School of BioSciences - Research Publications
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ItemMetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis(The Open Journal, 2023)MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics software suites and genomic databases to create an accurate taxonomic and functional characterization of the prokaryotic fraction of sequenced microbiomes. Written in the Workflow Definition Language (WDL), MGP produces output that can be explored and interpreted directly, or can be used for downstream analysis. MGP is a pipeline-development best practice tool that uses Singularity for containerization and includes a setup script that downloads the necessary databases for setup. The source code for MGP is freely available and distributed under the Apache 2.0 license.
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ItemLongitudinal spatial mapping of lipid metabolites reveals pre-symptomatic changes in the hippocampi of Huntington?s disease transgenic mice(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2023-01-01)In Huntington's disease (HD), a key pathological feature includes the development of inclusion-bodies of fragments of the mutant huntingtin protein in the neurons of the striatum and hippocampus. To examine the molecular changes associated with inclusion-body formation, we applied MALDI-mass spectrometry imaging and deuterium pulse labelling to determine lipid levels and synthesis rates in the hippocampus of a transgenic mouse model of HD (R6/1 line). The R6/1 HD mice lacked inclusions in the hippocampus at 6 weeks of age (pre-symptomatic), whereas inclusions were pervasive by 16 weeks of age (symptomatic). Hippocampal subfields (CA1, CA3 and DG), which formed the highest density of inclusion formation in the mouse brain showed a reduction in the relative abundance of neuron-enriched lipids that have roles in neurotransmission, synaptic plasticity, neurogenesis, and ER-stress protection. Lipids involved in the adaptive response to ER stress (phosphatidylinositol, phosphatidic acid, and ganglioside classes) displayed increased rates of synthesis in HD mice relative to WT mice at all the ages examined, including prior to the formation of the inclusion bodies. Our findings, therefore, support a role for ER stress occurring pre-symptomatically and potentially contributing to pathological mechanisms underlying HD.
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ItemNo Preview AvailableA metapopulation model reveals connectivity-driven hotspots in treatment resistance evolution in a marine parasite(Oxford University Press, 2022-11-30)In salmon aquaculture, the sustainable management of salmon lice (Lepeophtheirus salmonis) is limited by the adaptive capacity of the parasite. This is evident in the repeated evolution of pesticide resistance in the salmon louse population. To better prepare for resistance, we constructed a numerical metapopulation model that predicts the evolutionary dynamics of lice across an interconnected farm network. This model integrates within-farm population dynamics and between-farm louse dispersal, the latter using outputs from a state-of-the-art particle-tracking model. Distinct from previous metapopulation models, it also simulates spatial and temporal genetic variation arising from selection. The model was parameterized to simulate the evolution of resistance to the pesticide azamethiphos on farms in southern Norway. It successfully reproduced the rapid (within 10 years) evolution of azamethiphos resistance following extensive delousing treatments. It also identified strong spatial patterns in resistance, with regions of high farm connectivity being potential hotspots of louse adaptation. Rates of infestation and evolution were significantly reduced when highly connected farms were excluded from the simulation, compared to when low-connectivity or random sites were excluded. This model can be a valuable tool for coordinating pest management at a regional scale, in a way that slows or prevents the spread of resistance.
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ItemCharacterising a unique recreational hunting method: hound hunting of sambar deer (Cervus unicolor) in Victoria, Australia(CSIRO Publishing, 2022)Context: Scent-trailing dogs (‘hounds’) are used to hunt introduced sambar deer (Cervus unicolor) in south-eastern Australia, but little is known about this recreational hunting technique. Aim: The aim of this study was to characterise hound hunting of sambar deer in Victoria, Australia. Our study had three objectives as follows: (1) to report the hunting success of the technique; (2) to estimate pursuit times and distances; and (3) to investigate the landscape features associated with kill sites. Methods: Data were collected from four hound-hunting crews during 2020–2021. GPS data from collars fitted to hounds were used to quantify hunt duration (min) and hunt distance (m). Logistic regression was used to estimate the effects of deer sex and hound pack size on the probability of hunting success. We used a Bayesian multinomial regression resource selection function (RSF) to identify the characteristics of sites where deer were killed (elevation, aspect, and distances to water and roads). Key results: The four hunting teams ranged in size from 2 to 10 people and from one to eight hounds. Of 136 hunts, most (88%) harvested a deer, with pursued deer escaping on the other 12% of occasions. Pursuit times and distances were highly variable, with pursuit time >60 min for 46% of hunts and pursuit distance >5 km for 30% of hunts. The probability of killing a pursued male and female deer were similar, and there was not a positive relationship between pack size and hunt success. The RSF showed that both male and female deer were more likely to be killed on steeper slopes and closer to roads. Conclusions: Successful hound hunting of sambar deer involves pursuits of considerable duration and requires a network of roads, with geographical features associated with deer kills sites being related to hunter access. Implications: Hound hunting may be a useful wildlife management tool for land managers, but further studies are needed to assess its efficacy for achieving management goals.
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ItemModel-based estimation of the impact on rotavirus disease of RV3-BB vaccine administered in a neonatal or infant schedule(TAYLOR & FRANCIS INC, 2022-11-20)Rotavirus infection is a common cause of severe diarrheal disease and a major cause of deaths and hospitalizations among young children. Incidence of rotavirus has declined globally with increasing vaccine coverage. However, it remains a significant cause of morbidity and mortality in low-income countries where vaccine access is limited and efficacy is lower. The oral human neonatal vaccine RV3-BB can be safely administered earlier than other vaccines, and recent trials in Indonesia have demonstrated high efficacy. In this study, we use a stochastic individual-based model of rotavirus transmission and disease to estimate the anticipated population-level impact of RV3-BB following delivery according to either an infant (2, 4, 6 months) and neonatal (0, 2, 4 months) schedule. Using our model, which incorporated an age- and household-structured population and estimates of vaccine efficacy derived from trial data, we found both delivery schedules to be effective at reducing infection and disease. We estimated 95-96% reductions in infection and disease in children under 12 months of age when vaccine coverage is 85%. We also estimate high levels of indirect protection from vaccination, including 78% reductions in infection in adults over 17 years of age. Even for lower vaccine coverage of 55%, we estimate reductions of 84% in infection and disease in children under 12 months of age. While open questions remain about the drivers of observed lower efficacy in low-income settings, our model suggests RV3-BB could be effective at reducing infection and preventing disease in young infants at the population level.
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ItemMolecular Markers for Identifying Resistance Genes in Brassica napus(MDPI, 2022-05-01)Blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, is the most devastating disease of canola (Brassica napus, oilseed rape) worldwide. Breeding for genetic resistance is the most widely used tool for controlling this disease and minimizing the impact on yield. To date, five resistance genes (Rlm2, LepR3, Rlm4, Rlm7, Rlm9) have been cloned from B. napus, representing alleles of two different gene loci, Rlm2-LepR3 and Rlm4-7-9. We report on the development and validation of Kompetitive Allele-Specific PCR (KASP) markers that can discriminate between the resistant and susceptible alleles of each resistance gene. These markers will provide valuable tools for both researchers and industry through the ability to characterize resistance genes without phenotyping.
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ItemGenetic Improvement of Heat Stress Tolerance in Cereal Crops(MDPI, 2022-05-01)Crop heat stress is a threat to food supply, with heatwaves expected to increase in frequency and intensity globally. In addition to yield loss, heat stress dramatically reduces fertility and seed-setting rate, grain quality and weight, and seed germination and growth. Genetic variability for heat stress tolerance can be used in breeding programs to develop tolerant genotypes. The availability of genome assemblies with high-confidence sequences for many cereal crops, including rice, maize, wheat and barley, now allows the identification of heat stress tolerance-associated genes and gene networks. This review focuses on synthesizing current advances in understanding the detrimental effects of heat stress on cereal crop production at the physiological and genetic levels. It provides an account of available genomic resources, genetic variation, candidate genes, and molecular markers for heat stress tolerance. Lastly, this review offers insight into crop genetic improvement for heat stress tolerance, including germplasm screening in glasshouse and field trials, marker-assisted selection, mapping genomic loci and identification of candidate genes, and genomic-assisted breeding.
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ItemConsidering health damages and co-benefits in climate change policy assessment.(Elsevier BV, 2022-09)
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ItemImpacts of Recreational Angling on Fish Population Recovery after a Commercial Fishing Ban(MDPI, 2022-10-01)It is often assumed that recreational fishing has negligible influences on fish stocks compared to commercial fishing. However, for inland water bodies in densely populated areas, this assumption may not be supported. In this study, we demonstrate variable stock recovery rates among different fish species with similar life histories in a large productive inland freshwater ecosystem (Kaunas Reservoir, Lithuania), where previously intensive commercial fishing has been banned since 2013. We conducted over 900 surveys of recreational anglers from 2016 to 2021 to document recreational fishing catches and combined these catch estimates with drone and fishfinder device-based assessments of recreational fishing effort. Fish population recovery rates were assessed using a standardized catch-per-unit-effort time series in independent scientific surveys. We show that recreational fishing is slowing the recovery of predatory species, such as pikeperch Sander lucioperca (Linnaeus, 1758) and Eurasian perch Perca fluviatilis Linnaeus, 1758. The estimated annual recreational catches for these species were 19 tons (min-max of 7–55 tons) and 9 tons (4–28), respectively, which was considerably higher than the average commercial catch before the fishery closure (10 and 1 tons, respectively). In contrast, the recovery of roach Rutilus rutilus (Linnaeus, 1758), rarely caught by anglers (annual recreational catch of ca 3 tons compared to ca 100 tons of commercial catch), has been rapid, and the species is now dominating the ecosystem. Our study demonstrates that recreational fishing can have strong and selective impacts on fish species, reduce predator abundance, alter relative species composition and potentially change ecosystem state and dynamics.
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ItemInsights into the Antennal Characteristics and Olfactory Strategy of the Endangered Rhino Stomach Bot Fly Gyrostigma rhinocerontis (Diptera: Oestridae).(MDPI AG, 2022-09-29)Gyrostigma rhinocerontis (Diptera: Oestridae) is a rare obligate intestinal parasite of both white and black rhinoceroses, which can induce severe myiasis, cause secondary infection, and lead to enormous economic and scientific loss. Antennae are the main sensory organs of G. rhinocerontis, which may have evolved a series of specialized adaptive structures to facilitate the exploitation of their hosts. Here, we thoroughly examine the antennae of G. rhinocerontis via light and scanning electron microscopy. Only microtrichia and chaetic sensilla were observed on the scape and pedicel, and the latter is enlarged, half-enveloping the postpedicel. Four types of sensilla (trichoid sensilla, basiconic sensilla, coeloconic sensilla, and clavate sensilla) and sensory pits are detected on the postpedicel. A set of coeloconic sensilla and a chaetic sensillum are located on the arista. Distribution, type, size, and ultrastructure of antennal sensilla are presented. The antennae of G. rhinocerontis are the largest among Oestridae species, with the most sensilla and the most sensory pits. These antennal characteristics could be correlated to their adaptation for more sensitive and accurate olfactory organs, used to locate their rare and endangered hosts. Accordingly, this morphological evidence supports that the host is an important driving factor in the diversity of antennal morphology in the bot flies.