Shutdown of turbulent convection as a new criterion for the onset of spring phytoplankton blooms

The onset of phytoplankton blooms in late winter, early spring has been traditionally associated with the shoaling of the mixed layer above a critical depth. Here we show that the onset of a bloom can also be triggered by a reduction in air–sea fluxes at the end of winter. When net cooling subsides at the end of winter, turbulent mixing becomes weak, thereby increasing the residence time of phytoplankton cells in the euphotic layer and allowing a bloom to develop. The necessary change in the air–sea flux generally precedes mixed-layer shoaling, and may provide a better indicator for the onset of the spring bloom than the mixed-layer depth alone. Our hypothesis is supported by numerical simulations and remote sensing data.United States. Office of Naval Research (Award N00014-08-1-1060

On the development of thermohaline correlations as a result of nonlinear diffusive parameterizations

Some oceanographic mixing parameterizations assume that transports depend nonlinearly on the buoyancy gradient; e.g., diffusivities are proportional to some power of the buoyancy gradient. In this paper we examine the consequences of these nonlinear-diffusion parameterizations by solving an initial value problem in which the t = 0 thermohaline fields are prepared as random and uncorrelated distributions of temperature and salinity. Solutions of the nonlinear diffusion equation as a ‘rundown’ problem show that correlations develop between the temperature and salinity. These correlations are such that the evolving thermohaline gradients tend to be strongly compensating in their joint effect on buoyancy

Shutdown of convection triggers increase of surface chlorophyll

The long-standing explanation of the triggering cause of the surface increase of phytoplankton visible in spring satellite images argues that phytoplankton biomass accumulation begins once the mixed layer depths become shallower than a ‘critical depth’. However, a series of recent studies have found evidence for phytoplankton increase in deep mixed layers, and several hypotheses have been proposed to explain this early increase. In this manuscript it is suggested that the surface concentration of phytoplankton increases rapidly in a ‘surface bloom’ when atmospheric cooling of the ocean turns into an atmospheric heating at the end of winter. The hypothesis is supported by analysis of satellite observations of chlorophyll and of heat fluxes from atmospheric reanalysis from the North Atlantic.National Science Foundation (U.S.) (Award OCE-1155205

Atlantic Ocean Heat Transport Enabled by Indo-Pacific Heat Uptake and Mixing

The ocean transports vast amounts of heat around the planet, helping to regulate regional climate. One important component of this heat transport is the movement of warm water from equatorial regions toward the poles, with colder water flowing in return. Here, we introduce a framework relating meridional heat transport to the diabatic processes of surface forcing and turbulent mixing that move heat across temperature classes. Applied to a (1/4)° global ocean model the framework highlights the role of the tropical Indo‐Pacific in the global ocean heat transport. A large fraction of the northward heat transport in the Atlantic is ultimately sourced from heat uptake in the eastern tropical Pacific. Turbulent mixing moves heat from the warm, shallow Indo‐Pacific circulation to the cold deeper‐reaching Atlantic circulation. Our results underscore a renewed focus on the tropical oceans and their role in global circulation pathways

Weighted protein interaction network analysis of frontotemporal dementia

The genetic analysis of complex disorders has undoubtedly led to the identification of a wealth of associations between genes and specific traits. However, moving from genetics to biochemistry one gene at a time has, to date, rather proved inefficient and under-powered to comprehensively explain the molecular basis of phenotypes. Here we present a novel approach, weighted protein−protein interaction network analysis (W-PPI-NA), to highlight key functional players within relevant biological processes associated with a given trait. This is exemplified in the current study by applying W-PPI-NA to frontotemporal dementia (FTD): We first built the state of the art FTD protein network (FTD-PN) and then analyzed both its topological and functional features. The FTD-PN resulted from the sum of the individual interactomes built around FTD-spectrum genes, leading to a total of 4198 nodes. Twenty nine of 4198 nodes, called inter-interactome hubs (IIHs), represented those interactors able to bridge over 60% of the individual interactomes. Functional annotation analysis not only reiterated and reinforced previous findings from single genes and gene-coexpression analyses but also indicated a number of novel potential disease related mechanisms, including DNA damage response, gene expression regulation, and cell waste disposal and potential biomarkers or therapeutic targets including EP300. These processes and targets likely represent the functional core impacted in FTD, reflecting the underlying genetic architecture contributing to disease. The approach presented in this study can be applied to other complex traits for which risk-causative genes are known as it provides a promising tool for setting the foundations for collating genomics and wet laboratory data in a bidirectional manner. This is and will be critical to accelerate molecular target prioritization and drug discovery

2014 program ot study : climate physics and dynamics

From the Preface: The 2014 Geophysical Fluid Dynamics Summer Study Program started on June 16th, with the topic of Climate Physics and Dynamics. The topic proved very timely and attracted an unprecedented number of applications from brilliant students. Professors Kerry Emanuel (MIT) and Geoff Vallis (Exeter) gave the principal lectures. They began with the simplest energy balance models and then included adjustment of the vertical profiles by convection (dry and moist). Kerry delved more deeply into convection and the processes found in "cloud-permitting" models, including island effects and the spontaneous formation of clusters surrounded by dry regions. Geoff discussed the larger-scale dynamics of the atmosphere and oceans, including the transports by eddies and the thermohaline circulation.Funding was provided by the National Science Foundation Grant No. OCE-133275

Transport and emergent stratification in the equilibrated Eady model: the vortex gas scaling regime

We numerically and theoretically investigate the Boussinesq Eady model, where a rapidly rotating density-stratified layer of fluid is subject to a meridional temperature gradient in thermal wind balance with a uniform vertically sheared zonal flow. Through a suite of numerical simulations, we show that the transport properties of the resulting turbulent flow are governed by quasi-geostrophic (QG) dynamics in the rapidly rotating strongly stratified regime. The 'vortex gas' scaling predictions put forward in the context of the two-layer QG model carry over to this fully 3D system: the functional dependence of the meridional flux on the control parameters is the same, the two ajustable parameters entering the theory taking slightly different values. In line with the QG prediction, the meridional buoyancy flux is depth-independent. The vertical buoyancy flux is such that turbulence transports buoyancy along isopycnals, except in narrow layers near the the top and bottom boundaries, the thickness of which decreases as the diffusivities go to zero. The emergent (re)stratification is set by a simple balance between the vertical buoyancy flux and diffusion along the vertical direction. Overall, this study demonstrates how the vortex-gas scaling theory can be adapted to quantitatively predict the magnitude and vertical structure of the meridional and vertical buoyancy fluxes, and of the emergent stratification, without additional fitting parameters.Comment: Accepted versio

Atlantic Ocean Heat Transport Enabled by Indo-Pacific Heat Uptake and Mixing

The ocean transports vast amounts of heat around the planet, helping to regulate regional climate. One important component of this heat transport is the movement of warm water from equatorial regions toward the poles, with colder water flowing in return. Here, we introduce a framework relating meridional heat transport to the diabatic processes of surface forcing and turbulent mixing that move heat across temperature classes. Applied to a (1/4)° global ocean model the framework highlights the role of the tropical Indo‐Pacific in the global ocean heat transport. A large fraction of the northward heat transport in the Atlantic is ultimately sourced from heat uptake in the eastern tropical Pacific. Turbulent mixing moves heat from the warm, shallow Indo‐Pacific circulation to the cold deeper‐reaching Atlantic circulation. Our results underscore a renewed focus on the tropical oceans and their role in global circulation pathways

Protein interaction network analysis reveals genetic enrichment of immune system genes in frontotemporal dementia

To further unravel the complex genetic etiology of frontotemporal dementia (FTD), we hypothesized that interactors of the protein products of known FTD genes might be involved in the molecular pathways towards disease. We therefore applied protein interaction network (PIN) analysis to prioritize candidate genes for rare variant association. We created an FTD-PIN starting from known FTD genes downloading their physical interactors and performed functional enrichment analyses. We identified overrepresented processes in FTD and selected genes (n=440) belonging to the FTD processes for rare variant analysis in a Belgian cohort of 228 FTD patients and 345 controls. SKAT-O analysis suggested TNFAIP3 as the top gene (P = 0.7 × 10−3) reaching near test-wide significance (P = 2.5 × 10−4). We then analyzed the TNFAIP3-subnetwork within the FTD-PIN which indicated enrichment of several immune signaling networks, suggesting that disrupted immune signaling may be implicated in TNFAIP3-related FTD. Our study demonstrates that integration of PINs with genetic data is a useful approach to increase the power for rare variant association analysis. Furthermore, we present a computational pipeline for identifying potential novel therapeutic targets and risk-modifying variants

Screening for C9ORF72 repeat expansion in FTLD

In the present study we aimed to determine the prevalence of {C9ORF72} {GGGGCC} hexanucleotide expansion in our cohort of 53 frontotemporal lobar degeneration (FTLD) patients and 174 neurologically normal controls. We identified the hexanucleotide repeat, in the pathogenic range, in 4 (2 bv-frontotemporal dementia (FTD) and 2 FTD-amyotrophic lateral sclerosis ALS) out of 53 patients and 1 neurologically normal control. Interestingly, 2 of the \{C9ORF72\} expansion carriers also carried 2 novel missense mutations in \{GRN\} (Y294C) and in PSEN-2(I146V). Further, 1 of the \{C9ORF72\} expansion carriers, for whom pathology was available, showed amyloid plaques and tangles in addition to \{TAR\} (trans-activation response) DNA-binding protein (TDP)-43 pathology. In summary, our findings suggest that the hexanucleotide expansion is probably associated with ALS, FTD, or FTD-ALS and occasional comorbid conditions such as Alzheimer's disease. These findings are novel and need to be cautiously interpreted and most importantly replicated in larger numbers of samples