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Award Detail

Awardee:UNIVERSITY OF HAWAII SYSTEMS
Doing Business As Name:University of Hawaii
PD/PI:
  • Petra H Lenz
  • (808) 956-8003
  • petra@pbrc.hawaii.edu
Award Date:07/15/2010
Estimated Total Award Amount: $ 213,960
Funds Obligated to Date: $ 213,960
  • FY 2010=$213,960
Start Date:07/15/2010
End Date:06/30/2014
Transaction Type:Grant
Agency:NSF
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.050
Primary Program Source:040100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:EAGER: Application of transcriptomics to investigate organism-environment relationships in marine zooplankton
Federal Award ID Number:1040597
DUNS ID:965088057
Parent DUNS ID:009438664
Program:BIOLOGICAL OCEANOGRAPHY

Awardee Location

Street:2440 Campus Road, Box 368
City:Honolulu
State:HI
ZIP:96822-2234
County:Honolulu
Country:US
Awardee Cong. District:01

Primary Place of Performance

Organization Name:University of Hawaii
Street:2440 Campus Road, Box 368
City:Honolulu
State:HI
ZIP:96822-2234
County:Honolulu
Country:US
Cong. District:01

Abstract at Time of Award

Intellectual Merit: This project will develop transcriptomics approaches to investigate gene regulation as a function of environmental cycles and in response to experimental manipulation. Currently, there are few tools to establish physiological state of marine zooplankton, in particular for oceanic species. Molecular approaches based on quantifying the transcriptome could serve as powerful tools to obtain a physiological profile for individuals and groups of individuals collected in the field. In combination with laboratory experiments, transcriptome analysis will provide a new approach to understanding organism-environment interactions in the pelagic zone. The PI will focus on a model planktonic crustacean, Calanus finmarchicus, to develop the molecular tools. C. finmarchicus, a calanoid copepod, is highly abundant in the North Atlantic, with populations extending from the Gulf of Maine and Labrador Sea to the North Sea. Pyrosequencing and microarray technologies will be used to develop a diagnostic tool to determine physiological state in C. finmarchicus. The goal of having a measurement of physiological state is to determine if individuals in the population are growing, are synthesizing or catabolizing storage lipids, and are metabolically active and/or experiencing environmental stress. Specific objectives of this project include: 1. High throughput sequencing of C. finmarchicus transcriptome from pre-adult (copepodid stage V [CV]) individuals representing distinct phases of the annual cycle (late spring-early summer, early fall, diapausing individuals). 2. Analysis of the sequence data for discovery of seasonally regulated genes for the development of an ecologically relevant microarray. Probes for this microarray will include seasonally regulated genes, genes involved in the environmental stress response and control genes. 3. Preliminary testing of microarray on existing samples collected from the Gulf of Maine and stored in liquid nitrogen, as well as on experimentally manipulated animals. Broader Impacts: 1) Training of graduate and undergraduate students in these techniques will occur. At least two graduate students in Marine Sciences/Biological Oceanography will participate in the project and be trained in transcriptomics at the bench and in bioinformatics. Undergraduate students will participate in the project at the Mount Desert Island Biological Laboratory through the NSF REU-site funding. Undergraduate training will be interdisciplinary and include both biological oceanography and molecular biology techniques. 2) Results and sequences obtained in this study will be contributed to databanks and made available to the general public. Sequences will be analyzed using clustering tools and annotated using gene ontology software, followed by sequence submission to the National Center for Biotechnology Information (NCBI) database. Gene sequence data for copepods in general are still sparse, and the planned submission will increase information available for calanoid copepods by ten-fold or more.

Publications Produced as a Result of this Research

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Christie, A.E., Roncalli, V., Batta Lona, P., McCoole, M.D., King, B.L., Bucklin, A., Hartline, D.K. and Lenz, P.H. "In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda)" Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, v.8, 2012, p.45-57. doi:dx.doi.org/10.1016/j.cbd.2012.11.002 

Unal, E., Bucklin, A., Lenz, P.H., Towle, D.W. "Gene expression of the marine copepod Calanus finmarchicus: responses to small-scale environmental variation in the Gulf of Maine (NW Atlantic Ocean)" Journal of experimental marine biology and ecology, v.446, 2013, p.76-85. doi:dx.doi.org/10.1016/j.jembe.2013.04.020 

Christie, A.E., Fontanilla, T.M., Nesbit, K.T., Lenz, P.H. "Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome" Comparative Biochemistry and Physiology, Part D, v.8, 2013, p.165-193. doi:dx.doi.org/10.1016/j.cbd.2013.04.002 

Christie, A. E., T. M. Fontanilla, V. Roncalli, M. C. Cieslak, and P. H. Lenz "Diffusible gas transmitter signaling in the copepod crustacean Calanus finmarchicus: Identification of the biosynthetic enzymes of nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) using a de novo assembled transcriptome" General & Comparative Endocrinology, v.202, 2014, p.76.

Lenz, P.H., Unal, E., Hassett, R.P., Smith, C.M., Bucklin, A., Christie, A.E. and Towle, D.W. "Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray" Comparative Biochemistry Physiology D Genomics and Proteomics, v.7, 2012, p.110. doi:10.1016/j.bbr.2011.03.031 

Lenz, P.H., Unal, E., Hassett, R.P., Smith, C.M., Bucklin, A., Christie, A.E. and Towle, D.W. "Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray" Comparative Biochemistry Physiology D Genomics and Proteomics, v.7, 2012, p.110. doi:10.1016/j.bbr.2011.03.031 

Christie, A. E., T. M. Fontanilla, V. Roncalli, M. C. Cieslak, and P. H. Lenz "Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus." General & Comparative Endocrinology, v.195, 2014, p.28.

Christie, A.E., Roncalli, V., Wu, L.-S., Garrote, C.L., Doak, T. and Lenz, P.H "Peptidergic signaling in Calanus finmarchicus (Crustacea: Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome." General and Comparative Endocrinology, v.187, 2013, p.117-135. doi:dx.doi.org/10.1016/j.ygcen.2013.03.018 

Christie, A.E., McCoole, M.D., Harmon, S.M., Baer, K.N., Lenz, P.H. "Genomic analyses of the Daphnia pulex peptidome" General and Comparative Endocrinology, v.171, 2011, p.131. doi:10.1016/j.ygcen.2011.01.002 

Christie, A.E., Nolan, D.H., Garcia, Z.A., McCoole, M.D., Harmon, S.M., Congdon-Jones, B., Ohno, P., Hartline, N., Congdon, C.B., Baer, K.N., Lenz, P.H. "Bioinformatic prediction of arthropod/nematode-like peptides in non-arthropod, non-nematode members of the Ecdysozoa" General and Comparative Endocrinology, v.170, 2011, p.480. doi:10.1016/j.ygcen.2010.11.002 

Lenz, P. H., Roncalli, V., Hassett, R.P., Wu, L.-S., Cieslak, M.C., Hartline, D.K. and Christie, A.E. "De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda) - The dominant zooplankter of the North Atlantic Ocean." PLOS One, v.9, 2014, p.journal.p.


Project Outcomes Report

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Overview:  Global climate change is affecting all environments on our planet benefiting some organisms while hurting others.  However, predicting winners and losers is difficult, because biologists have in depth knowledge of only a few model species.  Therefore, it has become critical to study how ecologically important species respond to their environment.   Throughout the Gulf of Maine and the North Atlantic, young fishes feed primarily on the copepod, a planktonic crustacean smaller than a grain of rice.   Its small size and vast habitat make the copepod a poor subject for traditional physiological studies aimed at understanding how environmental factors affect their life cycle. 

Recent breakthroughs in molecular biology now allow scientists to take a snapshot of an animal’s messenger RNAs.  Known as transcriptomics, this technique catalogs the messages used by the cells to control the animal’s life processes.  In essence, scientists are now able to listen in on the instructions being sent out directing an organism’s response to its changing environment.  With respect to copepods, the challenge is to identify and understand each message, in order to track down the causes of population changes.

 

Intellectual Merit:  The first transcriptome for the key North Atlantic copepod Calanus finmarchicus has now been published and made available for scientists everywhere. Highlights of the study include: 1) the observation of large percentages of silent genes in any particular life stage of this copepod; 2) the identification of messages that are only highly expressed in individuals preparing to enter dormancy (diapause), a critical event in the annual population cycle; and 3) the discovery of a number of previously unknown genes, suggesting a more complex genome than those of model arthropods, such as the fruit fly and the water flea. 

 

The project has led to eleven peer-reviewed publications that were fully or partially supported under this award. The reference transcriptome generated is being used to study how exposure to the toxic alga, Alexandrium fundyense affects the biology of C. finmarchicus.  This toxic alga is responsible for the red tide in the Gulf of Maine and is a recurring health problem in the region. The results from the exposure experiments will become part of a Ph.D. dissertation (expected graduation: May 2015).  Microarray and platform data for C. finmarchicus are available at The Gene Expression Omnibus (GEO), accession numbers GSE34322 and GPL14742 and RNA-Seq data are available at BioProject PRJNA236528 (www.ncbi.nlm.nih.gov).  Custom Perl scripts for data processing are publicly available through: github.com/LenzLab/RNA-seq-scripts.

 

Broader Impacts: The broader impacts of the project fall into three separate categories:  1) training of future STEM workforce; 2) exposure of scientific research and its significance to a broader audience; and 3) generating resources for the scientific community.  1) NSF funding was leveraged to provide training from high school to post-doctoral levels.  Four high-school students participated in the collection, identification, maintenance and culture of marine organisms as well as engaged in data mining using national databases and bioinformatics tools at the Mt. Desert Island Biological Laboratory.  They also attended seminars and other scientific activities.  One g...

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