Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them

Sediment release of dissolved organic matter in the oxygen minimum zone off Peru

In combination to sluggish ventilation by ocean currents, the nutrient upwelling and high surface productivity, followed by organic matter remineralization, leads to a pronounced oxygen minimum zone (OMZ) in the eastern tropical South Pacific (ETSP). There, oxygen concentrations drop below 1 �mol/kg at a water depth <80 m. The high productivity results in the supply of organic matter (OM) to the anoxic sediments and its utilization by heterotrophic communities. The microbial utilization of OM under anoxia leads to nitrogen loss processes, and an accumulation of sulphide and methane. The proximity of the OMZ to the ocean surface in the ETSP may lead to an active outgassing of climate relevant products of the anoxic OM remineralization. The degradation of OM in sediments is associated with production of dissolved organic matter (DOM) from organic particles (POM) that is further remineralized into inorganic nutrients and dissolved inorganic carbon, which then can be released back to the water column, fuelling productivity. Part of the DOM pool may be released to the overlying water column and serve as ligands for micronutrients, such as iron, or provide an additional substrate for microbial communities to respire, affecting overlying water column biogeochemistry. Despite the potential relevance for biogeochemical processes, the quality of the DOM in the pore waters that may be released to the overlying water column has been barely studied in the ETSP off Peru. High spatial resolution measurements of DOM fluorescence (FDOM) during the research cruise M93 (Feb-March 2013) indicated elevated intensities near the sediments in the ETSP off Peru. Those intensities were interpreted as a sediment release of DOM, the quantification of dissolved organic carbon (DOC) flux, however, was not possible at the time. To estimate DOM fluxes and DOM quality, DOC and DOM samples were collected from the sediment pore waters and from benthic incubation chambers from six stations along the 12°S transect in the Peruvian upwelling in 2017 (cruises M136, M137). Samples were collected using a multiple-corer and by Biogeochemical Observatories, respectively. Here, we evaluate DOC fluxes from the sediments and relate them to the measurements of FDOM. We evaluate the quality of DOM by Excitation Emission spectroscopy, followed by parallel factor analysis. The possible implications of the DOM release for water column biogeochemistry are discussed

The contribution of surface and submesoscale processes to turbulence in the open ocean surface boundary layer

The ocean surface boundary layer is a critical interface across which momentum, heat, and trace gases are exchanged between the oceans and atmosphere. Surface processes (winds, waves, and buoyancy forcing) are known to contribute significantly to fluxes within this layer. Recently, studies have suggested that submesoscale processes, which occur at small scales (0.1–10 km, hours to days) and therefore are not yet represented in most ocean models, may play critical roles in these turbulent exchanges. While observational support for such phenomena has been demonstrated in the vicinity of strong current systems and littoral regions, relatively few observations exist in the open‐ocean environment to warrant representation in Earth system models. We use novel observations and simulations to quantify the contributions of surface and submesoscale processes to turbulent kinetic energy (TKE) dissipation in the open‐ocean surface boundary layer. Our observations are derived from moorings in the North Atlantic, December 2012 to April 2013, and are complemented by atmospheric reanalysis. We develop a conceptual framework for dissipation rates due to surface and submesoscale processes. Using this framework and comparing with observed dissipation rates, we find that surface processes dominate TKE dissipation. A parameterization for symmetric instability is consistent with this result. We next employ simulations from an ocean front‐resolving model to reestablish that dissipation due to surface processes exceeds that of submesoscale processes by 1–2 orders of magnitude. Together, these results suggest submesoscale processes do not dramatically modify vertical TKE budgets, though such dynamics may be climatically important owing to their ability to remove energy from the ocean

Testing the reconstruction of modelled particulate organic carbon from surface ecosystem components using PlankTOM12 and machine learning

Understanding the relationship between surface marine ecosystems and the export of carbon to depth by sinking organic particles is key to representing the effect of ecosystem dynamics and diversity, and their evolution under multiple stressors, on the carbon cycle and climate in models. Recent observational technologies have greatly increased the amount of data available, both for the abundance of diverse plankton groups and for the concentration and properties of particulate organic carbon in the ocean interior. Here we use synthetic model data to test the potential of using machine learning (ML) to reproduce concentrations of particulate organic carbon within the ocean interior based on surface ecosystem and environmental data. We test two machine learning methods that differ in their approaches to data-fitting, the random forest and XGBoost methods. The synthetic data are sampled from the PlankTOM12 global biogeochemical model using the time and coordinates of existing observations. We test 27 different combinations of possible drivers to reconstruct small (POCS) and large (POCL) particulate organic carbon concentrations. We show that ML can successfully be used to reproduce modelled particulate organic carbon over most of the ocean based on ecosystem and modelled environmental drivers. XGBoost showed better results compared to random forest thanks to its gradient boosting trees' architecture. The inclusion of plankton functional types (PFTs) in driver sets improved the accuracy of the model reconstruction by 58 % on average for POCS and by 22 % for POCL. Results were less robust over the equatorial Pacific and some parts of the high latitudes. For POCS reconstruction, the most important drivers were the depth level, temperature, microzooplankton and PO4, while for POCL it was the depth level, temperature, mixed-layer depth, microzooplankton, phaeocystis, PO4 and chlorophyll a averaged over the mixed-layer depth. These results suggest that it will be possible to identify linkages between surface environmental and ecosystem structure and particulate organic carbon distribution within the ocean interior using real observations and to use this knowledge to improve both our understanding of ecosystem dynamics and of their functional representation within models.</p

Coherent multi-flavour spin dynamics in a fermionic quantum gas

Microscopic spin interaction processes are fundamental for global static and dynamical magnetic properties of many-body systems. Quantum gases as pure and well isolated systems offer intriguing possibilities to study basic magnetic processes including non-equilibrium dynamics. Here, we report on the realization of a well-controlled fermionic spinor gas in an optical lattice with tunable effective spin ranging from 1/2 to 9/2. We observe long-lived intrinsic spin oscillations and investigate the transition from two-body to many-body dynamics. The latter results in a spin-interaction driven melting of a band insulator. Via an external magnetic field we control the system's dimensionality and tune the spin oscillations in and out of resonance. Our results open new routes to study quantum magnetism of fermionic particles beyond conventional spin 1/2 systems.Comment: 9 pages, 5 figure

Quarkonium correlators and spectral functions at zero and finite temperature

We study quarkonium correlators and spectral functions at zero and finite temperature using the anisotropic Fermilab lattice formulation with anisotropy xi=2 and 4. To control cutoff effects we use several different lattice spacings. The spectral functions were extracted from lattice correlators with Maximum Entropy Method based on a new algorithm. We find evidence for the survival of 1S quarkonium states in the deconfined medium till relatively high temperatures as well as for dissolution of 1P quarkonium states right above the deconfinement temperature.Comment: 22 pages, 31 figures, uses revtex styl

Lyman alpha Radiative Transfer with Dust: Escape Fractions from Simulated High-Redshift Galaxies

The Lyman alpha emission line is an essential diagnostic tool for probing galaxy formation and evolution. Not only is it commonly the strongest observable line from high-redshift galaxies but from its shape detailed information about its host galaxy can be revealed. However, due to the scattering nature of Lya photons increasing their path length in a non-trivial way, if dust is present in the galaxy the line may be severely suppressed and its shape altered. In order to interpret observations correctly, it is thus of crucial significance to know how much of the emitted light actually escapes the galaxy. In the present work, using a combination of high-resolution cosmological hydro-simulations and an adaptively refinable Monte Carlo Lya radiative transfer code including an advanced model of dust, the escape fractions f_esc of Lya radiation from high-redshift (z = 3.6) galaxies are calculated. In addition to the average escape fraction, the variation of f_esc in different directions and from different parts of the galaxies is investigated, as well as the effect on the emergent spectrum. Escape fractions from a sample of simulated galaxies of representative physical properties are found to decrease for increasing galaxy virial mass M_vir, from f_esc approaching unity for M_vir ~ 10^9 M_sun to f_esc less than 10% for M_vir ~ 10^12 M_sun. In spite of the dust being almost grey, it is found that the emergent spectrum is affected non-uniformly, with the escape fraction of photons close to the line center being much higher than of those in the wings, thus effectively narrowing the Lya line.Comment: Submitted to ApJ; comments are very welcom

Effects of external nutrient sources and extreme weather events on the nutrient budget of a Southern European coastal lagoon

The seasonal and annual nitrogen (N), phosphorus (P), and carbon (C) budgets of the mesotidal Ria Formosa lagoon, southern Portugal, were estimated to reveal the main inputs and outputs, the seasonal patterns, and how they may influence the ecological functioning of the system. The effects of extreme weather events such as long-lasting strong winds causing upwelling and strong rainfall were assessed. External nutrient inputs were quantified; ocean exchange was assessed in 24-h sampling campaigns, and final calculations were made using a hydrodynamic model of the lagoon. Rain and stream inputs were the main freshwater sources to the lagoon. However, wastewater treatment plant and groundwater discharges dominated nutrient input, together accounting for 98, 96, and 88 % of total C, N, and P input, respectively. Organic matter and nutrients were continuously exported to the ocean. This pattern was reversed following extreme events, such as strong winds in early summer that caused upwelling and after a period of heavy rainfall in late autumn. A principal component analysis (PCA) revealed that ammonium and organic N and C exchange were positively associated with temperature as opposed to pH and nitrate. These variables reflected mostly the benthic lagoon metabolism, whereas particulate P exchange was correlated to Chl a, indicating that this was more related to phytoplankton dynamics. The increase of stochastic events, as expected in climate change scenarios, may have strong effects on the ecological functioning of coastal lagoons, altering the C and nutrient budgets.Portuguese Science and Technology Foundation (FCT) [POCI/MAR/58427/2004, PPCDT/MAR/58427/2004]; Portuguese Science and Technology Foundation (FCT