A small-scale test for rapid assessment of the soil development potential in post-mining soils
- Authors: Bucka, Franziska , Pihlap, Evelin , Kaiser, Jara , Baumgartl, Thomas , Kögel-Knabner, Ingrid
- Date: 2021
- Type: Text , Journal article
- Relation: Soil and Tillage Research Vol. 211, no. (2021), p.
- Full Text: false
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- Description: When ceasing brown coal mining activities, the restoration of the disturbed landscape is required, and a rapid development of functional soils is of utter importance for the rehabilitation of these areas. In order to accelerate soil development and rehabilitation, soils are designed or engineered by applying alternative approaches in order to construct a soil-like substrate, e.g., by mixing different substrates and organic carbon (OC) sources. We used a rapid and easy to perform laboratory approach to simulate the initial steps of soil development. We investigated the mixtures’ properties and the initial development of soil structure, in order to identify suitable soil mixtures for subsequent field trials. We tested six different mixtures composed of increasing complexity, based on the mixture used for a rehabilitation program at a coal mine in southern Australia. The components were overburden, fly ash, paper mulch, brown coal and plant litter. We performed a short-term laboratory incubation in regularly irrigated microcosms for forty days at constant water tension. Our results showed that the addition of fly ash to the overburden led to a higher moisture content. Fly ash together with paper mulch and brown coal improved nutrient supply and OC content, but led also to a very wide C/N ratio >95. The molecular composition of the paper mulch and brown coal OC shows the potential for long-term OC storage because of slow microbial degradation. Microbial activity, as measured by CO2 release, was high in all mixtures with litter addition, but only the additional presence of fly ash, brown coal and paper mulch led to a higher microbial carbon use efficiency (CUE). Soil structure formation, as measured by isolating water-stable aggregates, was induced in all mixtures and intensified in the presence of litter. In the mixtures with litter, there was a predominant formation of large macroaggregates (0.63−30 mm) which stored >80 % of the total OC. We suggest that the complex rehabilitation mixture indicates the potential for soil structure development within a short timeframe also in field scale, because the tested substrates are known to store moisture, deliver nutrients and OC for sustainable microbial growth. © 2021 Elsevier B.V.
Ancylostoma ceylanicum
- Authors: Colella, Vito , Bradbury, Richard , Traub, Rebecca
- Date: 2021
- Type: Text , Journal article
- Relation: Trends in Parasitology Vol. 37, no. 9 (2021), p. 844-845
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Community structure and ecological responses to hydrological changes in benthic algal assemblages in a regulated river : application of algal metrics and multivariate techniques in river management
- Authors: Atazadeh, Ehsan , Gell, Peter , Mills, Keely , Barton, Andrew , Newall, Peter
- Date: 2021
- Type: Text , Journal article
- Relation: Environmental Science and Pollution Research Vol. 28, no. 29 (2021), p. 39805-39825
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- Description: The flow regime of the Wimmera River was substantially modified due to the construction of a water supply reservoir. Samples of diatoms and soft algae and measurements of water quality were analysed at ten sampling sites for 3 years (between February 2012 and November 2014) along the MacKenzie River, a tributary of the Wimmera River, in different seasons and under different flow regimes, to understand the spatial and temporal variation in the relationship between algal communities, water quality and stream condition. Baseline information on algal communities and water quality was collected during base flow conditions, while experiments on the effect of water releases on algal communities were based on flow regime variations (manipulated flow regimes), specifically on the algae community structure, water quality and ecosystem function. Algal species composition changed along the river under different flow regimes and different seasons. Under base flow, Bacillariophyta (diatoms) were more abundant upstream, and filamentous green algae were more abundant downstream. The results showed that the algal composition shifted downstream after water release events. Chlorophyta (green algae), Cyanophyta (blue-green algae) and Chrysophyta gradually increased from upstream to downstream under base flow conditions and before water releases, whereas diatoms were greater upstream and increased downstream after water releases. The results are presented to tailor discharge and duration of the river flows by amalgamation of consumptive and environmental flows to improve the condition of the stream thereby supplementing the flows dedicated to environmental outcomes. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes
- Authors: Sloan, Shelly , Jenvey, C. J. , Piedrafita, David , Preston, Sarah , Stear, Michael
- Date: 2021
- Type: Text , Journal article
- Relation: Bmc Biotechnology Vol. 21, no. 1 (May 17 2021), p.
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Convergence of social strategies in carrion breeding insects
- Authors: Charabidze, Damien , Trumbo, Stephen , Grzywacz, Andrze , Costa, James , Barton, Philip
- Date: 2021
- Type: Text , Journal article , Review
- Relation: BioScience Vol. 71, no. 10 (2021), p. 1028-1037
- Full Text: false
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- Description: Carrion is a highly ephemeral and nutrient rich resource, characterized by extreme biotic and abiotic stressors. We hypothesized that specific constraints of the carrion ecosystem, and especially its nutrient richness, ephemerality, and competition with microbes, have promoted the evolution of social behaviors in necrophagous insects. We show that group living is prevalent among early succession carrion breeding insects, suggesting that this trait has emerged as an adaptation to facilitate survival in the highly competitive environment of fresh carrion. We then highlight how developmental niche construction allows larvae to compete with microbes, efficiently feed on fresh cadavers, and rapidly reach maturity. We observed that larval societies and parental care are two different strategies responding to similar competitive and environmental constraints. We conclude that intra and interspecific competition on carrion are mitigated by social behavior. © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the American Institute of Biological Sciences. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record**
Differential associations of hypoxia, sleep fragmentation, and depressive symptoms with cognitive dysfunction in obstructive sleep apnea
- Authors: Alomri, Ridwan , Kennedy, Gerard , Wali, Siraj , Ahejaili, Faris , Robinson, Stephen
- Date: 2021
- Type: Text , Journal article
- Relation: Sleep Vol. 44, no. 4 (2021), p.
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- Description: Obstructive sleep apnea (OSA) is characterized by recurrent episodes of partial or complete cessation of breathing during sleep and increased effort to breathe. This study examined patients who underwent overnight polysomnographic studies in a major sleep laboratory in Saudi Arabia. The study aimed to determine the extent to which intermittent hypoxia, sleep disruption, and depressive symptoms are independently associated with cognitive impairments in OSA. In the sample of 90 participants, 14 had no OSA, 30 mild OSA, 23 moderate OSA, and 23 severe OSA. The findings revealed that hypoxia and sleep fragmentation are independently associated with impairments of sustained attention and reaction time (RT). Sleep fragmentation, but not hypoxia, was independently associated with impairments in visuospatial deficits. Depressive symptoms were independently associated with impairments in the domains of sustained attention, RT, visuospatial ability, and semantic and episodic autobiographical memories. Since the depressive symptoms are independent of hypoxia and sleep fragmentation, effective reversal of cognitive impairment in OSA may require treatment interventions that target each of these factors. © Sleep Research Society 2020. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.
Do primary rainforest tree species recruit into passively and actively restored tropical rainforest?
- Authors: Pohlman, Catherine , Tng, David , Florentine, Singarayer
- Date: 2021
- Type: Text , Journal article
- Relation: Forest Ecology and Management Vol. 496, no. (2021), p.
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- Description: Restoring tropical rainforests is becoming increasingly urgent. However, in most restoration plantings it is not possible to include the full suite of species found in the original rainforest. Full recovery of species composition thus depends on the dispersal and recruitment of species that are not planted. In many restoration projects, however, recruitment is dominated by a low diversity of regionally-abundant pioneer species and species with small, easily dispersed seeds. These species are characteristic of secondary rainforest and do not include the far more diverse suite of species characteristic of the original, primary rainforest. Such primary rainforest species are usually more vulnerable to the effects of fragmentation than disturbance-adapted pioneers and thus are of greater conservation concern, as well as being required for the full recovery of many important ecosystem functions. As restoring ecosystem processes is one of the central goals of restoration, this raises the question of which, if any, of the available rainforest restoration methods may be used to promote the recruitment of primary rainforest species. We compared the species composition and functional group composition of recruited trees and shrubs in a 25-year-old restoration experiment with those of the originally planted trees, and with nearby primary rainforest and secondary rainforest reference sites in an area of upland rainforest in north-eastern Australia. Our objective was to compare the performance of four commonly-used restoration methods: (i) unassisted (passive) regeneration, (ii) Pioneer Monoculture plantings, (iii) Framework Method plantings, and (iv) Maximum Diversity plantings. The species composition and functional group composition of recruited individuals within all treatments were similar to those of secondary rainforest and highly dissimilar to both primary rainforest and plantations. Pioneer species, species with small, biotically-dispersed diaspores, and canopy trees were over-represented among both recruited individuals and in secondary rainforest. Conversely, climax species, species with large, biotically-dispersed diaspores, species with abiotically-dispersed diaspores, and understorey trees were under-represented among both recruited individuals and secondary rainforest. Restoration treatments had little effect on the species or functional group composition of recruited individuals. Our results indicate that species from nearby primary rainforest almost completely failed to recruit into any of the restoration treatments. We argue that this failure was most likely due to the absence of frugivores able to disperse larger diaspores from both secondary forest and restored forest in our study site. Further direct management intervention will be required to restore primary rainforest plant species to restored forests in this region. © 2021 Elsevier B.V.
Effect of contamination and purity priming on attitudes to vaccination and other health interventions : a randomised controlled experiment
- Authors: Bryden, Gabrielle , Rockloff, Matthew , Browne, Matthew , Unsworth, Carolyn
- Date: 2021
- Type: Text , Journal article
- Relation: Vaccine Vol. 39, no. 45 (2021), p. 6653-6659
- Full Text: false
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- Description: The objective of this experiment is to assess whether priming for contamination and purity causes a change in attitudes to health interventions, including vaccination, and complementary and alternative medicines (CAMs). An online priming experiment was conducted with four between-subject experimental conditions including photos of: 1) biological contamination, 2) chemical contamination, 3) pure environments, such as pristine landscapes, and 4) hazard signs/icons indicating physical threats. Two control conditions included photos of neutral scenes and neutral icons, whereby experimental groups were compared against the related control groups (photograph for conditions 1–3 and neutral icons for condition 4). Subjects were randomly assigned to one of the six conditions, and after exposure to the images they were asked to rate 10 conventional and alternative health interventions for effectiveness and safety, as well being assessed for disgust sensitivity using the reduced-item DPSS-R [10]. A total of 642 adults completed the experiment. Exposure to primes did not cause a differential change in ratings of health interventions. Nevertheless, higher levels of sensitivity to disgust were associated with lower ratings of the effectiveness of MMR vaccination, tetanus injection, antibiotics, and surgery; and higher levels of sensitivity to disgust were associated with higher ratings of effectiveness of vitamins/minerals. In conclusion, this online experiment did not find an experimental effect of priming for contamination and purity on subjects’ ratings of the safety and effectiveness of conventional and alternative health interventions. This indicates that attitudes to these health interventions are not influenced by a temporary increase in the salience of feelings of contamination or purity. However, individual differences in disgust sensitivity are related to their attitudes to vaccination and CAM interventions. © 2021 Elsevier Ltd
Historical reports of quolls in Victoria’s south-west
- Authors: Wallis, Robert
- Date: 2021
- Type: Text , Journal article
- Relation: Victorian Naturalist Vol. 138, no. 3 (2021), p. 78-84
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- Description: The Eastern Quoll Dasyurus viverrinus is now extinct on mainland Australia, but was once common in southwestern Victoria. It was persecuted by landholders for its predation of poultry, but also suffered dramatic declines in population through an unknown disease from about 140 years ago. Eastern Quolls were also considered significant predators of young European Rabbits Oryctolagus cuniculus. The Spot-tailed Quoll D. maculatus was historically widespread though uncommon in south-western Victoria, but now is confined there to only a couple of sites. © 2021, Field Naturalists Club of Victoria. All rights reserved.
Insights from long-term shorebird monitoring for tracking change in ecological character of Australasian Ramsar sites
- Authors: Hansen, Birgita , Szabo, Judit , Fuller, Richard , Clemens, Robert , Rogers, Danny , Milton, David
- Date: 2021
- Type: Text , Journal article
- Relation: Biological Conservation Vol. 260, no. (2021), p.
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- Description: The Ramsar Convention is the centrepiece of international efforts for wetland conservation, aiming to maintain the ecological character of wetlands through holistic ecosystem management. Here, we review studies on shorebird populations at individual Australasian Ramsar sites and compare these against original listings under Criterion 6 to determine if there have been potential changes in ecological character. One to 12 migratory shorebird species have declined at four New Zealand and 18 Australian Ramsar sites over a 12 to 36-year period, resulting in 22 species (at 13 sites) no longer reaching Criterion 6 thresholds for Ramsar designation. In addition, 10 species at six Australian sites had exceeded the Limits of Acceptable Change. Despite these concerning results, there were remarkably few published site-based determinations of listed shorebird species' trends (and even fewer that were ≤5 years old). This is especially surprising since shorebird populations are regularly monitored at 27 out of 35 Australasian Ramsar sites (listed on the basis of one or more shorebird species). Thus, despite the volume of data available for analysis, long-term shorebird monitoring provides only limited insights about Ramsar ecological character. The value of these data would be greatly enhanced through complementary monitoring of other ecological characters at sites, particularly where shorebird populations provide early warning signs of potential deterioration. The main impediment to achieving a good understanding of how Ramsar sites are changing in Australasia appears to be a lack of analysis and centralised system for data and analytics, rather than a lack of monitoring data. © 2021 Elsevier Ltd
Is resource change a useful predictor of carrion insect succession on pigs and humans?
- Authors: Dawson, Blake , Wallman, James , Evans, Maldwyn , Barton, Philip
- Date: 2021
- Type: Text , Journal article
- Relation: Journal of Medical Entomology Vol. 58, no. 6 (2021), p. 2228-2235
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- Description: Carrion is a dynamic and nutrient-rich resource that attracts numerous insect species that undergo succession due to the rapid change in the carrion resource. Despite this process being well-understood, few studies have examined resource change as a driver of carrion insect succession, and instead have focused on the effects of time per se, or on coarse, qualitative measures such as decay stage. Here we report on three field succession experiments using pig carcasses and human cadavers encompassing two winters and one summer. We quantified the effects of resource change (measured as total body score, TBS), carrion type, initial carrion mass, ambient temperature, and season on insect species richness and community composition. We found that all variables had an effect on different taxonomic or trophic components of the insect community composition, with the exception of initial carrion mass which had no effect. We found significant positive effects of TBS on beetle species richness and composition, while fly species richness was not significantly affected by TBS, but was by ambient temperature. TBS had a significant positive effect on all trophic groups, while ambient temperature also had a significant positive effect on the necrophages and predator/parasitoids. Our study indicates that resource change, as indicated by TBS, is an important driver of carrion insect species turnover and succession on carrion, and that TBS can provide information about insect ecological patterns on carrion that other temporal measures of change cannot.
Laboratory experimental study of the evaporation and mechanical behaviour of deposited tailings
- Authors: Zheng, Binbin , Wang, Jiahe , Zhang, Dongming , Zhao, Lei , Wang, Wensong
- Date: 2021
- Type: Text , Journal article
- Relation: Environmental Science and Pollution Research Vol. 28, no. 47 (2021), p. 67565-67576
- Full Text: false
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- Description: Surface deposition has been widely used in the mining industry to manage mill tailings. Tailings are generally discharged in the form of a slurry into tailings ponds. The slurried tailings are deposited in layers that undergo complex processes, e.g. evaporation, desiccation and consolidation. The evaporation of the deposited tailings controls their geotechnical engineering behaviour, which is necessary to characterise the physical properties. In this study, a constant temperature device was employed in evaporation tests to investigate two classes of deposited tailings, and the effects of the initial concentration, particle size, exposure area and deposited layer thickness on the evaporation processes were analysed. The test results showed four stages in the evaporation processes of deposited coarse and fine tailings. Dewatering of the deposited tailings occurred during the first two stages, which were keys to improving the desiccation efficiency of the tailings in the pond. The exposure area and deposited layer thickness also had a considerable influence on evaporation. The evaporation rate increased with the exposure area and layer thickness. Direct shear tests were performed to measure the shear strength of intact tailings during evaporation and used to determine the variation law of the mechanical properties of the test tailings. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Lack of effectiveness of 13-valent pneumococcal conjugate vaccination against pneumococcal carriage density in Papua New Guinean infants
- Authors: Britton, Kathryn , Pickering, Janessa , Pomat, William , de Gier, Camilla , Greenhill, Andrew
- Date: 2021
- Type: Text , Journal article
- Relation: Vaccine Vol. 39, no. 38 (2021), p. 5401-5409
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- Description: Background: Papua New Guinea (PNG) introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2014, with administration at 1, 2, and 3 months of age. PCV13 has reduced or eliminated carriage of vaccine types in populations with low pneumococcal carriage prevalence, carriage density and serotype diversity. This study investigated PCV13 impact on serotype-specific pneumococcal carriage prevalence, density, and serotype diversity in PNG infants, who have some of the highest reported rates of pneumococcal carriage and disease in the world. Methods: Nasopharyngeal swabs were collected at 1, 4 and 9 months of age from PCV13-vaccinated infants (n = 57) and age-/season-matched, unvaccinated infants (at approximately 1 month, n = 53; 4 months, n = 57; 9 months, n = 52). Serotype-specific pneumococcal carriage density and antimicrobial resistance genes were identified by qPCR and microarray. Results: Pneumococci were present in 89% of swabs, with 60 different serotypes and four non-encapsulated variants detected. Multiple serotype carriage was common (47% of swabs). Vaccine type carriage prevalence was similar between PCV13-vaccinated and unvaccinated infants at 4 and 9 months of age. The prevalence of non-vaccine type carriage was also similar between cohorts, with non-vaccine types present in three-quarters of samples (from both vaccinated and unvaccinated infants) by 4 months of age. The median pneumococcal carriage density was high and similar at each age group (~7.0 log10 genome equivalents/mL). PCV13 had no effect on overall pneumococcal carriage density, vaccine type density, non-vaccine type density, or the prevalence of antimicrobial resistance genes. Conclusion: PNG infants experience dense and diverse pneumococcal colonisation with concurrent serotypes from 1 month of age. PCV13 had no impact on pneumococcal carriage density, even for vaccine serotypes. The low prevalence of vaccine serotypes, high pneumococcal carriage density and abundance of non-vaccine serotypes likely contribute to the lack of PCV13 impact on carriage in PNG infants. Indirect effects of the infant PCV programs are likely to be limited in PNG. Alternative vaccines with broader coverage should be considered. © 2021 The Authors. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Andrew Greenhill" is provided in this record**
Outfoxing the fox : effect of prey odor on fox behavior in a pastoral landscape
- Authors: Andrewartha, Tim , Evans, Maldwyn , Batson, William , Manning, Adrian , Barton, Philip
- Date: 2021
- Type: Text , Journal article
- Relation: Conservation Science and Practice Vol. 3, no. 12 (2021), p.
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- Description: Invasive mammalian predators have had a devastating effect on native species globally. The European red fox (Vulpes vulpes) is one such species where it has been introduced in Australia. A novel but unexplored tactic to reduce the impact of mammalian predators is the use of unrewarded prey odors to undermine the effectiveness of olfactory hunting behavior. To test the viability of unrewarded prey odors in an applied setting we investigated how foxes responded to the odors of three different prey species. We used the odors of two locally extinct native Australian marsupials; the eastern quoll (a smaller carnivore) and eastern bettong (a fungivore), and the European rabbit, an introduced herbivore. Conducting our research over a period of 3 weeks in a pastoral environment in South-eastern Australia, we used video observations of foxes' behaviors, as they encountered the different odors. We found a reduction in the number of fox visits to bettong odors in the third week. In contrast, we observed a sustained number of visits to rabbit odors. Foxes also spent more time investigating rabbit odors and displayed longer durations of vigilance behavior at quoll odors. Our results support the hypothesis that the exposure of wild foxes to unrewarded odors of novel prey species can reduce their interest in these odors, which might translate to a reduction in predation pressure. Our results also suggest, however, that olfactory pre-exposure may not be as effective at reducing fox interest in a competitor species' odor. © 2021 The Authors. Conservation Science and Practice published by Wiley Periodicals LLC. on behalf of Society for Conservation Biology
Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney
- Authors: Eales, James , Jiang, Xiao , Xu, Xiaoguang , Prestes, Priscilla , Charchar, Fadi
- Date: 2021
- Type: Text , Journal article
- Relation: Nature Genetics Vol. 53, no. 5 (2021), p. 630-637
- Full Text: false
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- Description: The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterize the effects of BP index variants from genome-wide association studies (GWASs) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired 49 BP-GWAS kidney genes with 210 licensed drugs. Our colocalization and Mendelian randomization analyses identified 179 unique kidney genes with evidence of putatively causal effects on BP. Through Mendelian randomization, we also uncovered effects of BP on renal outcomes commonly affecting patients with hypertension. Collectively, our studies identified genetic variants, kidney genes, molecular mechanisms and biological pathways of key relevance to the genetic regulation of BP and inherited susceptibility to hypertension. © 2021, Crown.
Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial
- Authors: Zilko, Joseph , Harley, Dan , Hansen, Birgita , Pavlova, Alexandra , Sunnucks, Paul
- Date: 2020
- Type: Text , Journal article
- Relation: Molecular Ecology Vol. 29, no. 16 (2020), p. 2978-2993
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- Description: Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, FH and F^III, to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. FH estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated FH and F^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179–237 per trait), and computed revised coefficients, FHby group and F^IIIby group, adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using FH or F^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^IIIby group (but not FHby group) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population. © 2020 John Wiley & Sons Ltd
Blood and saliva-derived exomes from healthy Caucasian subjects do not display overt evidence of somatic mosaicism
- Authors: Hall, Nathan , Mamrot, Jared , Frampton, Chris , Read, Prue , Steele, Edward , Bischoff, Robert , Lindley, Robyn
- Date: 2020
- Type: Text , Journal article
- Relation: Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis Vol. 821, no. (2020), p.
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- Description: Somatic mosaicism is a normal occurrence during development in the tissues and organs. As part of establishing a “healthy population “(HP) background or base-line, we investigated whether such mosaicism can be routinely detected in the circulating DNA secured from a rigorously designed healthy human liquid biopsy clinical trial (saliva, blood). We deployed next generation (NG) whole exome sequencing (WES) at median exome coverage rates of 97.2 % (-to-30x) and 70.0 % (-to-100x). We found that somatic mosaicism is not detectable by such standard bulk WES sequencing assays in saliva and blood DNA in 24 normal healthy Caucasians of both sexes from 18 to 60 years of age. We conclude that for circulating DNA using standard WES no novel somatic mutational variants can be detected in protein-coding regions of normal healthy subjects. This implies that the extent within normal tissues of somatic mosaicism must be at a lower level, below the detection threshold, for these circulating DNA WES read depths. © 2020 The Author(s)
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals
- Authors: Surendran, Praveen , Feofanova, Elena , Lahrouchi, Najim , Ntalla, Ionna , Karthikeyan, Savita , Cook, James , Chen, Lingyan , Mifsud, Borbala , Yao, Chen , Kraja, Aldi , Cartwright, James , Hellwege, Jacklyn , Giri, Ayush , Tragante, Vinicius , Thorleifsson, Gudmar , Liu, Dajiang , Prins, Bram , Stewart, Isobel , Cabrera, Claude , Eales, James , Akbarov, Artur , Auer, Paul , Charchar, Fadi , Howson, Joanna , LifeLines Cohort, Study , Epic, C. V. D. , Epic InterAct , Understanding Society Scientific, Group , Million Veteran, Program
- Date: 2020
- Type: Text , Journal article
- Relation: Nature Genetics Vol. 52, no. 12 (2020), p. 1314-1332
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- Description: Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to ~1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency ≤ 0.01) variant BP associations (P < 5 × 10−8), of which 32 were in new BP-associated loci and 55 were independent BP-associated single-nucleotide variants within known BP-associated regions. Average effects of rare variants (44% coding) were ~8 times larger than common variant effects and indicate potential candidate causal genes at new and known loci (for example, GATA5 and PLCB3). BP-associated variants (including rare and common) were enriched in regions of active chromatin in fetal tissues, potentially linking fetal development with BP regulation in later life. Multivariable Mendelian randomization suggested possible inverse effects of elevated systolic and diastolic BP on large artery stroke. Our study demonstrates the utility of rare-variant analyses for identifying candidate genes and the results highlight potential therapeutic targets. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. There are 286 authors of this articles not all are listed in this record.
GCNA interacts with spartan and topoisomerase II to regulate genome stability
- Authors: Dokshin, Gregoriy , Davis, Gregory , Sawle, Ashley , Eldridge, Matthew , Nicholls, Peter , Gourley, Taylin , Romer, Katherine , Molesworth, Luke , Tatnell, Hannah , Ozturk, Ahmet , de Rooij, Dirk , Hannon, Gregory , Page, David , Mello, Craig , Carmell, Michelle
- Date: 2020
- Type: Text , Journal article
- Relation: Developmental Cell Vol. 52, no. 1 (2020), p. 53-68.e6
- Full Text: false
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- Description: GCNA proteins are expressed across eukarya in pluripotent cells and have conserved functions in fertility. GCNA homologs Spartan (DVC-1) and Wss1 resolve DNA-protein crosslinks (DPCs), including Topoisomerase-DNA adducts, during DNA replication. Here, we show that GCNA mutants in mouse and C. elegans display defects in genome maintenance including DNA damage, aberrant chromosome condensation, and crossover defects in mouse spermatocytes and spontaneous genomic rearrangements in C. elegans. We show that GCNA and topoisomerase II (TOP2) physically interact in both mice and worms and colocalize on condensed chromosomes during mitosis in C. elegans embryos. Moreover, C. elegans gcna-1 mutants are hypersensitive to TOP2 poison. Together, our findings support a model in which GCNA provides genome maintenance functions in the germline and may do so, in part, by promoting the resolution of TOP2 DPCs. DNA topoisomerases help unwind DNA but occasionally get trapped, resulting in DNA-protein crosslinks (DPCs). DPCs damage DNA and threaten genomic integrity. Dokshin et al. find that GCNA protein family complements standard DPC processing machinery in resolving topoisomerase II DPCs to ensure heritable genome stability and germline immortality. © 2019 Elsevier Inc.
- Description: We thank S. Cheloufi, D. Bellott, D. Durning, L. Okumura, L. Teitz, and members of the Page and Mello labs for advice and discussion. We thank E. Spooner for mass spectrometry and K. Igarashi for technical assistance. We thank P. Boag and R. Pocock for access to microscopes and technical advice. Some strains provided by the CGC were supported by NIH ( P40 OD010440 ) and the International C. elegans Gene Knockout Consortium . This work was supported by the Life Sciences Research Foundation to M.A.C.; American Cancer Society 129916-PF16-232-RMC to G.A.D.; and NIH grants (R37 GM058800 and P01 HD078253 ) to C.C.M. G.J.H. is supported by Cancer Research UK and by a Royal Society Wolfson Research Professorship. D.C.P. and C.C.M. are Howard Hughes Medical Institute Investigators.
Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea
- Authors: Jonduo, Marinjho , Wawae, Lorry , Masiria, Geraldine , Suda, Wataru , Hattori, Masahira , Takayasu, Lena , Abdad, Mohammad , Greenhill, Andrew , Horwood, Paul , Pomat, William , Umezaki, Masahiro
- Date: 2020
- Type: Text , Journal article
- Relation: FEMS microbiology letters Vol. 367, no. 19 (2020), p.
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- Description: Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.