Laboratory procedures manual for the firefly luciferase assay for adenosine triphosphate (ATP)

A manual on the procedures and instruments developed for the adenosine triphosphate (ATP) luciferase assay is presented. Data cover, laboratory maintenance, maintenance of bacterial cultures, bacteria measurement, reagents, luciferase procedures, and determination of microbal susceptibility to antibiotics

Habitat-based density models of pack-ice seal distribution in the southern Weddell Sea, Antarctica

Climate variability and changes in sea ice dynamics have caused several ice-obligate or krill-dependent populations of marine predators to decline, eliciting concern about their demographic persistence and the indirect ecological consequences that predator depletions may have on marine ecosystems. Pack-ice seals are dominant ice-obligate predators in the Antarctic marine ecosystem, but there is considerable uncertainty about their abundance and population trends. We modelled the density and distribution of pack-ice seals as a function of environmental covariates in the southern Weddell Sea, Antarctica. Our density surface modelling approach used data from aerial surveys of pack-ice seals collected in the 2013/14 austral summer. Crabeater seals Lobo don carcinophaga, the most numerous pack-ice seal we observed, occurred at the highest densities in areas with extensive sea ice near the continental shelf break, but were almost absent in areas of similar sea ice concentration in the southern extent of the Weddell Sea. The highest densities of Weddell seals Leptonychotes weddelli, which were less abundant than crabeater seals within the pack-ice habitat, were predicted to occur over the continental shelf, near the shelf break. The distribution of both seal species broadly corresponded with the distribution and relative abundance of their main prey (Antarctic krill Euphausia superba and Antarctic silverfish Pleuragramma antarctica) obtained from concurrent ecosystem surveys. Ross seals Ommatophoca rossii and leopard seals Hydrurga leptonyx were not detected at all and are apparently rare within the southern Weddell Sea. These results can contribute to biodiversity assessments in the context of marine protected area planning in this region of the Southern Ocean

The warm, the excited, and the molecular gas: GRB 121024A shining through its star-forming galaxy

We present the first reported case of the simultaneous metallicity determination of a gamma-ray burst (GRB) host galaxy, from both afterglow absorption lines as well as strong emission-line diagnostics. Using spectroscopic and imaging observations of the afterglow and host of the long-duration Swift GRB121024A at z = 2.30, we give one of the most complete views of a GRB host/environment to date. We observe a strong damped Ly-alpha absorber (DLA) with a hydrogen column density of log N(HI) = 21.88 +/- 0.10, H2 absorption in the Lyman-Werner bands (molecular fraction of log(f)~ -1.4; fourth solid detection of molecular hydrogen in a GRB-DLA), the nebular emission lines H-alpha, H-beta, [O II], [O III] and [N II], as well as metal absorption lines. We find a GRB host galaxy that is highly star-forming (SFR ~ 40 solar masses/yr ), with a dust-corrected metallicity along the line of sight of [Zn/H]corr = -0.6 +/- 0.2 ([O/H] ~ -0.3 from emission lines), and a depletion factor [Zn/Fe] = 0.85 +/- 0.04. The molecular gas is separated by 400 km/s (and 1-3 kpc) from the gas that is photoexcited by the GRB. This implies a fairly massive host, in agreement with the derived stellar mass of log(M/M_solar ) = 9.9+/- 0.2. We dissect the host galaxy by characterising its molecular component, the excited gas, and the line-emitting star-forming regions. The extinction curve for the line of sight is found to be unusually flat (Rv ~15). We discuss the possibility of an anomalous grain size distributions. We furthermore discuss the different metallicity determinations from both absorption and emission lines, which gives consistent results for the line of sight to GRB 121024A.Comment: 20 pages, 11 figures, accepted by MNRA

The mysterious optical afterglow spectrum of GRB140506A at z=0.889

Context. Gamma-ray burst (GRBs) afterglows probe sightlines to star-forming regions in distant star-forming galaxies. Here we present a study of the peculiar afterglow spectrum of the z = 0.889 Swift GRB 140506A. Aims. Our aim is to understand the origin of the very unusual properties of the absorption along the line-of-sight. Methods. We analyse spectroscopic observations obtained with the X-shooter spectrograph mounted on the ESO/VLT at two epochs 8.8 h and 33 h after the burst as well as imaging from the GROND instrument. We also present imaging and spectroscopy of the host galaxy obtained with the Magellan telescope. Results. The underlying afterglow appears to be a typical afterglow of a long-duration GRB. However, the material along the line-of- sight has imprinted very unusual features on the spectrum. Firstly, there is a very broad and strong flux drop below 8000 AA (4000 AA in the rest frame), which seems to be variable between the two spectroscopic epochs. We can reproduce the flux-drops both as a giant 2175 AA extinction bump and as an effect of multiple scattering on dust grains in a dense environment. Secondly, we detect absorption lines from excited H i and He i. We also detect molecular absorption from CH+ . Conclusions. We interpret the unusual properties of these spectra as reflecting the presence of three distinct regions along the line-of-sight: the excited He i absorption originates from an H ii-region, whereas the Balmer absorption must originate from an associated photodissociation region. The strong metal line and molecular absorption and the dust extinction must originate from a third, cooler region along the line-of-sight. The presence of (at least) three separate regions is reflected in the fact that the different absorption components have different velocities relative to the systemic redshift of the host galaxy.Comment: 8 pages, 4 figures. Accepted for publications in A&

IκB kinase 2 determines oligodendrocyte loss by non-cell-autonomous activation of NF-κB in the central nervous system

The IκB kinase complex induces nuclear factor kappa B activation and has recently been recognized as a key player of autoimmunity in the central nervous system. Notably, IκB kinase/nuclear factor kappa B signalling regulates peripheral myelin formation by Schwann cells, however, its role in myelin formation in the central nervous system during health and disease is largely unknown. Surprisingly, we found that brain-specific IκB kinase 2 expression is dispensable for proper myelin assembly and repair in the central nervous system, but instead plays a fundamental role for the loss of myelin in the cuprizone model. During toxic demyelination, inhibition of nuclear factor kappa B activation by conditional ablation of IκB kinase 2 resulted in strong preservation of central nervous system myelin, reduced expression of proinflammatory mediators and a significantly attenuated glial response. Importantly, IκB kinase 2 depletion in astrocytes, but not in oligodendrocytes, was sufficient to protect mice from myelin loss. Our results reveal a crucial role of glial cell-specific IκB kinase 2/nuclear factor kappa B signalling for oligodendrocyte damage during toxic demyelination. Thus, therapies targeting IκB kinase 2 function in non-neuronal cells may represent a promising strategy for the treatment of distinct demyelinating central nervous system disease

A genome-wide resource for the analysis of protein localisation in Drosophila

The Drosophila genome contains >13000 protein-coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here, we present a genome-wide fosmid library of 10000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins, we created transgenic lines, and for a total of 207 lines, we assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we visualised many proteins at endogenous expression levels and found a large fraction of them localising to subcellular compartments. By applying genetic complementation tests, we estimate that about two-thirds of the tagged proteins are functional. Moreover, these tagged proteins enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will boost systematic analysis of protein expression and localisation in various cellular and developmental contexts

The evolution of superluminous supernova LSQ14mo and its interacting host galaxy system

We present and analyse an extensive dataset of the superluminous supernova (SLSN) LSQ14mo (z = 0.256), consisting of a multi-colour light curve from-30 d to +70 d in the rest-frame (relative to maximum light) and a series of six spectra from PESSTO covering-7 d to +50 d. This is among the densest spectroscopic coverage, and best-constrained rising light curve, for a fast-declining hydrogen-poor SLSN. The bolometric light curve can be reproduced with a millisecond magnetar model with 4 M⊙ ejecta mass, and the temperature and velocity evolution is also suggestive of a magnetar as the power source. Spectral modelling indicates that the SN ejected 6 M⊙ of CO-rich material with a kinetic energy of 7 × 1051 erg, and suggests a partially thermalised additional source of luminosity between-2 d and +22 d. This may be due to interaction with a shell of material originating from pre-explosion mass loss. We further present a detailed analysis of the host galaxy system of LSQ14mo. PESSTO and GROND imaging show three spatially resolved bright regions, and we used the VLT and FORS2 to obtain a deep (five-hour exposure) spectra of the SN position and the three star-forming regions, which are at a similar redshift. The FORS2 spectrum at + 300 days shows no trace of SN emission lines and we place limits on the strength of [O i] from comparisons with other Ic supernovae. The deep spectra provides a unique chance to investigate spatial variations in the host star-formation activity and metallicity. The specific star-formation rate is similar in all three components,as is the presence of a young stellar population. However, the position of LSQ14mo exhibits a lower metallicity, with 12 + log (O/H) = 8.2 in both the R23 and N2 scales (corresponding to 0.3 Z⊙). We propose that the three bright regions in the host system are interacting, which could induce gas flows triggering star formation in low-metallicity regions. © ESO, 2017

The optical/NIR afterglow of GRB 111209A: Complex yet not unprecedented

Context. Afterglows of gamma-ray bursts (GRBs) are simple in the most basic model, but can show many complex features. The ultra-long duration GRB 111209A, one of the longest GRBs ever detected, also has the best-monitored afterglow in this rare class of GRBs. Aims. We want to address the question whether GRB 111209A was a special event beyond its extreme duration alone, and whether it is a classical GRB or another kind of high-energy transient. The afterglow may yield significant clues. Methods. We present afterglow photometry obtained in seven bands with the GROND imager as well as in further seven bands with the Ultraviolet/Optical Telescope (UVOT) on-board the Neil Gehrels Swift Observatory. The light curve is analysed by multi-band modelling and joint fitting with power-laws and broken power-laws, and we use the contemporaneous GROND data to study the evolution of the spectral energy distribution. We compare the optical afterglow to a large ensemble we have analysed in earlier works, and especially to that of another ultra-long event, GRB 130925A. We furthermore undertake a photometric study of the host galaxy. Results. We find a strong, chromatic rebrightening event at ≈0.8 days after the GRB, during which the spectral slope becomes redder. After this, the light curve decays achromatically, with evidence for a break at about 9 days after the trigger. The afterglow luminosity is found to not be exceptional. We find that a double-jet model is able to explain the chromatic rebrightening. The afterglow features have been detected in other events and are not unique. Conclusions. The duration aside, the GRB prompt emission and afterglow parameters of GRB 111209A are in agreement with the known distributions for these parameters. While the central engine of this event may differ from that of classical GRBs, there are multiple lines of evidence pointing to GRB 111209A resulting from the core-collapse of a massive star with a stripped envelope