Remote Sensing-Driven Pacific Oyster (Crassostrea gigas) Growth Modeling to Inform Offshore Aquaculture Site Selection

Aquaculture increasingly contributes to global seafood production, requiring new farm sites for continued growth. In France, oyster cultivation has conventionally taken place in the intertidal zone, where there is little or no further room for expansion. Despite interest in moving production further offshore, more information is needed regarding the biological potential for offshore oyster growth, including its spatial and temporal variability. This study shows the use of remotely-sensed chlorophyll-a and total suspended matter concentrations retrieved from the Medium Resolution Imaging Spectrometer (MERIS), and sea surface temperature from the Advanced Very High Resolution Radiometer (AVHRR), all validated using in situ matchup measurements, as input to run a Dynamic Energy Budget (DEB) Pacific oyster growth model for a study site along the French Atlantic coast (Bourgneuf Bay, France). Resulting oyster growth maps were calibrated and validated using in situ measurements of total oyster weight made throughout two growing seasons, from the intertidal zone, where cultivation currently takes place, and from experimental offshore sites, for both spat (R2 = 0.91; RMSE = 1.60 g) and adults (R2 = 0.95; RMSE = 4.34 g). Oyster growth time series are further digested into industry-relevant indicators, such as time to achieve market weight and quality index, elaborated in consultation with local producers and industry professionals, and which are also mapped. Offshore growth is found to be feasible and to be as much as two times faster than in the intertidal zone (p < 0.001). However, the potential for growth is also revealed to be highly variable across the investigated area. Mapping reveals a clear spatial gradient in production potential in the offshore environment, with the northeastern segment of the bay far better suited than the southwestern. Results also highlight the added value of spatiotemporal data, such as satellite image time series, to drive modeling in support of marine spatial planning. The current work demonstrates the feasibility and benefit of such a coupled remote sensing modeling approach within a shellfish farming context, responding to real and current interests of oyster producers

Earth Mover’s Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations

Changes in the frequencies of cell subsets that (co)express characteristic biomarkers, or levels of the biomarkers on the subsets, are widely used as indices of drug response, disease prognosis, stem cell reconstitution, etc. However, although the currently available computational “gating” tools accurately reveal subset frequencies and marker expression levels, they fail to enable statistically reliable judgements as to whether these frequencies and expression levels differ significantly between/among subject groups. Here we introduce flow cytometry data analysis pipeline which includes the Earth Mover’s Distance (EMD) metric as solution to this problem. Well known as an informative quantitative measure of differences between distributions, we present three exemplary studies showing that EMD 1) reveals clinically-relevant shifts in two markers on blood basophils responding to an offending allergen; 2) shows that ablative tumor radiation induces significant changes in the murine colon cancer tumor microenvironment; and, 3) ranks immunological differences in mouse peritoneal cavity cells harvested from three genetically distinct mouse strains

Introduction to special section on Recent Advances in the Study of Optical Variability in the Near-Surface and Upper Ocean

Optical variability occurs in the near-surface and upper ocean on very short time and space scales (e.g., milliseconds and millimeters and less) as well as greater scales. This variability is caused by solar, meteorological, and other physical forcing as well as biological and chemical processes that affect optical properties and their distributions, which in turn control the propagation of light across the air-sea interface and within the upper ocean. Recent developments in several technologies and modeling capabilities have enabled the investigation of a variety of fundamental and applied problems related to upper ocean physics, chemistry, and light propagation and utilization in the dynamic near-surface ocean. The purpose here is to provide background for and an introduction to a collection of papers devoted to new technologies and observational results as well as model simulations, which are facilitating new insights into optical variability and light propagation in the ocean as they are affected by changing atmospheric and oceanic conditions

Introduction to special section on Recent Advances in the Study of Optical Variability in the Near-Surface and Upper Ocean

Optical variability occurs in the near-surface and upper ocean on very short time and space scales (e.g., milliseconds and millimeters and less) as well as greater scales. This variability is caused by solar, meteorological, and other physical forcing as well as biological and chemical processes that affect optical properties and their distributions, which in turn control the propagation of light across the air-sea interface and within the upper ocean. Recent developments in several technologies and modeling capabilities have enabled the investigation of a variety of fundamental and applied problems related to upper ocean physics, chemistry, and light propagation and utilization in the dynamic near-surface ocean. The purpose here is to provide background for and an introduction to a collection of papers devoted to new technologies and observational results as well as model simulations, which are facilitating new insights into optical variability and light propagation in the ocean as they are affected by changing atmospheric and oceanic conditions

Diel cycles of the particulate beam attenuation under varying trophic conditions in the NW Mediterranean Sea: Observations and modeling

The effects of the diel cycle of light intensity, while often neglected, have been reported for a variety of biogeochemical and optical quantities. In particular, a diel cycle in the particle beam attenuation coefficient (cp) appears to be a near ubiquitous feature of the optical variability in the euphotic zone and has been associated primarily with the daytime accumulation and night-time removal of particles in the size range ~0.1 to 20 microns. However, generally, in situ investigation of the cp daily variability is limited to a few days. The development of instrumented moorings allows in situ measurements to be performed at high-frequency, over long periods (years) and under varying environmental conditions (trophic state, vertical distribution of the water properties, composition of the particle community). A time series of inherent and apparent optical properties (cp, chlorophyll fluorescence, downward irradiances) has been collected at an open ocean mooring (BOUSSOLE project) in the North western Mediterranean Sea (60 km offshore Nice, France). All data are simultaneously recorded every 15 minutes at 9 m depth. This database allows us to characterize the diel variability in cp, with consideration of the physical forcing and the phytoplankton population composition (as described by monthly HPLC analyses).Using this two years time-series, we studied the changes in shape, amplitude and timing in the cp diel variability under contrasted physical and trophic situations. A diel cycle is observed whatever the season, during winter mixing, development of bloom, its collapse, and summer oligotrophic situations. The relative amplitude of the cycle is about 10-20% during mixing and oligotrophy, and at least twice as large during the spring bloom. Diel cp minima generally occur around sunrise and maxima a few hours before sunset. The specific particle rate of variation (1/cp dcp/dt) generally reaches maximum before noon, suggesting that the particle growth is more important in the first half of the photoperiod. A new model is proposed to reproduce this singular morning maximum. The rate of variation of cp is modeled as a light-dependent particle growth rate, using three parameters: maximum growth rate, growth efficiency and saturation irradiance. These parameters show important and consistent diel and seasonal variability. These results highlight the importance of considering the time-dependency of these parameters to improve the accuracy of predictive models of photosynthetic and heterotrophic particle growth in the ocean

Diel cycles of the particulate beam attenuation coefficient under varying trophic conditions in the northwestern Mediterranean Sea: observations and modeling

The changes in shape, amplitude, and timing in the diel variability of the particulate beam attenuation coefficient (cp) were investigated at 4 and 9 m during two seasonal cycles at an oceanic site in the northwestern Mediterranean Sea under contrasting physical and trophic situations. We observed a diel cycle in cp during the winter mixing of the water column, the development of the spring phytoplankton bloom, its collapse, and during the summer oligotrophy. The relative amplitude of the cp diel cycle was about 10–20% during winter mixing and summer oligotrophy and at least twice as large during the spring bloom. Diel cp minima generally occurred around sunrise and maxima a few hours before sunset. The specific particle rate of variation (r) was consistent over the diel cycle, with positive and negative values during daytime and nighttime, respectively. A striking feature of the r diel cycle was a morning maximum, i.e., before solar noon, which was successfully reproduced by a new model of particle assemblage growth rate based on three parameters: maximum growth rate, growth efficiency, and saturation irradiance. Each model parameter undergoes a diel cycle and shows a seasonal variation. A cp-based estimation of the particle net community production is computed from the measurements and model outputs. Results compare favorably with modeled primary production on the basis of continuous measurements of surface chlorophyll using fluorescence