Optical calibration hardware for the Sudbury Neutrino Observatory

The optical properties of the Sudbury Neutrino Observatory (SNO) heavy water Cherenkov neutrino detector are measured in situ using a light diffusing sphere ("laserball"). This diffuser is connected to a pulsed nitrogen/dye laser via specially developed underwater optical fibre umbilical cables. The umbilical cables are designed to have a small bending radius, and can be easily adapted for a variety of calibration sources in SNO. The laserball is remotely manipulated to many positions in the D2O and H2O volumes, where data at six different wavelengths are acquired. These data are analysed to determine the absorption and scattering of light in the heavy water and light water, and the angular dependence of the response of the detector's photomultiplier tubes. This paper gives details of the physical properties, construction, and optical characteristics of the laserball and its associated hardware.Comment: 17 pages, 8 figures, submitted to Nucl. Inst. Meth.

Breeding home range movements of pre-fledged brolga chicks, Antigone rubicunda (Gruidae) in Victoria, Australia - Implications for wind farm planning and conservation

Built infrastructure, such as wind farms and power lines, can impair wildlife movement. These barriers may displace individuals from important habitats due to direct mortality or disturbance. Understanding animal movement patterns can help avoid such impacts and manage population level effects. Avoiding impacts and implementing mitigation strategies is difficult when movement and home range information is lacking. Impact at breeding sites may negatively affect population recruitment. The number of wind farm developments is increasing in southern Australia within the core range of the south-eastern brolga (Antigone rubicunda) population. The main threats to this wetland bird include habitat loss, chick predation and collisions with power lines and fences. Wind farms may increase collision and mortality risk, and habitat displacement but the impact is difficult to assess or mitigate, as movement patterns and home range size are unknown. We deployed 11 GPS transmitters on pre-fledged brolga chicks at breeding sites in 2010-2012, including one at a wind farm, to investigate movement and home range use of brolga chicks. Brolga chicks moved 442m on average, to and from night roost wetlands (range: 0m-1964 m). The average breeding home range was 232 ha, estimated with a Brownian bridge movement model at 95% UD, but varied greatly between individuals (70 ha-523 ha). Brolgas used either single or multiple wetlands, and those using multiple wetlands either switched between them or relocated permanently. Information from this study can be used to design turbine-free buffers at brolga breeding sites and to manage breeding wetlands. (c) 2019 Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Identification and characterization of a novel peptide from rainbow trout (<i>Oncorhynchus mykiss</i>) with antimicrobial activity against <i>Streptococcus iniae</i>

The overuse and misuse of antibiotics has led to the emergence of antibiotic-resistant bacterial species which remain a challenge to treat therapeutically. Novel and efficacious drugs are desperately needed to combat pathogens. One method to facilitate these discoveries is the use of in silico methods. Computational biology has the power to scan large data sets and screen for potential molecules with antibacterial function. In the current study, an in silico approach was used to identify an antimicrobial peptide (AMP) derived from rainbow trout von Willebrand Factor. The AMP was tested against a panel of aquatic bacterial pathogens and was found to possess antibacterial activity against Streptococcus iniae (S. iniae). Since S. iniae is a zoonotic pathogen, this may be useful in other species as well. The peptide was non-hemolytic and non-cytotoxic at the concentrations tested in rainbow trout cells. Pre-treatment of rainbow trout cells with the peptide did not result in an upregulation of immune genes but stimulating the rainbow trout macrophage/monocyte-like cell line, RTS11, with heat-killed S. iniae, did result in a significant upregulation of the tumor necrosis factor alpha (tnfa) gene. In this study, a new AMP has been identified but its expression, synthesis and role in vivo remains unknown. Nevertheless, the findings presented improve our understanding of fish gill and macrophage responses towards this important zoonotic pathogen.</p

Pathway-Wide Association Study Implicates Multiple Sterol Transport and Metabolism Genes in HDL Cholesterol Regulation

Pathway-based association methods have been proposed to be an effective approach in identifying disease genes, when single-marker association tests do not have sufficient power. The analysis of quantitative traits may be benefited from these approaches, by sampling from two extreme tails of the distribution. Here we tested a pathway association approach on a small genome-wide association study (GWAS) on 653 subjects with extremely high high-density lipoprotein cholesterol (HDL-C) levels and 784 subjects with low HDL-C levels. We identified 102 genes in the sterol transport and metabolism pathways that collectively associate with HDL-C levels, and replicated these association signals in an independent GWAS. Interestingly, the pathways include 18 genes implicated in previous GWAS on lipid traits, suggesting that genuine HDL-C genes are highly enriched in these pathways. Additionally, multiple biologically relevant loci in the pathways were not detected by previous GWAS, including genes implicated in previous candidate gene association studies (such as LEPR, APOA2, HDLBP, SOAT2), genes that cause Mendelian forms of lipid disorders (such as DHCR24), and genes expressing dyslipidemia phenotypes in knockout mice (such as SOAT1, PON1). Our study suggests that sampling from two extreme tails of a quantitative trait and examining genetic pathways may yield biological insights from smaller samples than are generally required using single-marker analysis in large-scale GWAS. Our results also implicate that functionally related genes work together to regulate complex quantitative traits, and that future large-scale studies may benefit from pathway-association approaches to identify novel pathways regulating HDL-C levels