| 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 S2 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 S2 from Drake et al. 2014:
Proteins from coral, mollusk, and sea urchin direct COM sequencing, RT-PCR, or GO and KEGG annotation. 1076 proteins, including redundancy when noted by multiple sources, reduced to 1031 non-redundant sequences.
BCO-DMO Processing Notes:
- Replaced blanks with 'nd' to indicate 'no data'.
- Replaced alpha symbols with the word "alpha" and beta symbols with "beta".
- Created code list ("SI_Table_2_sequence_codes.csv") for long sequences contained in the 'detection_type' column.
- Created reference list ("SI_Table_2_references.csv") for full references of names in the 'reference' column.
| File |
|---|
SI_Table2.csv (Comma Separated Values (.csv), 131.92 KB) MD5:eef20978ad572b1e7ea5e6751c9a006d Primary data file for dataset ID 536485 |
| File |
|---|
SI_Table_2_references.csv (Comma Separated Values (.csv), 17.34 KB) MD5:bc997b3b68e1f4363701c99256fca7c9 Complete reference information for "Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin" dataset (dataset 536485; PI: Falkowski).
The "abbrev" column contains the abbreviated reference as cited in dataset 536485.
The "full_reference" column contains the complete citation for that paper.
|
SI_Table_2_sequence_codes.csv (Comma Separated Values (.csv), 1.68 KB) MD5:b3968320952b0f70c9409d1b32496fa9 Full sequences for those abbreviated in the "detection_type" column of "Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin" dataset (dataset 536485; PI: Falkowski).
The "code" column contains the sequence code as listed in dataset 536485.
The "sequence" column contains the full sequence.
|
| Parameter | Description | Units |
| protein_name | Name of the protein. | text |
| cluster_num | Cluster numbers were assigned to each batch of proteins that clustered together with 30% similarity or higher based on a clustering method using the CD-HIT suite web server. This was done progressively from 100% sequence similarity down to 30% with the cluster numbers carrying through. However, if a protein showed 30% similarity to another batch of proteins, then, for the final cut-off of 30%, the proteins from the previously independent batch were grouped in with the new batch. For instance, Cluster005744 has a cluster_num of 12. That means that it has 30% sequence similarity with proteins from proteins 5955, 00152 1(a), and 19987. In a previous clustering (with a higher similarity cutoff), it also showed sequence similarity with proteins Cluster020987, Cluster020227, and Cluster015890 (so they were previously in cluster #12). However, now proteins Cluster020987, Cluster020227, and Cluster015890 show at least 30% sequence similarity with one of the Cluster000783, Cluster050768, Cluster050003, or lotgi1|230171 proteins (that were previously assigned to cluster #0). So now since at least 1 protein in cluster #12 is similar to cluster #0, all #12 proteins were assigned to cluster #0. | unitless |
| group_num | Group number. | unitless |
| genus | Genus name. | text |
| species | Species name. | text |
| taxon | Taxonomic grouping (coral, echinoderm, or mollusk). | text |
| reference | Reference paper. Refer to Supplemental Files for full citations. | text |
| ID1 | The accession number, author's assigned protein number, or other note about a designator for the individual protein. | text |
| detection_type | Method used to sequence the protein.The strings of letters are the individual peptide sequences detected by LC-MS/MS. | text |
| type | Indicates if the protein can be assigned the name of a type of protein based on BLAST similarity. Also contains notes, such as if the protein was assigned its own accession number but was the same protein as found in another row. | 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) |