Large scale international replication and meta-analysis study confirms association of the 15q14 locus with myopia. The CREAM consortium

Myopia is a complex genetic disorder and a common cause of visual impairment among working age adults. Genome-wide association studies have identified susceptibility loci on chromosomes 15q14 and 15q25 in Caucasian populations of European ancestry. Here, we present a confirmation and meta-analysis study in which we assessed whether these two loci are also associated with myopia in other populations. The study population comprised 31 cohorts from the Consortium of Refractive Error and Myopia (CREAM) representing 4 different continents with 55,177 individuals; 42,845 Caucasians and 12,332 Asians. We performed a meta-analysis of 14 single nucleotide polymorphisms (SNPs) on 15q14 and 5 SNPs on 15q25 using linear regression analysis with spherical equivalent as a quantitative outcome, adjusted for age and sex. We calculated the odds ratio (OR) of myopia versus hyperopia for carriers of the top-SNP alleles using a fixed effects meta-analysis. At locus 15q14, all SNPs were significantly replicated, with the lowest P value 3.87 × 10 -12 for SNP rs634990 in Caucasians, and 9.65 × 10 -4 for rs8032019 in Asians. The overall meta-analysis provided P value 9.20 × 10 -23 for the top SNP rs634990. The risk of myopia versus hyperopia was OR 1.88 (95 % CI 1.64, 2.16, P < 0.001) for homozygous carriers of the risk allele at the top SNP rs634990, and OR 1.33 (95 % CI 1.19, 1.49, P < 0.001) for heterozygous carriers. SNPs at locus 15q25 did not replicate significantly (P value 5.81 × 10 -2 for top SNP rs939661). We conclude that common variants at chromosome 15q14 influence susceptibility for myopia in Caucasian and Asian populations world-wide. © The Author(s) 2012

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways

Animal welfare testing for shooting and darting free-ranging wildlife: a review and recommendations

Several important techniques for managing wildlife rely on ballistics (the behaviour of projectiles), including killing techniques (shooting) as well as capture and marking methods (darting). Because all ballistic techniques have the capacity to harm animals, animal welfare is an important consideration. Standardised testing approaches that have allowed refinement for other physical killing and capture methods (e.g. traps for mammals) have not been applied broadly to ballistic methods. At the same time, new technology is becoming available for shooting (e.g. subsonic and lead-free ammunition) and darting (e.g. dye-marker darts). We present several case studies demonstrating (a) how basic ballistic testing can be performed for novel firearms and/or projectiles, (b) the benefits of identifying methods producing undesirable results before operational use, and (c) the welfare risks associated with bypassing testing of a technique before broad-scale application. Following the approach that has been used internationally to test kill-traps, we suggest the following four-step testing process: (1) range and field testing to confirm accuracy and precision, the delivery of appropriate kinetic energy levels and projectile behaviour, (2) post-mortem assessment of ballistic injury in cadavers, (3) small-scale live animal pilot studies with predetermined threshold pass/fail levels, and (4) broad-scale use with reporting of the frequency of adverse animal welfare outcomes. Wepresent this as a practical approach for maintaining and improving animal welfare standards when considering the use of ballistic technology for wildlife management

Increasing the Yield and Cryosurvival of Spermatozoa from Rhinoceros Ejaculates Using the Enzyme Papain

The preservation of rhinoceros semen is vital for captive breeding programs. While successful collection and cryopreservation of rhinoceros semen has been reported, the volume and quality of semen produced is often low due to the high viscosity associated with ejaculates collected via electroejaculation. Reducing semen viscosity would enable access to previously unusable spermatozoa from viscous fractions and could improve quality post-thaw. The enzyme papain successfully reduced the viscosity of camelid semen but has yet to be tested in wildlife species. This study assessed the influence of papain on the in vitro quality of rhinoceros spermatozoa during cryopreservation using advanced semen assessment. In experiment 1, the motility of spermatozoa from the viscous fraction of an ejaculate, either untreated or treated with papain and its inhibitor E-64 prior to cryopreservation, was assessed post-thaw. In experiment 2, spermatozoa from papain-treated viscous fractions were compared to spermatozoa frozen from untreated sperm-rich fractions pre-freeze, as well as after 0, 1.5 and 3 h of incubation post-thaw (37 &deg;C). Papain significantly increased the quantity of spermatozoa collected from ejaculates, as well as the motility prior to freezing. Papain also improved the post-thaw motility, velocity, linearity and straightness of samples compared to sperm-rich samples, with no detriment to sperm viability, lipid membrane disorder, production of ROS or DNA integrity (p &lt; 0.05). Results show the benefit of supplementing rhinoceros spermatozoa with papain prior to cryopreservation on sperm cryosurvival and demonstrates the potential of using papain to improve the success of cryopreservation protocols, not only for the rhinoceros, but also for other wildlife species

Sequence analyses at mitochondrial and nuclear loci reveal a novel Theileria sp. and aid in the phylogenetic resolution of piroplasms from Australian marsupials and ticks.

The order Piroplasmida encompasses two main families: Babesiidae and Theileriidae, containing tick-borne pathogens of veterinary and medical importance worldwide. While only three genera (Babesia, Cytauxzoon and Theileria) comprising piroplasm parasites are currently recognised, phylogenetic studies at the 18S rRNA (18S) gene suggest that these organisms represent at least ten lineages, one of which comprises the relatively unique and highly diverse Theileria spp. from Australian marsupials and ticks. As an alternative to analysing 18S sequences alone, sequencing of mitochondrial genes has proven to be useful for the elucidation of evolutionary relationships amongst some groups of piroplasms. This research aimed to characterise piroplasms from Australian native mammals and ticks using multiple genetic markers (18S, cytochrome c, oxidase subunit III (cox3) and cytochrome B (cytB)) and microscopy. For this, nearly complete piroplasm-18S sequences were obtained from 32 animals belonging to six marsupial species: eastern bettong (Bettongia gaimardi), eastern quoll (Dasyurus viverrinus), eastern grey kangaroo (Macropus giganteus), swamp wallaby (Wallabia bicolor), quokka (Setonix brachyurus) and Gilbert's potoroo (Potorous gilbertii). The organisms detected represented eight novel Theileria genotypes, which formed five sub-clades within the main marsupial clade containing previously reported Australian marsupial and tick-derived Theileria spp. A selection of both novel and previously described Australian piroplasms at the 18S were also successfully characterised, for the first time, at the cox3 and cytB loci, and corroborated the position of Australian native theilerias in a separate, well-supported clade. Analyses of the cox3 and cytB genes also aided in the taxonomic resolution within the clade of Australian Piroplasmida. Importantly, microscopy and molecular analysis at multiple loci led to the discovery of a unique piroplasm species that clustered with the Australian marsupial theilerias, for which we propose the name Theileria lupei n. sp

Animal welfare testing for shooting and darting free-ranging wildlife: a review and recommendations

Several important techniques for managing wildlife rely on ballistics (the behaviour of projectiles), including killing techniques (shooting) as well as capture and marking methods (darting). Because all ballistic techniques have the capacity to harm animals, animal welfare is an important consideration. Standardised testing approaches that have allowed refinement for other physical killing and capture methods (e.g. traps for mammals) have not been applied broadly to ballistic methods. At the same time, new technology is becoming available for shooting (e.g. subsonic and lead-free ammunition) and darting (e.g. dye-marker darts). We present several case studies demonstrating (a) how basic ballistic testing can be performed for novel firearms and/or projectiles, (b) the benefits of identifying methods producing undesirable results before operational use, and (c) the welfare risks associated with bypassing testing of a technique before broad-scale application. Following the approach that has been used internationally to test kill-traps, we suggest the following four-step testing process: (1) range and field testing to confirm accuracy and precision, the delivery of appropriate kinetic energy levels and projectile behaviour, (2) post-mortem assessment of ballistic injury in cadavers, (3) small-scale live animal pilot studies with predetermined threshold pass/fail levels, and (4) broad-scale use with reporting of the frequency of adverse animal welfare outcomes. We present this as a practical approach for maintaining and improving animal welfare standards when considering the use of ballistic technology for wildlife management. ethics, fertility control, human dimensions, pest control, population control

The ‘Goldilocks Zone’ of predation:the level of fox control needed to select predator resistance in a reintroduced mammal in Australia

A large component of the anthropogenic biodiversity crisis is the loss of animal species. In response, there has been significant investment in reintroductions of species to their historical ranges. Predation by native and exotic predators, however, remains a barrier to success. Over the past 200 years, Australia has seen the highest rate of mammal extinction on earth, with mammals within a critical weight range (CWR: 35 g–5.5 kg) most affected due to predation by exotic predators. Populations of some threatened species now exist only in Tasmania, offshore islands, or predator-proof sanctuaries. The next critical step is to return native populations outside of predator-free areas, ‘beyond-the-fence’, on the continental mainland. Given our current inability to completely remove exotic predators from mainland ecosystems, how can we achieve successful mammal reintroductions? A potential solution is to drive adaptation of reintroduced animals towards predator-resistance by exposing them to low levels of predation. We propose the concept of a ‘Goldilocks Zone’—the ‘just right’ levels of predation needed to drive selection for predator-resistant native species, while ensuring population viability. We experimentally reintroduced a mammal, the eastern bettong (Bettongia gaimardi), to mainland Australia, 100 years after its local extinction. Using an intense baiting regime, we reduced the population density of the red fox (Vulpes vulpes), the main factor behind the eastern bettong’s extirpation from the continent. Reducing bait take to 15% of previous levels allowed differential survival among bettongs; some surviving under 100 days and others over 450 (~ 4 times longer than some similar trials with related species). Surviving individuals were generally larger at release than those that died earlier, implying selection for larger bettongs. Our results suggest that reducing predation could establish a Goldilocks Zone that could drive selection for bettongs with predator-resistant traits. Our work contributes to a growing body of literature that explores a shift towards harnessing evolutionary principles to combat the challenges posed by animal management and conservation.This project was supported by the ACT Government, the Australian National University, The Mulligans Flat—Goorooyarroo Woodland Experiment and the ACT Woodlands and Wetlands Trust. The research also received funding from the Australian Government’s National Environmental Science Program through the Threatened Species Recovery Hub to support WB and ME. EB was funded by The Woodlands and Wetlands Trust. ME was partly funded by the Japan Society for Promotion of Science (JSPS) as a Postdoctoral Research Fellow (P19084

Transition to density dependence in a reintroduced ecosystem engineer

When does a reintroduced population of animals become self-regulating? Quantifying this is critical in determining when interventions can be tapered off, or when they may need to be reinstated. We tracked the growth trajectory of a reintroduced population to establish whether it was irruptive and/or had transitioned to self-regulation. In 2012, we reintroduced 32 eastern bettongs (Bettongia gaimardi), a potoroid marsupial from Tasmania, Australia, to a 485 ha exotic predator-proof fenced reserve in the Australian Capital Territory. We established a 92 cage trap monitoring network to track population growth between the Austral Autumn 2014 and Summer 2018. We used capture-recapture models to track changes in the population through time, and modelled 'bettong weight', 'pouch occupancy' and 'age of pouch young' with population variation, to establish potential associations with changes in population size. The estimated population grew from 32 individuals in 2012 to 100 in 2014, 192 in Autumn 2016, and then declined to 151 in Summer 2018. Estimated survival of adults was high-above 92% between most sessions. Adult female weights ranged between 0.485 and 2.428 kg, and adult males between 0.470 and 2.775 kg. Our study showed density dependence was achieved over the 6 year period. Low adult mortality, and variable pouch occupancy related to female weight, suggested that food availability had influenced lactation in females, with flow-on impacts on juvenile survival. Long-term, broad-scale population dynamics were probably driven by a mix of direct (e.g. disease, harvesting for other reintroductions), and indirect (i.e. climate dependent availability of nutritious food) influences on population size

Univariable analysis assessing select epidemiological variables as predictors for the presence of herpesvirus DNA in Tasmanian devils ^a.

<p>^a Reference levels are indicated by odds ratio of 1.0. Results highlighted in bold (log likelihood p ≤ 0.25) represent variables included in the initial multivariable model, with the exception of season as it was directly influenced by timing of management procedures, and therefore correlated with captive status and was thus excluded. In the final model (n = 50) only captivity was identified as a significant factor (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133807#pone.0133807.t008" target="_blank">Table 8</a>). n/a = not applicable.</p><p>Univariable analysis assessing select epidemiological variables as predictors for the presence of herpesvirus DNA in Tasmanian devils <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133807#t006fn001" target="_blank">^a</a>.</p