NFAT5 genes are part of the osmotic regulatory system in Atlantic salmon (Salmo salar)

Acknowledgements This study was supported by a grant from the Biotechnology and Biological Sciences Research Council (BBSRC, BB/H008063/1), UK to DGH and SAM. Funding also came from Research Council Norway for project number 241016 for DGH and EJ. This work was carried out as part of a PhD thesis funded by the Marine Alliance of Science and Technology Scotland (MASTS).Peer reviewedPublisher PD

Optimizing the CLIC Beam Delivery System

The optimization of the new CLIC Final Focus System (FFS) with L*=3.5m is presented for a collection of CLIC beam parameters. The final performance is computed for the full Beam Delivery System including the new diagnostics section. A comparison to previous designs is also presented

Convex optimization problem prototyping for image reconstruction in computed tomography with the Chambolle-Pock algorithm

The primal-dual optimization algorithm developed in Chambolle and Pock (CP), 2011 is applied to various convex optimization problems of interest in computed tomography (CT) image reconstruction. This algorithm allows for rapid prototyping of optimization problems for the purpose of designing iterative image reconstruction algorithms for CT. The primal-dual algorithm is briefly summarized in the article, and its potential for prototyping is demonstrated by explicitly deriving CP algorithm instances for many optimization problems relevant to CT. An example application modeling breast CT with low-intensity X-ray illumination is presented.Comment: Resubmitted to Physics in Medicine and Biology. Text has been modified according to referee comments, and typos in the equations have been correcte

Absolute dimensions of solar-type eclipsing binaries. EF Aquarii: a G0 test for stellar evolution models

Recent studies have shown that stellar chromospheric activity, and its effect on convective energy transport in the envelope, is most likely the cause of significant radius and temperature discrepancies between theoretical evolution models and observations. We aim to determine absolute dimensions and abundances for the solar-type detached eclipsing binary EF Aqr, and to perform a detailed comparison with results from recent stellar evolutionary models. uvby-beta standard photometry was obtained with the Stromgren Automatic Telescope. The broadening function formalism was applied on spectra observed with HERMES at the Mercator telescope in La Palma, to obtain radial velocity curves. Masses and radii with a precision of 0.6% and 1.0% respectively have been established for both components of EF Aqr. The active 0.956 M_sol secondary shows star spots and strong Ca II H and K emission lines. The 1.224 M_sol primary shows signs of activity as well, but at a lower level. An [Fe/H] abundance of 0.00+-0.10 is derived with similar abundances for Si, Ca, Sc, Ti, V, Cr, Co, and Ni. Solar calibrated evolutionary models such as Yonsei-Yale, Victoria-Regina and BaSTI isochrones and evolutionary tracks are unable to reproduce EF Aqr, especially for the secondary, which is 9% larger and 400 K cooler than predicted. Models adopting significantly lower mixing length parameters l/H_p remove these discrepancies, as seen in other solar type binaries. For the observed metallicity, Granada models with a mixing length of l/H_p=1.30 (primary) and 1.05 (secondary) reproduce both components at a common age of 1.5+-0.6 Gyr. Observations of EF Aqr suggests that magnetic activity, and its effect on envelope convection, is likely to be the cause of discrepancies in both radius and temperature, which can be removed by adjusting the mixing length parameter of the models downwards.Comment: 11 pages, 8 figures, accepted for publication by A&

Electron transport in single wall carbon nanotube weak links in the Fabry-Perot regime

We fabricated reproducible high transparency superconducting contacts consisting of superconducting Ti/Al/Ti trilayers to gated single-walled carbon nanotubes (SWCNTs). The reported semiconducting SWCNT have normal state differential conductance up to $3e^2/h$ and exhibit clear Fabry-Perot interference patterns in the bias spectroscopy plot. We observed subharmonic gap structure in the differential conductance and a distinct peak in the conductance at zero bias which is interpreted as a manifestation of a supercurrent. The gate dependence of this supercurrent as well as the excess current are examined and compared to a coherent theory of superconducting point contacts with good agreement.Comment: 10 pages, 4 figure

Desulfuromonas svalbardensis sp nov and Desulfuromusa ferrireducens sp nov., psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard

Two psychrophilic, Gram-negative, rod-shaped, motile bacteria (strains 112T and 102T) that conserved energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation were isolated from permanently cold Arctic marine sediments. Both strains grew at temperatures down to -2 degrees C, with respective temperature optima of 14 degrees C and 14-17 degrees C for strains 112T and 102T. The isolated strains reduced Fe(III) using common fermentation products such as acetate, lactate, propionate, formate or hydrogen as electron donors, and they also grew with fumarate as the sole substrate. As alternatives to Fe(III), they reduced fumarate, S0 and Mn(IV). Based on 16S rRNA gene sequence similarity, strain 112T was most closely related to Desulfuromonas acetoxidans (97.0 %) and Desulfuromonas thiophila NZ27T (95.5 %), and strain 102T to Malonomonas rubra Gra Mal 1T (96.3 %) and Desulfuromusa succinoxidans GylacT (95.9 %) within the Deltaproteobacteria. Strains 112T and 102T therefore represent novel species, for which the names Desulfuromonas svalbardensis sp. nov. (type strain 112T=DSM 16958T=JCM 12927T) and Desulfuromusa ferrireducens sp. nov. (type strain 102T=DSM 16956T=JCM 12926T) are proposed

Sulfide assimilation by ectosymbionts of the sessile ciliate, Zoothamnium niveum

We investigated the constraints on sulfide uptake by bacterial ectosymbionts on the marine peritrich ciliate Zoothamnium niveum by a combination of experimental and numerical methods. Protists with symbionts were collected on large blocks of mangrove-peat. The blocks were placed in a flow cell with flow adjusted to in situ velocity. The water motion around the colonies was then characterized by particle tracking velocimetry. This shows that the feather-shaped colony of Z. niveum generates a unidirectional flow of seawater through the colony with no recirculation. The source of the feeding current was the free-flowing water although the size of the colonies suggests that they live partly submerged in the diffusive boundary layer. We showed that the filtered volume allows Z. niveum to assimilate sufficient sulfide to sustain the symbiosis at a few micromoles per liter in ambient concentration. Numerical modeling shows that sulfide oxidizing bacteria on the surfaces of Z. niveum can sustain 100-times higher sulfide uptake than bacteria on flat surfaces, such as microbial mats. The study demonstrates that the filter feeding zooids of Z. niveum are preadapted to be prime habitats for sulfide oxidizing bacteria due to Z. niveum’s habitat preference and due to the feeding current. Z. niveum is capable of exploiting low concentrations of sulfide in near norm-oxic seawater. This links its otherwise dissimilar habitats and makes it functionally similar to invertebrates with thiotrophic symbionts in filtering organs

Methanol maps of low-mass protostellar systems: the Serpens Molecular Core

Observations of Serpens have been performed at the JCMT using Harp-B. Maps over a 4.5'x5.4' region were made in a frequency window around 338 GHz, covering the 7-6 transitions of methanol. Emission is extended over each source, following the column density of H2 but showing up also particularly strongly around outflows. The rotational temperature is low, 15-20 K, and does not vary with position within each source. The abundance is typically 10^-9 - 10^-8 with respect to H2 in the outer envelope, whereas "jumps" by factors of up to 10^2 -10^3 inside the region where the dust temperature exceeds 100 K are not excluded. A factor of up to ~ 10^3 enhancement is seen in outflow gas. In one object, SMM4, the ice abundance has been measured to be ~ 3x10^-5 with respect to H2 in the outer envelope, i.e., a factor of 10^3 larger than the gas-phase abundance. Comparison with C18O J=3-2 emission shows that strong CO depletion leads to a high gas-phase abundance of CH3OH not just for the Serpens sources, but for a larger sample of protostars. The observations illustrate the large-scale, low-level desorption of CH3OH from dust grains, extending out to and beyond 7500 AU from each source, a scenario which is consistent with non-thermal (photo-)desorption from the ice. The observations also illustrate the usefulness of CH3OH as a tracer of energetic input in the form of outflows, where methanol is sputtered from the grain surfaces. Finally, the observations provide further evidence of CH3OH formation through CO hydrogenation proceeding on grain surfaces in low-mass envelopes.Comment: Accepted for publication in A&A

Singlet-Triplet Physics and Shell Filling in Carbon Nanotube Double Quantum Dots

An artifcial two-atomic molecule, also called a double quantum dot (DQD), is an ideal system for exploring few electron physics. Spin-entanglement between just two electrons can be explored in such systems where singlet and triplet states are accessible. These two spin-states can be regarded as the two states in a quantum two-state system, a so-called singlet-triplet qubit. A very attractive material for realizing spin based qubits is the carbon nanotube (CNT), because it is expected to have a very long spin coherence time. Here we show the existence of a gate-tunable singlet-triplet qubit in a CNT DQD. We show that the CNT DQD has clear shell structures of both four and eight electrons, with the singlet-triplet qubit present in the four-electron shells. We furthermore observe inelastic cotunneling via the singlet and triplet states, which we use to probe the splitting between singlet and triplet, in good agreement with theory.Comment: Supplement available at: http://www.fys.ku.dk/~hij/public/singlet-triple_supp.pd

Penicillium verrucosum occurrence and Ochratoxin A contents in organically cultivated grain with special reference to ancient wheat types and drying practice

This study addresses the relationship between the ochratoxigenic strains of Penicillium verrucosum and ochratoxin A (OTA) contents in organically cultivated grain. It included 37 combined, non-dried grain samples from farmers with no drying facilities as well as 19 non-dried and 22 dried samples from six farms with on-farm drying facilities (Case studies 1-6). The study focused on the ancient wheat type spelt but also included samples of wheat, rye, barley, oats, triticale, emmer, and einkorn. All 78 samples were analysed for moisture content (MC) and occurrence of P. verrucosum. The latter was assessed by plating non-disinfected kernels on DYSG agar and counting those contaminated by the fungus. Fiftyfive samples were analysed for OTA. Most of the combine harvested samples (82%) were contaminated with P. verrucosum prior to drying. This was ascribed to difficult harvest conditions and many samples of spelt, which was significantly more contaminated by P. verrucosum than oats, wheat and barley. Though not statistically significant, the results also indicated that spelt was more contaminated than rye, which is usually regarded the most sensitive small grain cereal. No correlation was found between number of kernels contaminated by P. verrucosum and OTA content. Despite many non-dried samples being contaminated by P. verrucosum, only two exceeded the EU maximum limit for grain (5 ng OTA g-1), both being spring spelt with 18 and 92 ng g-1, respectively. The problems were most likely correlated to a late harvest and high MC of the grain. The case studies showed exceedings of the maximum limit in a batch of dried oats and spring wheat, respectively, probably to be explained by insufficient drying of late harvested grain with high MC. Furthermore, our results clearly indicate that OTA is not produced in significant amounts in samples with MCs below 17%. All dried samples with MCs above 18% exceeded the 5 ng OTA g-1 limit in grain. However, no correlation between MC and the amount of OTA produced was found