATIONS: No major changes are reported.
Impacts
Disease is one of the biggest challenges for aquaculture, the fastest growing sector of world agriculture. This program is in the process of generating experts capable to addressing the complex scientific, social, and economical issues related to the management of infectious diseases in a rapidly growing aquaculture industry and that can apply the tools of genomics, bioinformatics, and proteomics to solving research problems in the area of diseases of marine organisms. The NNF-DIMO graduate program has helped in the recruitment of new faculty, led to the development of specialized new courses in the area of marine genomics, increased the exposure of URI in the area of marine genomics, and led to a surge in interest and applications to the various graduate programs involved. The NNF DIMO program has also significantly contributed and benefited from the newly funded Rhode Island NSF EPSCoR program, which has a research focus on the effects of climate change on marine communities, including effects on diseases or marine organisms. This program has also contributed to the revision and strengthening of graduate programs in Biological and Environmental Sciences at URI, providing a model for specialized training, leading to the creation of new curriculum that emphasizes communication, and capitalizing on the cohort approach and the sharing of technical resources and common approaches.
Publications
- Harvey EL*, Menden-Deuer S. 2011. Avoidance, movement, and mortality: the interactions between a protistan grazer and Heterosigma akashiwo, a harmful algal bloom species. Limnology &Oceanography. 56(1): 371-378.
- Harvey, EL*, Menden-Deuer S. 2012. In review. Avoidance of a protistan predator by the toxic phytoplankter, Heterosigma akashiwo (Raphidophyceae). Submitted to PNAS.
- Misner I*, P Lopez, E Bapteste, JC Bailey, C Lane. 2011. Using evolutionary gene networks to uncover HGT in pathogenic oomycetes. Society for General Microbiology August 2011. Invited Speaker.
- Misner I*. Visualizing transcriptome data using networks. 2011. Phycological Society of America Advanced Genomics Workshop. July 2011. Invited Speaker.
- Misner I*, P Lopez, E Bapteste, JC Bailey, C Lane. 2011. Utilizing Evolutionary Gene Networks to Uncover Genomic Consequences of Adopting a Parasitic Lifestyle. Phycological Society of America Meeting. July 2011. Hoshaw Travel Award.
- Misner I*, P Lopez, E Bapteste, JC Bailey, C Lane. 2011. Understanding oomycete gene evolution using evolutionary gene networks. Oomycete Molecular Genetics Network March 2011.
- Nelson PJ*, Grizotte M, Bromage E. 2011. A Practical Tool for Characterizing Immunity in a Flatfish: Summer Flounder (Paralichthys dentatus) Immunoglobulin Monoclonal Antibody. Poster presented at the 2nd Annual Discovery@URI, Kingston, RI.
- Nelson PJ*, Grizotte M, Bromage E. 2011. A Practical Tool for Characterizing Immunity in a Flatfish: Summer Flounder (Paralichthys dentatus) Immunoglobulin Monoclonal Antibody. Presented at the 36th Annual Eastern Fish Health Workshop, Mt. Pleasant, SC.
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Progress 01/01/10 to 12/31/10
Outputs
The three fellows in the DIMO program, including one minority fellow, continue to show excellent progress. One student has successfully passed the comprehensive examination. The other two students will be finished with coursework at the end of Spring 2011 and will take the comprehensive examination next academic year. In year 3 of the DIMO program, we continued our focus on the training of DIMO Fellows in using a combination of traditional and modern tools (genomics, bioinformatics, proteomics) and an integrated, collaborative approach to solve research problems in the area of diseases of marine organisms (objective 2). A new course, Special Topics in Genome Biology, was developed by DIMO faculty and was highly subscribed by both faculty (6) and students (18), resulting in new collaborations and a White Paper outlining needs, challenges and opportunities in the area of Genomics at URI, with a special emphasis in Marine Genomics. We have established collaborations with bioinformaticists at Brown University and designers at the Rhode Island School of Design, which led to our participation in the Innovation Studios, a platform for developing new ways to visualize complex scientific datasets. One of our fellows has been involved in the development of a new tool to analyze genomic data using novel networks, participated in the Skate Genome Annotation workshop, and chaired a session at the Evolution 2010 meetings in Portland, Oregon. In order to supply DIMO Fellows with a culturally diverse and supportive environment that provides the foundation to succeed in a career addressing complex issues in the area of diseases of marine organisms (objective 3), we continue our collaborations with international groups in South Korea, Mexico, and Europe, leading to increased opportunities for student exchange. A student from South Korea performed a one year stay at URI, and one of the DIMO fellows will be performing a NNF-sponsored IRTA in South Korea during the summer of 2011. The students have attended and presented at international and national meetings. DIMO fellows also helped in the organization of the Baird Symposium in Lobster Shell Disease, held in the summer of 2010 at URI. This Symposium provided opportunities to interact with scientists, members of the fishing industry, and government management agencies, and provided a great example on how science and management interact. The students were encouraged to apply for travel and other awards, and they all received at least one competitive award in 2010, such as the Ada L. Sawyer Award for Oceanography, University of Rhode Island and a URI Graduate Research Grant. PRODUCTS: Products of the program include: a) a White Paper on "Genome Biology URI Research Needs"; b) creation of new curriculum and international research experiences; and c) building up international collaborations, as well as those with faculty at URI and at neighboring institutions, like the Center for Computer Science at Brown University and the Rhode Island School for Design; d) participation of fellows in the Baird Symposium in Lobster Shell Disease and in the Skate Genome Annotation Workshop. OUTCOMES: The NNF-DIMO program has helped in the recruitment of new faculty, led to the development of specialized new courses in the area of marine genomics, increased the exposure of URI in the area of marine genomics, and led to a surge in interest and applications to the various graduate programs involved. DISSEMINATION ACTIVITIES: Dissemination activities include the DIMO website, several presentations at national and international meetings, and a white paper on "Genome Biology URI Research Needs". FUTURE INITIATIVES: We are still in the process of organizing a Workshop in Marine Genomics that will bring experts in the area for an intensive week of lectures and laboratory training for our students and faculty. We are also establishing contacts for stays of two more fellows in laboratories abroad for an international experience.
Impacts
Disease is one of the biggest challenges for aquaculture, the fastest growing sector of world agriculture. This program will generate experts capable to addressing the complex scientific, social, and economical issues related to the management of infectious diseases in a rapidly growing aquaculture industry and that can apply the tools of genomics, bioinformatics, and proteomics to solving research problems in the area of diseases of marine organisms.
Publications
- Harvey EL*, Menden-Deuer S. 2010. The role of halo-tolerance in providing a refuge for the toxic raphidophyte alga, Heterosigma akashiwo from heterotrophic protists and enhancing bloom formation. Marine Microbes, Gordon Conference, Tilton, New Hampshire.
- Harvey EL*, Menden-Deuer S. 2011. Avoidance, movement, and mortality: the interactions between a protistan grazer and Heterosigma akashiwo, a harmful algal bloom species. Limnology & Oceanography. 56(1): 371-378.
- Harvey EL*. Menden-Deuer S. 2010. Anti-predator defense mechanisms of the toxic raphidophyte alga, Heterosigma akashiwo against potential heterotrophic protist predators. 14th International Harmful Algal Bloom Meeting, Crete, Greece. Travel award.
- Harvey EL, Strom S, Menden-Deuer S. 2010. Can the halo-tolerance of the toxic raphidophyte alga, Heterosigma akashiwo provide a refuge from microzooplankton predation Ocean Sciences, Portland, Oregon.
- Innis C, Davis D, Mandelman J, Gibson P*, Charron K, Schumacher I, Murphy W, Weber ES. 2010. Hematologic Values of Captive Acadian Redfish (Sebastes fasciatus) Journal of Zoo and Wildlife Medicine 41(3):432-437.
- Menden-Deuer S, Harvey EL*. 2010. Avoidance, movement, and mortality: the role of predator-prey interactions in harmful algal bloom dynamics. Eastern Pacific Ocean Conference, Mt. Hood, Oregon.
- Misner I*, Sommer K, Bailey JC, Lane CE. 2010. Evidence for a vestigial plastid in Saprolegnian Oomycetes. 18th Meeting of the International Society for Evolutionary Protistology - Kanazawa Japan. Travel award.
- Misner I* Lindsey H, Bailey JC, Lane C. 2010. Core photosynthetic genes in Saprolegnian oomycetes: evidence for a plastid Evolution 2010, Portland, Oregon.
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Progress 01/01/09 to 12/31/09
Outputs
The three fellows in the program, including one minority fellow, showed excellent progress in their programs of study and are in the process of finishing with course requirements. In year 2 of this program, we have focused on the training of DIMO Fellows in using a combination of traditional and modern tools (genomics, bioinformatics, proteomics) and an integrated, collaborative approach to solve research problems in the area (objective 2). In our second annual meeting, fellows were satisfied with the program and considered they had fulfilled most of the goals they had set for the year. The capstone course in the program, Diseases of Marine Organisms, was offered in the fall of 2009. As part of this course, DIMO fellows and other students in the Aquatic Pathology and Fisheries graduate program prepared a draft of a review manuscript showcasing different examples on the application of genomics to answer key questions the field of Aquatic Animal Health. This manuscript is being revised by the major advisors and will be submitted for publication in a peer-reviewed journal in the field of aquaculture. Recent faculty hires in the areas of Marine Genomics have developed several new graduate courses, including Symbiosis, Marine Molecular Ecology, Advanced Molecular Sequencing, and Special Topics in Genome Biology. In the process of the class discussions, journal clubs, and several other opportunities in which all program participants met, the fellows and faculty identified a few challenges to their research and gaps in their training, leading to a proposal to develop a Workshop in Marine Genomics for fall 2010, geared to bring to URI experts in the areas of functional genomics, bioinformatics, and data analysis and visualization. In order to supply DIMO Fellows with a culturally diverse and supportive environment that provides the foundation to succeed in a career addressing complex issues in the area of diseases of marine organisms (objective 3), several recognized international and national experts in the fields of evolution, genomics, ecology, and animal health have come to URI to give seminars, some of them as part of a seminar series organized to celebrate the 200th anniversary of Darwin's birth. These include Dr. Lavilla-Pitogo, a Fullbright Fellow from the Philippines and specialist in aquatic animal health, Dr. Erin Bromage (fish adaptive immunology), Dr. Mike Bell (stickleback evolution - parasites), Dr. McFall-Ngai (squid-vibrio symbiosis), and Dr. Debashish Bhattacharya (genomic approaches to red tides). These seminars have offered students invaluable networking opportunities and led to the establishment of an ongoing collaboration of one of the fellows with Dr. Bromage. The students have attended and presented at international and national meetings, some of which provided opportunities to interact with members of the aquaculture industry and government management agencies. PRODUCTS: Products of the program include: a) the NNF DIMO web site (http://cels.uri.edu/dimo), emphasizing the critical needs and great opportunities in the field of diseases of marine organisms, the research areas targeted in the program, the breath and depth of the marine programs at URI, and the wide variety of resources available to the Fellows; b) a review manuscript by fellows and faculty on the Applications of Genomics to Aquatic Animal Health, in preparation; c) creation of new curriculum and research experiences, including plans for a Marine Genomics Workshop; and d) several new collaborations with faculty at URI at neighboring institutions, some of them leading to successfully funded research proposals. OUTCOMES: This program has helped in the recruitment of new faculty, led to the development of specialized new courses in the area of marine genomics, increased the exposure of URI in the area of marine genomics, and led to a surge in interest and applications to the various graduate programs involved. DISSEMINATION ACTIVITIES: These included the DIMO web site, a press release to local media on the NNF-DIMO program, participation in the 2009 NNF-MSP meeting, with the poster of one of our fellows being showcased at the NNF site, as well as participation of fellows and faculty in several national and international scientific meetings. FUTURE INITIATIVES: We are in the process of organizing a Workshop in Marine Genomics that will bring experts in the area for an intensive week of lectures and laboratory training for our students and faculty. Students will also participate in a Symposium on Lobster Shell Disease to be held at URI during the summer of 2010, and which will provide further opportunities to educate DIMO Fellows in the implications and relevance of their research for the management of infectious diseases in the marine environment. Fellows will also participate in an outreach project that will allow fellows to interact with other graduate students in programs with emphasis in management of the coastal environment and policy, as well as with industry, governmental partners and other stakeholders. We are also establishing contacts for stays of the fellows in laboratories abroad for an international experience.
Impacts
Disease is one of the biggest challenges for aquaculture, the fastest growing sector of world agriculture. This program will generate experts capable to addressing the complex scientific, social, and economical issues related to the management of infectious diseases in a rapidly growing aquaculture industry and that can apply the tools of genomics, bioinformatics, and proteomics to solving research problems in the area of diseases of marine organisms.
Publications
- Gomez-Chiarri M. 2009. National Needs Graduate Program in Diseases of Marine Organisms. NNF-MSP National Needs Fellowship/Multicultural Scholars ProgramProject Directors and Beneficiaries Meeting, Washington DC (oral presentation) http://www.caes.uga.edu/unit/diversity/events/documents/MartaGomez-Ch iari.pdf
- Harvey, E.L., Strom S., Menden-Deuer, S. 2010. Can the halo-tolerance of the toxic raphidophyte alga, Heterosigma akashiwo provide a refuge from microzooplankton predation Ocean Sciences, Portland, OR (poster)
- Harvey, E.L. and Menden-Deuer, S. 2009. Distribution and swimming behaviors of heterotrophic protist predators in response to the toxic raphidophyte algal, Heterosigma akashiwo. Advancing the Science of Limnology and Oceanography, Nice, France.
- Menden-Deuer, S., Harvey, E., Fredrickson, K., Graham, S., Strom S. 2009. Predator impacts on the vertical distribution and population dynamics of the toxic raphidophyte, Heterosigma akashiwo. USA Harmful Algal Bloom Meeting, Washington DC (poster)
- Misner I, Sommer K, Bailey C, Lane CE. 2009. Is there a relic plastid in oomycetes 48th Annual NorthEast Algal Symposium (NEAS) Amherst, Massachusetts (poster)
- Misner I, Sommer K, Bailey C, Lane CE. 2009. Evidence for a photosynthetic ancestry of the oomycetes sensu lato. Society for Molecular Biology and Evolution, Iowa City. 2009.
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Progress 01/01/08 to 12/31/08
Outputs
The goal of this project is to train three doctoral students in an integrated, collaborative, multidisciplinary approach to solve research questions in the area of diseases of marine organisms. This program addresses the critical need for students that know how to apply genomics/proteomics and bioinformatics to identify the molecular and ecological mechanisms of disease in the marine environment and to use that knowledge to design novel, effective, economical, and safe prevention tools, therapeutants, and management strategies. The objectives of this proposal include the: 1) Recruitment and selection of a cohort of culturally and ethnically diverse graduate students interested in different aspects of the area of diseases of marine organisms, capable of understanding the complexity of the field, and willing to take an integrative, multidisciplinary, collaborative approach; 2) Training of DIMO Fellows in using a combination of traditional and modern tools (genomics, bioinformatics, proteomics) and an integrated, collaborative approach to solve research problems in the area; 3) Supplying DIMO Fellows with a culturally diverse and supportive environment that provides the foundation to succeed in a career addressing complex issues in the area of diseases of marine organisms; and 4) Educating DIMO Fellows in the implications and relevance of their research for the management of infectious diseases in aquaculture, as well as train students to effectively communicate with a diversity of audiences that includes scientists, decision-makers, business professionals, and citizens. We have fulfilled our goals for the first year of the project by successfully recruiting and appointing three Ph.D. fellows in the program, one in the Spring of 2008 and two in the Spring of 2009. This is an ethnically and culturally diverse set of students, including a student with expertise in ecology, another with expertise in parasite evolution, and a third one with expertise in aquatic pathology and job experience in the aquarium industry. We have also enlisted two new faculty in the program, Dr. Chris Lane, a new hire in the area of Marine Genomics with expertise in the evolution of protists, and Dr. Susanna Menden-Deuer, a new hire in Oceanography with expertise in ecology and modeling. Students have chosen their major advisors and started working on their research projects. We are now in the process of fulfilling the rest of our goals, by developing a solid curriculum and rich and diverse training experiences for our fellows. PRODUCTS: For our recruitment efforts, we have prepared web materials (http://cels.uri.edu/dimo) emphasizing the critical needs and great opportunities in the field of diseases of marine organisms, the research areas targeted in the program, the breath and depth of the marine programs at URI, and the wide variety of resources available to the Fellows. The fellows are actively participating in the design of content to be included in the website. During our first DIMO Orientation and Social, the students met the faculty, students, and staff in the program. We discussed expectations from faculty and students in the program and filled a survey that will be used in the future in assessment of the program. The Orientation was evaluated and considered a success by students and faculty. We have developed curriculum and research experiences that provide disciplinary depth in one of the targeted areas (ecology and evolution of host-pathogen interactions, mechanisms of pathogen virulence and survival, and management of infectious diseases in the marine environment), as well as interdisciplinary breath. Spring 2009 offerings include a course in Symbiosis with a molecular emphasis offered by our new hire in Marine Genomics, as well as Molecular Marine Ecology, Writing for the Life Sciences, and a Journal Club in Diseases of Marine Organisms. We have also established a seminar series and invited worldwide experts in diseases of marine organisms, with 2 seminars offered in the Spring 09 semester. The program has already attracted international attention, leading to the establishment of international links with groups in Chile, Mexico, Korea, and the Philippines that will provide the basis for an international experience for students in the DIMO program. Dr. Lavilla-Pitogo, a Fullbright Fellow from the Philippines, will be visiting URI in April 2009 and meeting with the fellows. Dr. Park, a professor expert in fish diseases from Korea, will be spending his sabbatical at URI starting in September 09 and collaborating with one of the fellows. OUTCOMES: Curriculum and research training experiences emphasized the strength of a multidisciplinary approach by encouraging the participation of faculty with expertise in the areas of genomics, oceanography, pathology, immunology, ecology, evolution, modeling, and medicinal chemistry in the advisory committees and the journal clubs. Additional elements of the program included a strong emphasis on mentoring, an international experience, workshops and seminars in career development, scientific writing, communication to the public, diversity issues, research ethics, and leadership, and an outreach project that will allow fellows to interact with other graduate students in programs with emphasis in management of the coastal environment and policy, as well as with industry, governmental partners and other stakeholders. DISSEMINATION ACTIVITIES: As an assignment in a writing class, one if the DIMO fellows is preparing content on the program that will be posted in the DIMO website. During this period, one of the students presented her work at the American Society of Limnology and Oceanography (ASLO) meeting (Fall 08), and another will be participating in the Eastern Fish Health Workshop (Spring 09). FUTURE INITIATIVES: With funding from Rhode Island NSF EPSCoR, we are in the process of organizing a Workshop in Marine Genomics that will bring experts in the area for an intensive week of lectures and laboratory training for our students and faculty. We are also organizing an intensive one-week course in Leadership in the Environmental Sciences that will be delivered by faculty in philosophy and communication.
Impacts
Disease is one of the biggest challenges for aquaculture, the fastest growing sector of world agriculture. This program will generate experts capable to addressing the complex scientific, social, and economical issues related to the management of infectious diseases in a rapidly growing aquaculture industry and that can apply the tools of genomics, bioinformatics, and proteomics to solving research problems in the area of diseases of marine organisms.
Publications
- No publications reported this period
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