Suspended solids, light penetration and primary production in the Scheldt estuary

In strong tidal estuaries such as the Scheldt, the hydrodynamic conditions display large variations, with current velocities ranging from zero during slacks up to 2 m.s-1 during ebbs and floods. This highly fluctuating water velocity induces a periodically varying shear stress at the sediment-water interface, resulting in a cyclic pattern of sedimentation and resuspension. As a result, the suspended solid concentration in the water column follows a marked tidal fluctuation which causes significant variations of the light-attenuation coefficient. Since the underwater light field depends on both the incident light and the light-attenuation coefficient, the instantaneous light availability (PAR) in the water column has to be computed from these two periodic signals. In this paper, we present some characteristics of the underwater light field in the Scheldt estuary. We show that the estimation of gross primary production (GPP) by phytoplankton is strongly affected by the time-variation of the light-attenuation coefficient (kd). In particular, the common practice of considering a constant (time-averaged) kd value leads to an erroneous assessment of the time- and depth-integrated GPP. Finally, we show some estimates of the phytoplankton net primary production (NPP) in the Scheldt, computed from a coupled model that takes into account the hydrodynamic conditions, the light penetration and the phytoplankton dynamics

The Destruction of Antiquity in Syria and Iraq - We Ought to Care About a Viable Solution

Syria and Iraq are home to numerous ancient civilizations which have been instrumental in helping modern humans understand the dawn of civilization. While human casualties are often the media focus, the permanent loss of historic sites and artifacts is a long term economic burden for local communities that rely on tourism, and the global cultural heritage within Syria and Iraq simply cannot be replaced once it is gone. This paper will explore the fundamentalist ideals which fuel the desecration of antiquity, the historic relevance of variety of damaged or destroyed sites, and we will argue that a long term solution involves targeting the illegal trade of antiquities, the economic foundation of ISIS, and the withdrawal of aggressive foreign military forces

Marine phytoplankton community composition data from the Belgian part of the North Sea, 1968-2010

The Belgian Phytoplankton Database (BPD) is a comprehensive data collection comprising quantitative phytoplankton cell counts from multiple research projects conducted since 1968. The collection is focused on the Belgian part of the North Sea, but also includes data from the French and the Dutch part of the North Sea. The database includes almost 300 unique sampling locations and more than 3,000 sampling events resulting in more than 86,000 phytoplankton cell count records. The dataset covers two periods: 1968 to 1978 and 1994 to 2010. The BPD can be accessed online and provides high quality phytoplankton count data. The species taxonomy is updated, and the count values are quality checked and standardized. Important metadata like sampling date, sampling location, sampling depth and methodology is provided and standardized. Additionally, associated abiotic data and biovolume values are available. The dataset allows to conduct analyses of long-term temporal and spatial trends in phytoplankton community structure in the southern part of the North Sea, including changes in phytoplankton phenology and seasonality

Marine phytoplankton community composition data from the Belgian part of the North Sea, 1968-2010

The Belgian Phytoplankton Database (BPD) is a comprehensive data collection comprising quantitative phytoplankton cell counts from multiple research projects conducted since 1968. The collection is focused on the Belgian part of the North Sea, but also includes data from the French and the Dutch part of the North Sea. The database includes almost 300 unique sampling locations and more than 3,000 sampling events resulting in more than 86,000 phytoplankton cell count records. The dataset covers two periods: 1968 to 1978 and 1994 to 2010. The BPD can be accessed online and provides high quality phytoplankton count data. The species taxonomy is updated, and the count values are quality checked and standardized. Important metadata like sampling date, sampling location, sampling depth and methodology is provided and standardized. Additionally, associated abiotic data and biovolume values are available. The dataset allows to conduct analyses of long-term temporal and spatial trends in phytoplankton community structure in the southern part of the North Sea, including changes in phytoplankton phenology and seasonality

4 Decades of Belgian Marine Monitoring: uplifting historical data to today’s needs - Final Report

Context : Long-term quality checked and integrated datasets for the Belgian Part of the North Sea (BPNS) are essential to detect changes in this complex ecosystem and support policy related decisions.Objectives: - Compile and safeguard quality checked, intercalibrated and integrated datasets and make them publicly accessible for further research and policy purposes.- Improve or develop methods and protocols to assess and interpret environmental change in the BPNS and compare trends with neighbouring areas.- Provide support and advice for policy related decisions and legal measures, like MSFD and OSPAR.Conclusions: A scheme with data management tools has been worked out for efficient data flow throughout the project. The scheme, including the mandatory metadata fields and standardization, can be used as a guideline for future projects. Inventories of datasources, projects and data-originators were compiled and the final datasets are available via the central dataportal. Even after compiling and quality checking the long-term datasets, the scientists had to consider some limitations, like changing methodologies and low data resolution, and incorporate these into their trend analyses procedures. Some remarkable environmental changes over time were observed. Model results of the contaminants showed decreasing trends for heavy metals and PCBs. Zn concentrations, however, were found increasing in marine sediments while As concentrations were found increasing in groyne mussels. Nearby the port of Zeebrugge and the mouth of the Scheldt, PCB concentrations were found slightly increasing again over the last decade. The study on eutrophication showed that nutrient (N, P) riverine concentrations and loads have decreased continuously from the end of the 1980‟s to now. However, this did not result in a comparable decrease of marine nutrient concentrations. No clear long-term trend effect was observed on in situ chlorophyll a concentrations following the nutrient decrease. However, a clear change in chlorophyll a phenology followed the increase in sea surface temperature in the period. Furthermore, biomass, seasonality and structure of diatom and dinoflagellate communities were compared between the 1970s and 2000s for the Belgian Part of the North Sea (BPNS), derived from the newly established Belgian Phytoplankton Database. Distinct changes were observed: changes in diatom and dinoflagellate biomass and shift of fulcrum; changes in community structure, with a trend towards seasonal homogenization in the diatom community; increased occurrence of harmful diatom (Pseudo-nitzschia) and dinoflagellate (e.g. Prorocentrum) genera. The observed changes correlate well with overall increases in temperature and changes in nutrient loads and ratios.And finally, for acidification, pH data reveal an increasing trend from the mid-70‟s to the mid-80‟s and a decrease of pH from the mid-80‟s onwards that seems consistent with changes in primary production patterns. The comparison of CH4 concentrations obtained in 1990 and 2016, showed a decreasing trend consistent with alleviation of eutrophication in the area.Based on the outcome of this successful project, the partners defined various recommendations regarding future monitoring strategies for policy makers

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology

Building blocks for protein interaction devices

Here, we propose a framework for the design of synthetic protein networks from modular protein–protein or protein–peptide interactions and provide a starter toolkit of protein building blocks. Our proof of concept experiments outline a general work flow for part–based protein systems engineering. We streamlined the iterative BioBrick cloning protocol and assembled 25 synthetic multidomain proteins each from seven standardized DNA fragments. A systematic screen revealed two main factors controlling protein expression in Escherichia coli: obstruction of translation initiation by mRNA secondary structure or toxicity of individual domains. Eventually, 13 proteins were purified for further characterization. Starting from well-established biotechnological tools, two general–purpose interaction input and two readout devices were built and characterized in vitro. Constitutive interaction input was achieved with a pair of synthetic leucine zippers. The second interaction was drug-controlled utilizing the rapamycin-induced binding of FRB(T2098L) to FKBP12. The interaction kinetics of both devices were analyzed by surface plasmon resonance. Readout was based on Förster resonance energy transfer between fluorescent proteins and was quantified for various combinations of input and output devices. Our results demonstrate the feasibility of parts-based protein synthetic biology. Additionally, we identify future challenges and limitations of modular design along with approaches to address them