Phase behaviour of DNA in presence of DNA-binding proteins

To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of the DNA collapse. For physiologically relevant values of the DNA-protein affinity, this collapse gives rise to a biphasic regime with a dense and a dilute phase; the corresponding phase diagram was computed. Using an approach based on Hamiltonian paths, we show that the dense phase has either a molten globule or a crystalline structure, depending on the DNA bending rigidity, which is influenced by the ionic strength. These results are valid at the thermodynamical equilibrium and should therefore be consistent with many biological processes, whose characteristic timescales range typically from 1 ms to 10 s. Our model may thus be applied to biological phenomena that involve DNA-binding proteins, such as DNA condensation with crystalline order, which occurs in some bacteria to protect their chromosome from detrimental factors; or transcription initiation, which occurs in clusters called transcription factories that are reminiscent of the dense phase characterized in this study.Comment: 20 pages, 9 figures, accepted for publication at The Biophysical Journa

Prediction of the water/oil interfacial tension from molecular simulations using the coarse-grained SAFT-γ Mie force field

This work is framed within the Ninth Industrial Fluid Properties Simulation Challenge, with the aim of assessing the capability of molecular simulation methods and force fields to accurately predict the interfacial tension of oil + water mixtures at high temperatures and pressures. The challenge focused on predicting the liquid-liquid interfacial tension of binary mixtures of dodecane + water, toluene + water and a 50:50 (wt%) mixture of dodecane:toluene + water at 1.825 MPa (250 psig) and temperatures from 110 to 170 °C. In our entry for the challenge, we employed coarse-grained intermolecular models parametrized via a top-down technique in which an accurate equation of state is used to link experimentally observed macroscopic properties of fluids with the force-field parameters. The state-of-the-art version of the statistical associating fluid theory (SAFT) for potentials of variable range as reformulated in terms of the Mie potential is employed here. Interfacial tensions are calculated through a direct method, where an elongated simulation cell is sampled through molecular dynamics in the isobaric-isothermal constant area ensemble (NPzzAT). The coarse-grained nature of the force field allows for the accelerated calculation of relatively large systems. The binary interaction parameters that describe the cross-interactions have been obtained in previous works by fitting to interfacial tensions of the constituent binaries at lower pressures and temperatures; these are taken as constant for all conditions and mixtures studied. After disclosure of the challenge results, we observe that the interfacial properties of the mixtures are described with an error of less than 5 mN/m over the whole range of conditions, demonstrating the accuracy and transferability of the top-down SAFT-γ Mie force field approach

Eliminacija kloramfenikola u kalifornijskoj pastrvi

Chloramphenicol muscle residue levels in rainbow trout were determined after oral administration of 84 μg kg−1d−1 of chloramphenicol for four days. Samples were taken one day before treatment and for 43 days after the treatment was over. Chloramphenicol was analysed using an in-house enzyme linked immunoassay (ELISA) validated against the criteria of the Commission Decision 2002/657/EC. Validation parameters confi rmed that the method was appropriate for the detection of chloramphenicol at levels below the minimum required performance limit (MRPL) of 0.3 μg kg−1. The highest chloramphenicol levels were observed on the fi rst day after the treatment had ended (144.3 μg kg−1). Elimination was signifi cant over the fi rst seven days; signifi cant differences were detected between days 1 and 3 (p<0.001), 3 and 5 (p<0.001), and 5 and 7 (p<0.05). Chloramphenicol levels dropped below MRPL to 0.17 μg kg−1 on day 9 after the end of treatment. From day 11 to 43, chloramphenicol residues were detectable in a range from 0.091 μg kg−1 (highest) to 0.011 μg kg−1 (lowest). Our results indicate that trout muscle tissue could be compliant with health requirements for consumption 10 days after withdrawal from chloramphenicol treatment.Određivani su ostaci kloramfenikola u mišićnom tkivu kalifornijske pastrve nakon oralne primjene u dozi od 84 μg kg−1d−1 tijekom 4 dana. Uzorkovanje je provedeno dan prije tretmana te tijekom 43 dana nakon tretmana. Maseni udjeli kloramfenikola određivani su primjenom in-house imunoenzimske metode (ELISA) validirane prema kriterijima Odluke Komisije 2002/657/EC. Dobiveni validacijski parametri pokazuju da je metoda prikladna za određivanje kloramfenikola na nivou manjem od vrijednosti granice najmanje zahtijevane učinkovitosti izvedbe metode (MRPL) od 0,3 μg kg−1. Najviši maseni udjeli kloramfenikola utvrđeni su prvog dana nakon završetka tretmana (144,3 μg kg−1). Statistički značajna eliminacija utvrđena je tijekom sedam dana te je značajno smanjenje određeno između prvog i trećeg (p<0,001), trećeg i petog (p<0,001) te petog i sedmog dana nakon tretmana (p<0,05). Razina kloramfenikola ispod MRPL vrijednosti utvrđena je devetog dana (0,17 μg kg−1) nakon tretmana. U vremenu od 11. do 43. dana nakon tretmana određeni su ostaci kloramfenikola od maksimalno 0,091 μg kg−1 do minimalno 0,011 μg kg−1. Prikazani rezultati pokazuju da se 10 dana nakon završetka tretmana tkivo pastrve može smatrati prikladnim za konzumaciju bez potencijalne štete za zdravlje

Aquaculture Site-Selection and Marine Spatial Planning: The Roles of GIS-Based Tools and Models

Around the globe, increasing human activities in coastal and offshore waters have created complex conflicts between different sectors competing for space and between the use and conservation of ocean resources. Like other users, aquaculture proponents evaluate potential offshore sites based primarily on their biological suitability, technical feasibility, and cost considerations. Recently, Marine Spatial Planning (MSP) has been promoted as an approach for achieving more ecosystem-based marine management, with a focus on balancing multiple management objectives in a holistic way. Both industry-specific and multiple-use planners all rely heavily on spatially-referenced data, Geographic Information System (GIS)-based analytical tools, and Decision Support Systems (DSS) to explore a range of options and assess their costs and benefits. Although ecological factors can currently be assessed fairly comprehensively, better tools are needed to evaluate and incorporate the economic and social considerations that will also be critical to identifying potential sites and achieving successful marine plans. This section highlights the advances in GIS-based DSS in relation to their capability for aquaculture site selection and their integration into multiple-use MSP. A special case of multiple-use planning—the potential co-location of offshore wind energy and aquaculture—is also discussed, including an example in the German EEZ of the North Sea