An Inverse Modeling Approach to Estimating Phytoplankton Pigment Concentrations from Phytoplankton Absorption Spectra

Phytoplankton absorption spectra and High-Performance Liquid Chromatography (HPLC) pigment observations from the Eastern U.S. and global observations from NASA's SeaBASS archive are used in a linear inverse calculation to extract pigment-specific absorption spectra. Using these pigment-specific absorption spectra to reconstruct the phytoplankton absorption spectra results in high correlations at all visible wavelengths (r(sup 2) from 0.83 to 0.98), and linear regressions (slopes ranging from 0.8 to 1.1). Higher correlations (r(sup 2) from 0.75 to 1.00) are obtained in the visible portion of the spectra when the total phytoplankton absorption spectra are unpackaged by multiplying the entire spectra by a factor that sets the total absorption at 675 nm to that expected from absorption spectra reconstruction using measured pigment concentrations and laboratory-derived pigment-specific absorption spectra. The derived pigment-specific absorption spectra were further used with the total phytoplankton absorption spectra in a second linear inverse calculation to estimate the various phytoplankton HPLC pigments. A comparison between the estimated and measured pigment concentrations for the 18 pigment fields showed good correlations (r(sup 2) greater than 0.5) for 7 pigments and very good correlations (r(sup 2) greater than 0.7) for chlorophyll a and fucoxanthin. Higher correlations result when the analysis is carried out at more local geographic scales. The ability to estimate phytoplankton pigments using pigment-specific absorption spectra is critical for using hyperspectral inverse models to retrieve phytoplankton pigment concentrations and other Inherent Optical Properties (IOPs) from passive remote sensing observations

Phytoplankton Assemblage Patterns in the Southern Mid-Atlantic Bight

As part of the Wallops Coastal Oceans Observing Laboratory (Wa-COOL) Project, we sampled a time-series transect in the southern Mid-Atlantic Bight (MAB) biweekly. Our 2-year time-series data included physical parameters, nutrient concentrations, and chlorophyll a concentrations. A detailed phytoplankton assemblage structure was examined in the second year. During the 2-year study, chlorophyll a concentration (and ocean color satellite imagery) indicated that phytoplankton blooms occurred in January/February during mixing conditions and in early autumn under stratified conditions. The chlorophyll a concentrations ranged from 0.25 microgram 1(exp -1) to 15.49 microgram 1(exp -1) during the 2-year period. We were able to discriminate approximately 116 different species under phase contrast microscopy. Dominant phytoplankton included Skeletonema costatum, Rhizosolenia spp., and Pseudo-nitzschia pungens. In an attempt to determine phytoplankton species competition/succession within the assemblage, we calculated a Shannon Weaver diversity index for our diatom microscopy data. Diatom diversity was greatest during the winter and minimal during the spring. Diatom diversity was also greater at nearshore stations than at offshore stations. Individual genera appeared patchy, with surface and subsurface patches appearing abruptly and persisting for only 1-2 months at a time. The distribution of individual species differed significantly from bulk variables of the assemblage (chlorophyll a ) and total phytoplankton assemblage (cells), which indicates that phytoplankton species may be limited in growth in ways that differ from those of the total assemblage. Our study demonstrated a highly diverse phytoplankton assemblage throughout the year, with opportunistic species dominating during spring and fall in response to seasonal changes in temperature and nutrients in the southern MAB

Absorption and Attenuation Coefficients Using the WET Labs ac-s in the Mid-Atlantic Bight: Field Measurements and Data Analysis

Ocean color algorithms are based on the parameterization of apparent optical properties as a function of inherent optical properties. WET Labs underwater absorption and attenuation meters (ac-9 and ac-s) measure both the spectral beam attenuation [c (lambda)] and absorption coefficient [a (lambda)]. The ac-s reports in a continuous range of 390-750 nm with a band pass of 4 nm, totaling approximately 83 distinct wavelengths, while the ac-9 reports at 9 wavelengths. We performed the ac-s field measurements at nine stations in the Mid-Atlantic Bight from water calibrations to data analysis. Onboard the ship, the ac-s was calibrated daily using Milli Q-water. Corrections for the in situ temperature and salinity effects on optical properties of water were applied. Corrections for incomplete recovery of the scattered light in the ac-s absorption tube were performed. The fine scale of spectral and vertical distributions of c (lambda) and a (lambda) were described from the ac-s. The significant relationships between a (674) and that of spectrophotometric analysis and chlorophyll a concentration of discrete water samples were observed

Report on IOCCG Workshop Phytoplankton Composition from Space: towards a validation\ud strategy for satellite algorithms

The IOCCG-supported workshop “Phytoplankton Composition from Space: towards a validation strategy for satellite algorithms” was organized as a follow-up to the Phytoplankton Functional Types from Space splinter session, held at the International Ocean Colour Science Meeting (Germany, 2013). The specific goals of the workshop were to: 1. Provide a summary of the status of activities from relevant IOCCG working groups, the 2nd PFT intercomparison working group, PFT validation data sets and other research developments. 2. Provide a PFT validation strategy that considers the different applications of PFT products: and seeks community consensus on datasets and analysis protocols. 3. Discuss possibilities for sustaining ongoing PFT algorithm validation and intercomparison activities. The workshop included 15 talks, breakout sessions and plenary discussions. Talks covered community algorithm intercomparison activity updates, review of established and novel methods for PFT validation, validation activities for specific applications and space-agency requirements for PFT products and validation. These were followed by general discussions on (a) major recommendations for global intercomparison initiative in respect to validation, intercomparison and user’s guide; (b) developing a community consensus on which data sets for validation are optimal and which measurement and analysis protocols should be followed to support sustained validation of PFT products considering different applications; (c) the status of different validation data bases and measurement protocols for different PFT applications, and (d) engagement of the various user communities for PFT algorithms in developing PFT product specifications. From these discussions, two breakout groups provided in depth discussion and recommendations on (1) validation of current algorithms and (2) work plan to prepare for validation of future missions. Breakout group 1 provided an action list for progressing the current international community validation and intercomparison activity. Breakout group 2 provided the following recommendations towards developing a future validation strategy for satellite PFT products: 1. Establish a number of validation sites that maintain measurements of a key set of variables. 2. This set of variables should include: • Phytoplankton pigments from HPLC, phycobilins from spectrofluorometry • Phytoplankton cell counts and ID, volume / carbon estimation and imaging (e.g. from flow cytometry, FlowCam, FlowCytobot type technologies) • Inherent optical properties (e.g. absorption, backscattering, VSF) • Hyperspectral radiometry (both above and in-water) • Particle size distribution • Size-fractionated measurements of pigments and absorption • Genetic / -omics data 3. Undertake an intercomparison of methods / instruments over several years at a few sites to understand our capabilities to fully characterize the phytoplankton community. 4. Organise workshops to address the following topics: • Techniques for particle analysis, characterization and classification • Engagement with modellers and understanding end-user requirements • Data storage and management, standards for data contributors, data challenges In conclusion, the workshop was assessed to have fulfilled its goals. A follow-on meeting will be organized during the International Ocean Colour Science Meeting 2015 in San Francisco. Specific follow-on actions are listed at the end of the report

Coastal and Inland Aquatic Data Products for the Hyperspectral Infrared Imager (HyspIRI)

The HyspIRI Aquatic Studies Group (HASG) has developed a conceptual list of data products for the HyspIRI mission to support aquatic remote sensing of coastal and inland waters. These data products were based on mission capabilities, characteristics, and expected performance. The topic of coastal and inland water remote sensing is very broad. Thus, this report focuses on aquatic data products to keep the scope of this document manageable. The HyspIRI mission requirements already include the global production of surface reflectance and temperature. Atmospheric correction and surface temperature algorithms, which are critical to aquatic remote sensing, are covered in other mission documents. Hence, these algorithms and their products were not evaluated in this report. In addition, terrestrial products (e.g., land use land cover, dune vegetation, and beach replenishment) were not considered. It is recognized that coastal studies are inherently interdisciplinary across aquatic and terrestrial disciplines. However, products supporting the latter are expected to already be evaluated by other components of the mission. The coastal and inland water data products that were identified by the HASG, covered six major environmental and ecological areas for scientific research and applications: wetlands, shoreline processes, the water surface, the water column, bathymetry and benthic cover types. Accordingly, each candidate product was evaluated for feasibility based on the HyspIRI mission characteristics and whether it was unique and relevant to the HyspIRI science objectives

A Compilation of Global Bio-Optical In Situ Data for Ocean-Colour Satellite Applications

A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi:10.1594/PANGAEA.854832 (Valente et al., 2015)

A Compilation of Global Bio-Optical In Situ Data for Ocean-Colour Satellite Applications

A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi:10.1594/PANGAEA.854832 (Valente et al., 2015)

Yeast Screens Identify the RNA Polymerase II CTD and SPT5 as Relevant Targets of BRCA1 Interaction

BRCA1 has been implicated in numerous DNA repair pathways that maintain genome integrity, however the function responsible for its tumor suppressor activity in breast cancer remains obscure. To identify the most highly conserved of the many BRCA1 functions, we screened the evolutionarily distant eukaryote Saccharomyces cerevisiae for mutants that suppressed the G1 checkpoint arrest and lethality induced following heterologous BRCA1 expression. A genome-wide screen in the diploid deletion collection combined with a screen of ionizing radiation sensitive gene deletions identified mutants that permit growth in the presence of BRCA1. These genes delineate a metabolic mRNA pathway that temporally links transcription elongation (SPT4, SPT5, CTK1, DEF1) to nucleopore-mediated mRNA export (ASM4, MLP1, MLP2, NUP2, NUP53, NUP120, NUP133, NUP170, NUP188, POM34) and cytoplasmic mRNA decay at P-bodies (CCR4, DHH1). Strikingly, BRCA1 interacted with the phosphorylated RNA polymerase II (RNAPII) carboxy terminal domain (P-CTD), phosphorylated in the pattern specified by the CTDK-I kinase, to induce DEF1-dependent cleavage and accumulation of a RNAPII fragment containing the P-CTD. Significantly, breast cancer associated BRCT domain defects in BRCA1 that suppressed P-CTD cleavage and lethality in yeast also suppressed the physical interaction of BRCA1 with human SPT5 in breast epithelial cells, thus confirming SPT5 as a relevant target of BRCA1 interaction. Furthermore, enhanced P-CTD cleavage was observed in both yeast and human breast cells following UV-irradiation indicating a conserved eukaryotic damage response. Moreover, P-CTD cleavage in breast epithelial cells was BRCA1-dependent since damage-induced P-CTD cleavage was only observed in the mutant BRCA1 cell line HCC1937 following ectopic expression of wild type BRCA1. Finally, BRCA1, SPT5 and hyperphosphorylated RPB1 form a complex that was rapidly degraded following MMS treatment in wild type but not BRCA1 mutant breast cells. These results extend the mechanistic links between BRCA1 and transcriptional consequences in response to DNA damage and suggest an important role for RNAPII P-CTD cleavage in BRCA1-mediated cancer suppression