Evaluating the impact of hydropower on downstream migrating anguillid eels: Catchment-wide and fine-scale approaches to identify cost-effective solutions

Hydropower is an increasingly popular source of renewable and ‘green’ (in terms of emissions) energy, but reduced longitudinal connectivity and diverting flow through turbines can have negative impacts on catadromous anguillid eel species that have declined globally. There is an urgent need for environmental managers to perform remediation actions, such as protecting flows for migratory fish and providing passage solutions at infrastructure, under increasing legislative pressure. To deliver this, a more comprehensive understanding of eel migration in catchments with hydropower is required. Here, we illustrate the importance of catchment-wide and fine-scale acoustic telemetry, coupled with the influence of eel maturation (i.e. sex steroid levels), to determine the impact of Wairua run-of-river Power Station (WPS) on downstream migrating shortfin eels (Anguilla australis; n = 25) in Wairua River, New Zealand. Migration speed through the unregulated reach upstream of WPS was positively correlated with flow, but not eel length or sex steroids. Three eels passed a diversion weir (DW) to follow the natural watercourse and eight entered the WPS canal. Eels predominantly entered (95.2%) and were last detected (85.7%) in WPS forebay during hours of darkness. Eleven (52%) of the 21 eels that entered WPS forebay were impinged or entrained, all when three or four turbines were in operation (power generation >3.04 MW). Ten (48%) passed WPS spillway during significantly higher spill than impinged or entrained eels, with four passing during no turbine operation, after experiencing high flows near the intake (multiple receivers in WPS forebay used to quantify fine-scale behaviour). On average, eels were impinged or entrained at WPS significantly quicker (6.40 ± 11.13 days) than eels that entered the spillway (25.17 ± 15.12 days), but eel length and sex steroids did not significantly influence fate. Of the eels that migrated through the entire 55 km study reach, passage time at DW and WPS equated to 0.01–0.02% and 47.62–92.17% of their migration, respectively. Mitigation for WPS (and similar power schemes) should focus on operational or physical changes at DW to minimise eels entering power station forebay(s). Turbine shutdowns, ensuring WPS spillway is available and the provision of a bypass channel in WPS forebay are also discussed as ways to conserve the species with the potential to save costs for water resource managers

A Bayesian spatio-temporal framework to identify outbreaks and examine environmental and social risk factors for infectious diseases monitored by routine surveillance

Spatio-temporal disease patterns can provide clues to etiological pathways, but can be complex to model. Using a flexible Bayesian hierarchical framework, we identify previously undetected space-time clusters and environmental and socio-demographic risk factors for reported giardiasis and cryptosporidiosis at the New Zealand small area level. For giardiasis, there was no seasonal pattern in outbreak probability and an inverse association with density of dairy cattle (β^₁= -0.09, Incidence Risk Ratio (IRR) 0.90 (95% CI 0.84, 0.97) per 1 log increase in cattle/km²). In dairy farming areas, cryptosporidiosis outbreaks were observed in spring. Reported cryptosporidiosis was positively associated with dairy cattle density: β^₁= 0.12, IRR 1.13 (95% CI 1.05, 1.21) per 1 log increase in cattle/km2 and inversely associated with weekly average temperature: β^₁=-0.07, IRR 0.92 (95% CI 0.87, 0.98) per 4°C increase. This framework can be generalized to determine the potential drivers of sporadic cases and latent outbreaks of infectious diseases of public health importance

Simulations and Measurements of the Background Encountered by a High-Altitude Balloon-Borne Experiment for Hard X-ray Astronomy

We have modelled the hard X-ray background expected for a high-altitude balloon flight of the Energetic X-ray Telescope Experiment (EXITE2), an imaging phoswich detector/telescope for the 20--600 keV energy range. Photon and neutron-induced contributions to the background are considered. We describe the code and the results of a series of simulations with different shielding configurations. The simulated hard X-ray background for the actual flight configuration agrees reasonably well (within a factor of $\sim$ 2) with the results measured on the first flight of EXITE2 from Palestine, Texas. The measured background flux at 100 keV is $\sim$ 4 $\times$ 10$^{-4}$ counts cm$^{-2}$ s$^{-1}$ keV$^{-1}$.Comment: 17 pages Latex (uses aaspp4.sty) plus 7 postscript figures: available in file figs.tar.g

Marked Campylobacteriosis Decline after Interventions Aimed at Poultry, New Zealand

A population-level food safety response successfully reduced disease incidence

Endogenous CRISPR/Cas systems for genome engineering in the acetogens Acetobacterium woodii and Clostridium autoethanogenum

Acetogenic bacteria can play a major role in achieving Net Zero through their ability to convert CO2 into industrially relevant chemicals and fuels. Full exploitation of this potential will be reliant on effective metabolic engineering tools, such as those based on the Streptococcus pyogenes CRISPR/Cas9 system. However, attempts to introduce cas9-containing vectors into Acetobacterium woodii were unsuccessful, most likely as a consequence of Cas9 nuclease toxicity and the presence of a recognition site for an endogenous A. woodii restriction–modification (R-M) system in the cas9 gene. As an alternative, this study aims to facilitate the exploitation of CRISPR/Cas endogenous systems as genome engineering tools. Accordingly, a Python script was developed to automate the prediction of protospacer adjacent motif (PAM) sequences and used to identify PAM candidates of the A. woodii Type I-B CRISPR/Cas system. The identified PAMs and the native leader sequence were characterized in vivo by interference assay and RT-qPCR, respectively. Expression of synthetic CRISPR arrays, consisting of the native leader sequence, direct repeats, and adequate spacer, along with an editing template for homologous recombination, successfully led to the creation of 300 bp and 354 bp in-frame deletions of pyrE and pheA, respectively. To further validate the method, a 3.2 kb deletion of hsdR1 was also generated, as well as the knock-in of the fluorescence-activating and absorption-shifting tag (FAST) reporter gene at the pheA locus. Homology arm length, cell density, and the amount of DNA used for transformation were found to significantly impact editing efficiencies. The devised workflow was subsequently applied to the Type I-B CRISPR/Cas system of Clostridium autoethanogenum, enabling the generation of a 561 bp in-frame deletion of pyrE with 100% editing efficiency. This is the first report of genome engineering of both A. woodii and C. autoethanogenum using their endogenous CRISPR/Cas systems

The pMTL70000 modular, plasmid vector series for strain engineering in Cupriavidus necator H16

Cupriavidus necator H16 can convert CO2 into industrial chemicals and fuels. To facilitate its engineering, we designed, built and tested the pMTL70000 modular plasmids comprising standardised Cupriavidus and E. coli replicons, selectable markers and application specific modules. Plasmids were characterised in terms of transmissibility, stability, copy number and compatibility

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering

The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami

Structural Transitions and Global Minima of Sodium Chloride Clusters

In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we determine reaction pathways between the low energy isomers of one of these clusters, (NaCl)35Cl-. The key process in these structural transitions is a highly cooperative rearrangement in which two parts of the nanocrystal slip past one another on a {110} plane in a direction. In this way the nanocrystals can plastically deform, in contrast to the brittle behaviour of bulk sodium chloride crystals at the same temperatures; the nanocrystals have mechanical properties which are a unique feature of their finite size. We also report and compare the global potential energy minima for (NaCl)NCl- using two empirical potentials, and comment on the effect of polarization.Comment: extended version, 13 pages, 8 figures, revte