Reconciling observed and modelled phytoplankton dynamics in a major lowland UK river system, the Thames

This study aims to elucidate the key mechanisms controlling phytoplankton growth and decay within the Thames basin through the application of a modified version of an established river-algal model and comparison with observed stream water chlorophyll-a concentrations. The River Thames showed a distinct simulated phytoplankton seasonality and behaviour having high spring, moderate summer and low autumn chlorophyll-a concentrations. Three main sections were identified along the River Thames with different phytoplankton abundance and seasonality: (i) low chlorophyll-a concentrations from source to Newbridge; (ii) steep concentration increase between Newbridge and Sutton; and (iii) high concentrations with a moderate increase in concentration from Sutton to the end of the study area (Maidenhead). However, local hydrologic (e.g. locks) and other conditions (e.g. radiation, water depth, grazer dynamics, etc.) affected the simulated growth and losses. The model achieved good simulation results during both calibration and testing through a range of hydrological and nutrient conditions. Simulated phytoplankton growth was controlled predominantly by residence time, but during medium–low flow periods available light, water temperature and herbivorous grazing defined algal community development. These results challenge the perceived importance of in-stream nutrient concentrations as the perceived primary control on phytoplankton growth and death.

Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae

Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ~200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.

Interface dynamics in planar neural field models

Neural field models describe the coarse-grained activity of populations of interacting neurons. Because of the laminar structure of real cortical tissue they are often studied in two spatial dimensions, where they are well known to generate rich patterns of spatiotemporal activity. Such patterns have been interpreted in a variety of contexts ranging from the understanding of visual hallucinations to the generation of electroencephalographic signals. Typical patterns include localized solutions in the form of traveling spots, as well as intricate labyrinthine structures. These patterns are naturally defined by the interface between low and high states of neural activity. Here we derive the equations of motion for such interfaces and show, for a Heaviside firing rate, that the normal velocity of an interface is given in terms of a non-local Biot-Savart type interaction over the boundaries of the high activity regions. This exact, but dimensionally reduced, system of equations is solved numerically and shown to be in excellent agreement with the full nonlinear integral equation defining the neural field. We develop a linear stability analysis for the interface dynamics that allows us to understand the mechanisms of pattern formation that arise from instabilities of spots, rings, stripes and fronts. We further show how to analyze neural field models with linear adaptation currents, and determine the conditions for the dynamic instability of spots that can give rise to breathers and traveling waves.

Mg/Ca partitioning between aqueous solution and aragonite mineral: a molecular dynamics study

We have calculated the concentrations of Mg in the bulk and surfaces of aragonite CaCO3 in equilibrium with aqueous solution, based on molecular dynamics simulations and grand-canonical statistical mechanics. Mg is incorporated in the surfaces, in particular in the (001) terraces, rather than in the bulk of aragonite particles. However, the total Mg content in the bulk and surface of aragonite particles was found to be too small to account for the measured Mg/Ca ratios in corals. We therefore argue that most Mg in corals is either highly metastable in the aragonite lattice, or is located outside the aragonite phase of the coral skeleton, and we discuss the implications of this finding for Mg/Ca paleothermometry.

Thermodynamics/dynamics coupling in weakly compressible turbulent stratified fluids

In traditional and geophysical fluid dynamics, it is common to describe stratified turbulent fluid flows with low Mach number and small relative density variations by means of the incompressible Boussinesq approximation. Although such an approximation is often interpreted as decoupling the thermodynamics from the dynamics, this paper reviews recent results and derive new ones that show that the reality is actually more subtle and complex when diabatic effects and a nonlinear equation of state are retained. Such an analysis reveals indeed: (1) that the compressible work of expansion/contraction remains of comparable importance as the mechanical energy conversions in contrast to what is usually assumed; (2) in a Boussinesq fluid, compressible effects occur in the guise of changes in gravitational potential energy due to density changes. This makes it possible to construct a fully consistent description of the thermodynamics of incompressible fluids for an arbitrary nonlinear equation of state; (3) rigorous methods based on using the available potential energy and potential enthalpy budgets can be used to quantify the work of expansion/contraction B in steady and transient flows, which reveals that B is predominantly controlled by molecular diffusive effects, and act as a significant sink of kinetic energy.

Efficient fully nonlinear data assimilation for geophysical fluid dynamics

A potential problem with Ensemble Kalman Filter is the implicit Gaussian assumption at analysis times. Here we explore the performance of a recently proposed fully nonlinear particle filter on a high-dimensional but simplified ocean model, in which the Gaussian assumption is not made. The model simulates the evolution of the vorticity field in time, described by the barotropic vorticity equation, in a highly nonlinear flow regime. While common knowledge is that particle filters are inefficient and need large numbers of model runs to avoid degeneracy, the newly developed particle filter needs only of the order of 10-100 particles on large scale problems. The crucial new ingredient is that the proposal density cannot only be used to ensure all particles end up in high-probability regions of state space as defined by the observations, but also to ensure that most of the particles have similar weights. Using identical twin experiments we found that the ensemble mean follows the truth reliably, and the difference from the truth is captured by the ensemble spread. A rank histogram is used to show that the truth run is indistinguishable from any of the particles, showing statistical consistency of the method.

Postglacial vegetation, fire and climate dynamics at Central Chilean Patagonia (Lake Shaman, 44ºS)

A 19 cal ka BP pollen and charcoal record from Lake Shaman (44°S; 71°W, Chile) was analyzed to establish vegetation, fire and climate dynamics of the forest-steppe ecotone in Central Chilean Patagonia. Lake Shaman record indicates that the upper Río Cisnes valley was free of ice at around 19 cal ka BP. From this date and until 14.8 cal ka BP, a grass steppe with high proportions of shrubs associated to colder and drier conditions than present developed in this area. A continuous increase of Nothofagus accompanied by a decline in the steppe shrubs and sudden dominance of paludal over aquatic plants from 11 cal ka BP was associated to effective moisture increase but still under modern values. The replacement of the cold-dry grass-shrub steppe by a similar-than-present forest-steppe ecotone suggests an increase in temperature indicating the onset of the Holocene. At the same time, moderate fire activity suggested by the charcoal record could be related to major fuel availability as consequence of Nothofagus forest expansion. Between 8 and 3 cal ka BP, the record indicates the easternmost position of the forest-steppe ecotone suggesting the highest effective moisture with the establishment of seasonality between 5 and 3 cal ka BP. From 3 cal ka BP, the record indicates a retraction of the forest-steppe ecotone accompanied by a high pollen record variability and an increased fire activity. These late changes suggest decreased effective moisture associated with a high climatic variability. At regional and extra-regional scale, climatic changes at Lake Shaman's record are mostly associated to changes (latitudinal shifts and/or strengthening/weakening) of past Southern Westerlies that were previously recorded along Patagonia from the Lateglacial to the mid-Holocene. During the Late Holocene, a regional pattern characterized by high record variability emerges throughout Central Chilean Patagonia. This variability would be related to (1) low magnitude Southern Westerlies changes probably associated to ENSO and/or SAM or (2) the complex relationships between vegetation, fire and human occupations during the last 3 cal ka.

Bond-selective energy redistribution in the chemisorption of CH3D and CD3H on Pt{1 1 0}-(1 2): a first-principles molecular dynamics study

We have investigated the chemisorption of CH3D and CD3H on Pt{11 0}-(1 2) by performing first-principles molecular dynamics simulations of the recombinative desorption of CH3D (from adsorbed methyl and deuterium) and of CD3H (from adsorbed trideuteromethyl and hydrogen). Vibrational analysis of the symmetry adapted internal coordinates of the desorbing molecules shows that excitation of the single C– D (C–H) bond in the parent molecule is strongly correlated with energy excess in the reaction coordinate. The results of the molecular dynamics simulations are consistent with observed mode- and bond-specific reactivity measurements for chemisorption of methane and its isotopomers on platinum and nickel surfaces.

TNF-α influences the lateral dynamics of TNF receptor I in living cells

In mammalian cells, inflammation is mainly mediated by the binding of tumor necrosis factor alpha to tumor necrosis factor receptor 1. In this study, we investigated lateral dynamics of TNF-R1 before and after ligand binding using high-density single-particle tracking in combination with photoactivated localization microscopy. Our single-molecule data indicates the presence of tumor necrosis factor receptor 1 with different mobilities in the plasma membrane, suggesting different molecular organizations. Cholesterol depletion led to a decrease of slow receptor species and a strong increase in the average diffusion coefficient. Moreover, as a consequence of tumor necrosis factor-alpha treatment, the mean diffusion coefficient moderately increased while its distribution narrowed. Based on our observation, we propose a refined mechanism on the structural arrangement and activation of tumor necrosis factor receptor 1 in the plasma membrane.

Comparative in situ analyses of cell wall matrix polysaccharide dynamics in developing rice and wheat grain

Cell wall polysaccharides of wheat and rice endosperm are an important source of dietary fibre. Monoclonal antibodies specific to cell wall polysaccharides were used to determine polysaccharide dynamics during the development of both wheat and rice grain. Wheat and rice grain present near synchronous developmental processes and significantly different endosperm cell wall compositions, allowing the localisation of these polysaccharides to be related to developmental changes. Arabinoxylan (AX) and mixed-linkage glucan (MLG) have analogous cellular locations in both species, with deposition of AX and MLG coinciding with the start of grain filling. A glucuronoxylan (GUX) epitope was detected in rice, but not wheat endosperm cell walls. Callose has been reported to be associated with the formation of cell wall outgrowths during endosperm cellularisation and xyloglucan is here shown to be a component of these anticlinal extensions, occurring transiently in both species. Pectic homogalacturonan (HG) was abundant in cell walls of maternal tissues of wheat and rice grain, but only detected in endosperm cell walls of rice in an unesterified HG form. A rhamnogalacturonan-I (RG-I) backbone epitope was observed to be temporally regulated in both species, detected in endosperm cell walls from 12 DAA in rice and 20 DAA in wheat grain. Detection of the LM5 galactan epitope showed a clear distinction between wheat and rice, being detected at the earliest stages of development in rice endosperm cell walls, but not detected in wheat endosperm cell walls, only in maternal tissues. In contrast, the LM6 arabinan epitope was detected in both species around 8 DAA and was transient in wheat grain, but persisted in rice until maturity.