| Contributors | Affiliation | Role |
|---|---|---|
| Falkowski, Paul G. | Rutgers University (Rutgers IMCS) | Principal Investigator, Contact |
| Rosenthal, Yair | Rutgers University | Co-Principal Investigator |
| Schofield, Oscar M.E. | Rutgers University | Co-Principal Investigator |
| Sherrell, Robert M. | Rutgers University | Co-Principal Investigator |
| Rauch, Shannon | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Cluster analysis and gene ontology to compare ~1500 proteins, from over 100 studies, extracted from calcium carbonates in stony corals, bivalve and gastropod mollusks, and adult and larval sea urchins. This dataset includes information presented in Supplemental Table S1 from Drake et al. 2014. Refer to Drake, et al. (2014) for more information on methodology and results.
Methodology described in Drake et al. 2014:
Sequences from over 100 biomineral proteome studies were grouped by hierarchical clustering using the CD-HIT suite web server (Li and Godzik, 2006; Huang et al., 2010; http://weizhong-lab.ucsd.edu/cd-hit/) and assigned gene ontology (GO) terms using Blast2Go software (Conesa et al., 2005). Although 1531 proteins reduced to 1051 clusters at 30% similarity, only 64 clusters showed sequence similarity across phyla. Studies published from the 1990s through June 2013, using N-terminal and mass spectrometry COM sequencing, RT-PCR, or GO and KEGG annotation of genomic and transcriptomic data sets are included. Mass spectrometry sequences were excluded if the experimental data were compared with gene models from a different species.
This dataset includes information presented in Supplemental Table S1 from Drake et al. 2014:
Cross-phyla clustering of non-redundant carbonate organic matrix proteins from N-terminal and mass spectrometry COM sequencing, RT-PCR, or GO and KEGG annotation of genomic and transcriptomic data sets (from over 100 studies) grouped by hierarchical clustering using the CD-HIT suite web server (http://weizhong-lab.ucsd.edu/cd-hit/). The gene accession numbers are included. 1531 proteins reduced to 1051 clusters at 30% or greater similarity, although only 64 clusters showed sequence similarity across phyla. Studies published from the 1990s through June 2013 are included. Clusters with the same name have been combined. Note: Mass spectrometry sequences were excluded if the experimental data were compared with gene models from a different species.
* indicates that non-homologous proteins with similar function were also observed. See Table 2 in Drake et al. 2014.
** indicates a likely cellular contaminant due to location based on cellular component GO term.
* in protein_name column indicates that non-homologous proteins with similar function were also observed. See Table 2 in Drake et al. 2014.
** in protein_name column indicates a likely cellular contaminant due to location based on cellular component GO term.
BCO-DMO Processing Notes:
- Replaced abbreviated species names with the full genus and species.
- Replaced blanks with 'nd' to indicate 'no data'.
- Created reference list (SI_Table_1_references.csv) for full references of names in the 'reference' column.
| File |
|---|
SI_Table1.csv (Comma Separated Values (.csv), 10.74 KB) MD5:876fd43d72e70ef9290d54fd086814eb Primary data file for dataset ID 536074 |
| File |
|---|
SI_Table_1_references.csv (Comma Separated Values (.csv), 6.32 KB) MD5:3339003b915c03b8cd4d6eb659fe2f28 Complete reference information for "Cross-phyla clustering of non-redundant carbonate organic matrix proteins" dataset (dataset 536074; PI: Falkowski).
The "abbrev" column contains the abbreviated reference as cited in dataset 536074.
The "full_reference" column contains the complete citation for that paper. |
| Parameter | Description | Units |
| protein_name | Name of the protein. | text |
| coral_species | Name(s) of the coral species. | text |
| coral_accession | The accession numbers corresponding to the coral species. | text |
| coral_reference | Reference paper for the coral species/coral accession number. See the Supplemental File "SI_Table_1_references.csv" for full citations. | text |
| mollusk_species | Name(s) of the mollusk species. | text |
| mollusk_accession | The accession numbers corresponding to the mollusk species. | text |
| mollusk_reference | Reference paper for the mollusk species/mollusk accession number. See the Supplemental File "SI_Table_1_references.csv" for full citations. | text |
| sea_urchin_species | Name(s) of the sea urchin species. | text |
| sea_urchin_accession | The accession numbers corresponding to the sea urchin species. | text |
| sea_urchin_reference | Reference paper for the sea urchin species/sea urchin accession number. See the Supplemental File "SI_Table_1_references.csv" for full citations. | text |
| cellular_component_GO_term | Cellular component gene ontology (GO) term. | text |
| Dataset-specific Instrument Name | Mass Spec |
| Generic Instrument Name | Mass Spectrometer |
| Generic Instrument Description | General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. |
| Website | |
| Platform | Rutgers_New_Brunswick |
| Start Date | 2010-09-01 |
| End Date | 2014-08-01 |
| Description | Laboratory-based research for the project "The Molecular Basis of Ocean Acidification Effects on Calcification in Zooxanthellate Corals" were conducted at Dr. Falkowski's lab at the Rutgers New Brunswick campus:
71 Dudley Road
New Brunswick, NJ 08901 |
From the NSF award abstract:
Ocean acidification (the decrease in seawater pH) is driven by the increase in atmospheric CO2. This is expected to have a dramatic effect on organisms that precipitate calcium carbonate. Coral reefs are formed and maintained by calcifying organisms, particularly reef-building corals. Current predictions are that coral species will be negatively impacted; however the limited number of available measurements exhibit significant variability for reasons that are not understood. This is critically important as coral reef ecosystems hold significant cultural and economic values both nationally and internationally. This program is therefore focused on the molecular basis for calcification in corals in order to understand how corals will respond to ocean acidification in the next century. Rutgers University has a state-of-art coral culture facility that will be used to simulate future ocean conditions. The work will utilize a unique set of coral tissue cultures that will allow scientists to assess the cellular biology that underlies the responses of corals to ocean acidification. The laboratory measurements will also determine how geochemical signatures of corals are affected by varying environmental conditions. These results are important because coral geochemical signatures are used to understand how corals have responded to changes in the ocean pH in the historical past. The project will be conducted by a research team at Rutgers, in collaboration with scientists in Taiwan and Israel.
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
| Funding Source | Award |
|---|---|
| NSF Emerging Frontiers Division (NSF EF) |