Oscillatory regulation of hes1: Discrete stochastic delay modelling and simulation

Discrete stochastic simulations are a powerful tool for understanding the dynamics of chemical kinetics when there are small-to-moderate numbers of certain molecular species. In this paper we introduce delays into the stochastic simulation algorithm, thus mimicking delays associated with transcription and translation. We then show that this process may well explain more faithfully than continuous deterministic models the observed sustained oscillations in expression levels of hes1 mRNA and Hes1 protein.

T-Q relation and exact solution for the XYZ chain with general non-diagonal boundary terms

We propose that the Baxter's Q-operator for the quantum XYZ spin chain with open boundary conditions is given by the j -> infinity limit of the corresponding transfer matrix with spin-j (i.e., (2j + I)-dimensional) auxiliary space. The associated T-Q relation is derived from the fusion hierarchy of the model. We use this relation to determine the Bethe Ansatz solution of the eigenvalues of the fundamental transfer matrix. The solution yields the complete spectrum of the Hamiltonian. (c) 2006 Elsevier B.V. All rights reserved.

Reconstructing the past? Low German and the creating of regional identity in public language display

This article deals with language contact between a dominant standard language -German - and a lesser-used variety - Low German - in a situation in which the minoritised language is threatened by language shift and language loss. It analyses the application of Low German in forms of public language display and the selfpresentation of the community in tourism brochures, focusing on bilingual linguistic practices on the one hand and on underlying discourses on the other. It reveals that top-down and bottom-up approaches to implementing Low German in public language display show a remarkable homogeneity, thus creating a regional 'brand'. The article asks whether a raised level of visibility will in itself guarantee better chances for linguistic maintenance and survival of the threatened language. © 2011 Taylor & Francis.

Professor Rudolf Gorenflo and his Contribution to Fractional Calculus

MSC 2010: 26A33 Dedicated to Professor Rudolf Gorenflo on the occasion of his 80th anniversary

Digital Humanities: Challenges of the Transformation of Tools and Objects of Knowledge in Contemporary Humanities

This paper aims to sketch some bases for the problematization of digital tools as objects of knowledge for Social Sciences and Humanities (SSH). Our purpose is to raise some relevant questions about the Digital Humanities (DH) and how SSH and Computer Sciences (CS) can work together to face new challenges. We discuss some tension points and propose a model for SSH and CS collaboration for joint projects in cultural digitization.

One-dimensional and two-dimensional polyacrylamide gel electrophoresis: a tool for protein characterisation in aquatic samples

Dissolved organic nitrogen (DON) represents the least understood part of the nitrogen cycle. Due to recent methodological developments, proteins now represent a potentially characterisable fraction of DON at the macromolecular level. We have applied polyacrylamide gel electrophoresis to characterise proteins in samples from a range of aquatic environments in the Everglades National Park, Florida, USA. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed that each sample has a complex and characteristic protein distribution. Some proteins appeared to be common to more than one site, and these might derive from dominant higher plant vegetation. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) provided better resolution; however, strong background hindered interpretation. Our results suggest that the two techniques can be used in parallel as a tool for protein characterisation: SDS-PAGE to provide a sample-specific fingerprint and 2D-PAGE to focus on the characterisation of individual protein molecules.

Spatial, geomorphological, and seasonal variability of CDOM in estuaries of the Florida Coastal Everglades

This paper demonstrates the usefulness of fluorescence techniques for long-term monitoring and assessment of the dynamics (sources, transport and fate) of chromophoric dissolved organic matter (CDOM) in highly compartmentalized estuarine regions with non-point water sources. Water samples were collected monthly from a total of 73 sampling stations in the Florida Coastal Everglades (FCE) estuaries during 2001 and 2002. Spatial and seasonal variability of CDOM characteristics were investigated for geomorphologically distinct sub-regions within Florida Bay (FB), the Ten Thousand Islands (TTI), and Whitewater Bay (WWB). These variations were observed in both quantity and quality of CDOM. TOC concentrations in the FCE estuaries were generally higher during the wet season (June–October), reflecting high freshwater loadings from the Everglades in TTI, and a high primary productivity of marine biomass in FB. Fluorescence parameters suggested that the CDOM in FB is mainly of marine/microbial origin, while for TTI and WWB a terrestrial origin from Everglades marsh plants and mangroves was evident. Variations in CDOM quality seemed mainly controlled by tidal exchange/mixing of Everglades freshwater with Florida Shelf waters, tidally controlled releases of CDOM from fringe mangroves, primary productivity of marine vegetation in FB and diagenetic processes such as photodegradation (particularly for WWB). The source and dynamics of CDOM in these subtropical estuaries is complex and found to be influenced by many factors including hydrology, geomorphology, vegetation cover, landuse and biogeochemical processes. Simple, easy to measure, high sample throughput fluorescence parameters for surface waters can add valuable information on CDOM dynamics to long-term water quality studies which can not be obtained from quantitative determinations alone.

Phosphorus Biogeochemistry and the Impact of Phosphorus Enrichment: Why Is the Everglades so Unique?

The Florida Everglades is extremely oligotrophic and sensitive to small increases in phosphorus (P) concentrations. P enrichment is one of the dominant anthropogenic impacts on the ecosystem and is therefore a main focus of restoration efforts. In this review, we synthesize research on P biogeochemistry and the impact of P enrichment on ecosystem structure and function in the Florida Everglades. There are clear patterns of increased P concentrations and altered structure and processes along nutrient-enrichment gradients in the water, periphyton, soils, macrophytes, and consumers. Periphyton, an assemblage of algae, bacteria, and associated microfauna, is abundant and has a large influence on phosphorus cycling in the Everglades. The oligotrophic Everglades is P-starved, has lower P concentrations and higher nitrogen–phosphorus (N:P) ratios, and has oxidized to only slightly reduced soil profiles compared to other freshwater wetland ecosystems. Possible general causes and indications of P limitation in the Everglades and other wetlands include geology, hydrology, and dominance of oxidative microbial nutrient cycling. The Everglades may be unique with respect to P biogeochemistry because of the multiple causes of P limitation and the resulting high degree of limitation.

Mapping Height and Biomass of Mangrove Forests in Everglades National Park with SRTM Elevation Data

We produced a landscape scale map of mean tree height in mangrove forests in Everglades National Park (ENP) using the elevation data from the Shuttle Radar Topography Mission (SRTM). The SRTM data was calibrated using airborne lidar data and a high resolution USGS digital elevation model (DEM). The resulting mangrove height map has a mean tree height error of 2.0 m (RMSE) over a pixel of 30 m. In addition, we used field data to derive a relationship between mean forest stand height and biomass in order to map the spatial distribution of standing biomass of mangroves for the entire National Park. The estimation showed that most of the mangrove standing biomass in the ENP resides in intermediate- height mangrove stands around 8 m. We estimated the total mangrove standing biomass in ENP to be 5.6 X 109 kg.

Determining Spatial and Temporal Inputs of Freshwater, Including Submarine Groundwater Discharge, to a Subtropical Estuary Using Geochemical Tracers, Biscayne Bay, South Florida

Geochemical mixing models were used to decipher the dominant source of freshwater (rainfall, canal discharge, or groundwater discharge) to Biscayne Bay, an estuary in south Florida. Discrete samples of precipitation, canal water, groundwater, and bay surface water were collected monthly for 2 years and analyzed for salinity, stable isotopes of oxygen and hydrogen, and Sr2+/Ca2+ concentrations. These geochemical tracers were used in three separate mixing models and then combined to trace the magnitude and timing of the freshwater inputs to the estuary. Fresh groundwater had an isotopic signature (δ 18O = −2.66‰, δD −7.60‰) similar to rainfall (δ 18O = −2.86‰, δD = −4.78‰). Canal water had a heavy isotopic signature (δ 18O = −0.46‰, δD  = −2.48‰) due to evaporation. This made it possible to use stable isotopes of oxygen and hydrogen to separate canal water from precipitation and groundwater as a source of freshwater into the bay. A second model using Sr2+/Ca2+ ratios was developed to discern fresh groundwater inputs from precipitation inputs. Groundwater had a Sr2+/Ca2+ ratio of 0.07, while precipitation had a dissimilar ratio of 0.89. When combined, these models showed a freshwater input ratio of canal/precipitation/groundwater of 37%:53%:10% in the wet season and 40%:55%:5% in the dry season with an error of ±25%. For a bay-wide water budget that includes saltwater and freshwater mixing, fresh groundwater accounts for 1–2% of the total fresh and saline water input.

Lake metabolism and the diel oxygen technique: State of the science

Significant improvements have been made in estimating gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP) from diel, “free-water” changes in dissolved oxygen (DO). Here we evaluate some of the assumptions and uncertainties that are still embedded in the technique and provide guidelines on how to estimate reliable metabolic rates from high-frequency sonde data. True whole-system estimates are often not obtained because measurements reflect an unknown zone of influence which varies over space and time. A minimum logging frequency of 30 min was sufficient to capture metabolism at the daily time scale. Higher sampling frequencies capture additional pattern in the DO data, primarily related to physical mixing. Causes behind the often large daily variability are discussed and evaluated for an oligotrophic and a eutrophic lake. Despite a 3-fold higher day-to-day variability in absolute GPP rates in the eutrophic lake, both lakes required at least 3 sonde days per week for GPP estimates to be within 20% of the weekly average. A sensitivity analysis evaluated uncertainties associated with DO measurements, piston velocity (k), and the assumption that daytime R equals nighttime R. In low productivity lakes, uncertainty in DO measurements and piston velocity strongly impacts R but has no effect on GPP or NEP. Lack of accounting for higher R during the day underestimates R and GPP but has no effect on NEP. We finally provide suggestions for future research to improve the technique.

Leaf Functional Traits and Forest Structure of Tropical Dry Forest Species Along a Rainfall Gradient in Florida and Puerto Rico

This study examined how different rainfall regimes affect a set of leaf functional traits related to plant stress and forest structure in tropical dry forest (TDF) species on limestone substrate. One hundred fifty eight individuals of four tree species were sampled in six ecological sites in south Florida and Puerto Rico, ranging in mean annual rainfall from 858 to 1933 mm yr-1. Leaf nitrogen content, specific leaf area (SLA), and N:P ratio of evergreen species, but not deciduous species, responded positively to increasing rainfall. Phosphorus content was unaffected in both groups. Canopy height and basal area reached maxima of 10.3 m and 31.4 m2 ha-1, respectively, at 1168 mm annual rainfall. Leaf traits reflected soil properties only to a small extent. This led us to the conclusion that water is a major limiting factor in TDF and some species that comprise TDF ecosystems are limited by nitrogen in limestone sites with less than ~1012 mm rainfall, but organismal, biological and/or abiotic forces other than rainfall control forest structure in moister sites.