The detection of Atlantic cod (Gadus morhua) using loop mediated isothermal amplification in conjunction with a simplified DNA extraction process

Atlantic cod (Gadus morhua) is a commercially important species of white fish, and one of three species legally identifiable as cod in the UK. Mislabelling of G. morhua does occur, as does the substitution of G. morhua for less expensive species. Sensitive molecular tests based on PCR have been developed for this species, but they have limitations, including the need for expensive thermal cycling equipment, and complex DNA extraction procedures. A loop mediated isothermal amplification (LAMP) assay was designed for the G. morhua cytochrome b gene, which was capable of detecting 0.1% w/w G. morhua in a homogenised raw fish mix. The LAMP assay was also able to detect G. morhua DNA when a rapid sample preparation was used, involving heating 100 mg of fish in a 1 ml aliquot of water and testing the supernatant, showing a higher tolerance of amplification inhibitors than a PCR assay. The LAMP assay did not generate a positive result when challenged with a range of non-target species, including Gadus macrocephalus, and Gadus chalcogrammus, indicating a high level of specificity. Direct detection of a positive reaction using propidium iodide was also demonstrated

Combustion of dried animal dung as biofuel results in the generation of highly redox active fine particulates.

BACKGROUND: The burning of biomass in the developing world for heating and cooking results in high indoor particle concentrations. Long-term exposure to airborne particulate matter (PM) has been associated with increased rates of acute respiratory infections, chronic obstructive lung disease and cancer. In this study we determined the oxidative activity of combustion particles derived from the biomass fuel dung cake by examining their capacity to deplete antioxidants from a model human respiratory tract lining fluid (RTLF). For comparison, the observed oxidative activity was compared with that of particles derived from industrial and vehicular sources. RESULTS: Incubation of the dung cake particle suspensions in the RTLF for 4 h resulted in a mean loss of ascorbate of 72.1 +/- 0.7 and 89.7 +/- 2.5% at 50 and 100 microg/ml, respectively. Reduced glutathione was depleted by 49.6 +/- 4.3 and 63.5 +/- 22.4% under the same conditions. The capacity of these samples to deplete ascorbate was in excess of that observed with diesel or gasoline particles, but comparable to that seen with residual oil fly ash and considerably in excess of all three control particles in terms of glutathione depletion. Co-incubation with the metal chelator diethylenetriaminepentaacetate inhibited these losses, whilst minimal inhibition was seen with superoxide dismutase and catalase treatment. The majority of the activity observed appeared to be contained within aqueous particle extracts. CONCLUSION: These data demonstrate that biomass derived particles have considerable oxidative activity, largely attributable to their transition metal content

The Broad Absorption Line Tidal Disruption Event iPTF15af: Optical and Ultraviolet Evolution

We present multi-wavelength observations of the tidal disruption event (TDE) iPTF15af, discovered by the intermediate Palomar Transient Factory (iPTF) survey at redshift $z=0.07897$. The optical and ultraviolet (UV) light curves of the transient show a slow decay over five months, in agreement with previous optically discovered TDEs. It also has a comparable black-body peak luminosity of $L_{\rm{peak}} \approx 1.5 \times 10^{44}$ erg/s. The inferred temperature from the optical and UV data shows a value of (3$-$5) $\times 10^4$ K. The transient is not detected in X-rays up to $L_X < 3 \times 10^{42}$erg/s within the first five months after discovery. The optical spectra exhibit two distinct broad emission lines in the He II region, and at later times also H$\alpha$ emission. Additionally, emission from [N III] and [O III] is detected, likely produced by the Bowen fluorescence effect. UV spectra reveal broad emission and absorption lines associated with high-ionization states of N V, C IV, Si IV, and possibly P V. These features, analogous to those of broad absorption line quasars (BAL QSOs), require an absorber with column densities $N_{\rm{H}} > 10^{23}$ cm$^{-2}$. This optically thick gas would also explain the non-detection in soft X-rays. The profile of the absorption lines with the highest column density material at the largest velocity is opposite that of BAL QSOs. We suggest that radiation pressure generated by the TDE flare at early times could have provided the initial acceleration mechanism for this gas. Spectral UV line monitoring of future TDEs could test this proposal.Comment: 20 pages, 12 figures, published in Ap

Assay of matrix metalloproteinases types 1, 2, 3 and 9 in breast cancer.

Matrix metalloproteinases (MMPs) are zinc dependent endopeptidases implicated in cancer invasion and metastasis. Gelatin zymography was performed on 84 human breast carcinomas and seven normal breast tissues. The precursor form of MMP-2 (72 kDa) was found in 11 (12%) samples, while its two activated forms, i.e. 62 kDa and 59 kDa, were found in three (6%) and 34 (40%) samples respectively. In contrast to MMP-2, most of the samples (52%) contained MMP-9 in its precursor form. Using ELISA, MMP-1 levels were found in 12% of the samples while MMP-3 levels were found in only 2% of the samples. Levels of MMP-2, -3 and -9 correlated inversely with numbers of nodal metastases. Neither MMP-2 nor -9 levels were significantly related to patient outcome. However, patients with high levels of a 50-kDa gelatinase band after zymography had a significantly better survival than patients with low levels. This species was never observed in normal breast tissue

Tracking of Salmonella Positive Pigs from Farm to Fork in the Republic of Ireland

In this study, individual pigs from selected herds of known Salmonella serological status were tracked through the slaughter and dressing process. From all tracked animals, caecal contents, rectal faeces, carcasses (before washing and chilling and after chilling) and pork primal cuts were examined for the presence of Salmonella. All samples were screened for Salmonella using real time PCR and all suspect positive samples were confirmed using the ISO 6579 method for Salmonella. To determine the relationship between Salmonella isolates from different parts of the chain , all isolates are being characterised by Pulse Field Gel Electrophoresis (PFGE). The results suggest that the slaughter and dressing operations have a significant effect on the incidence of Salmonella and that even if pigs are presented for slaughter with caecal or rectal carriage of Salmonella then good slaughter practices can prevent carcass contamination. All data generated in the study is being fed into a quantitative risk assessment model for Salmonella in pork

Towards modelling language innovation acceptance in online social networks

Language change and innovation is constant in online and offline communication, and has led to new words entering people’s lexicon and even entering modern day dictionaries, with recent additions of ‘e-cig’ and ‘vape’. However the manual work required to identify these ‘innovations’ is both time consuming and subjective. In this work we demonstrate how such innovations in language can be identified across two different OSN’s (Online Social Networks) through the operationalisation of known language acceptance models that incorporate relatively simplistic statistical tests. From grounding our work in language theory, we identified three statistical tests that can be applied, variation in; frequency, form and meaning; each showing different success rates across the two networks (Geo-bound Twitter sample and a sample of Reddit). These tests were also applied to different community levels within the two networks allow- ing for different innovations to be identified across different community structures over the two networks, for instance: identifying regional variation across Twitter, and variation across groupings of Subreddits, where identified example in- novations included ‘casualidad’ and ‘cym’

Excitons in type-II quantum dots: Finite offsets

Quantum size effects for an exciton attached to a spherical quantum dot are calculated by a variational approach. The band line-ups are assumed to be type-II with finite offsets. The dependence of the exciton binding energy upon the dot radius and the offsets is studied for different sets of electron and hole effective masses

Issues in Performance Assessments for Disposal of U.S. Department of Energy Low-Level Waste

The US Department of Energy (DOE) and its contractors have long been pioneers in the field of radiological performance assessment (PA). Much effort has been expended in developing technology and acquiring data to facilitate the assessment process. This is reflected in DOE Order 5820.2A, Radioactive Waste Management Chapter III of the Order lists policy and requirements to manage the DOEs low-level waste; performance objectives for low-level waste management are stated to ensure the protection of public health and the environment. A radiological PA is also required to demonstrate compliance with the performance objectives. DOE Order 5820.2A further requires that an Oversight and Peer Review Panel be established to ensure consistency and technical quality around the DOE complex in the development and application of PA models that include site-specific geohydrology and waste composition. The DOE has also established a Performance Assessment Task Team (PATT) to integrate the activities of sites that are preparing PAs. The PATT`s purpose is to recommend policy and guidance to DOE on issues that impact PAs so that the approaches taken are as consistent as possible across the DOE complex