| 1. |
- Janssen, Michael, et al.
(author)
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Event Horizon Telescope observations of the jet launching and collimation in Centaurus A
- 2021
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In: Nature Astronomy. - : Springer Science and Business Media LLC. - 2397-3366. ; 5:10, s. 1017-1028
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Journal article (peer-reviewed)abstract
- Very-long-baseline interferometry (VLBI) observations of active galactic nuclei at millimetre wavelengths have the power to reveal the launching and initial collimation region of extragalactic radio jets, down to 10–100 gravitational radii (rg ≡ GM/c2) scales in nearby sources1. Centaurus A is the closest radio-loud source to Earth2. It bridges the gap in mass and accretion rate between the supermassive black holes (SMBHs) in Messier 87 and our Galactic Centre. A large southern declination of −43° has, however, prevented VLBI imaging of Centaurus A below a wavelength of 1 cm thus far. Here we show the millimetre VLBI image of the source, which we obtained with the Event Horizon Telescope at 228 GHz. Compared with previous observations3, we image the jet of Centaurus A at a tenfold higher frequency and sixteen times sharper resolution and thereby probe sub-lightday structures. We reveal a highly collimated, asymmetrically edge-brightened jet as well as the fainter counterjet. We find that the source structure of Centaurus A resembles the jet in Messier 87 on ~500 rg scales remarkably well. Furthermore, we identify the location of Centaurus A’s SMBH with respect to its resolved jet core at a wavelength of 1.3 mm and conclude that the source’s event horizon shadow4 should be visible at terahertz frequencies. This location further supports the universal scale invariance of black holes over a wide range of masses5,6.
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| 2. |
- Craddock, Nick, et al.
(author)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Journal article (peer-reviewed)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 3. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 4. |
- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Journal article (peer-reviewed)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 5. |
- Jarvis, Erich D., et al.
(author)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Journal article (peer-reviewed)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 6. |
- Richards, Stephen, et al.
(author)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Journal article (peer-reviewed)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 7. |
- Diment, Bethany, et al.
(author)
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Exercise Intensity and Duration Effects on In Vivo Immunity
- 2015
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In: Medicine & Science in Sports & Exercise. - 0195-9131 .- 1530-0315. ; 47:7, s. 1390-1398
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Journal article (peer-reviewed)abstract
- Purpose: To examine the effects of intensity and duration of exercise stress on induction of in vivo immunity in humans using experimental contact hypersensitivity (CHS) with the novel antigen diphenylcyclopropenone (DPCP).Methods: Sixty-four healthy males completed either 30 min running at 60% V˙O2peak (30MI), 30 min running at 80% V˙O2peak (30HI), 120 min running at 60% V˙O2peak (120MI), or seated rest (CON). Twenty min later, the subjects received a sensitizing dose of DPCP; and 4 wk later, the strength of immune reactivity was quantified by measuring the cutaneous responses to a low dose-series challenge with DPCP on the upper inner arm. Circulating epinephrine, norepinephrine and cortisol were measured before, after, and 1 h after exercise or CON. Next, to understand better whether the decrease in CHS response on 120MI was due to local inflammatory or T-cell-mediated processes, in a crossover design, 11 healthy males performed 120MI and CON, and cutaneous responses to a dose series of the irritant, croton oil (CO), were assessed on the upper inner arm.Results: Immune induction by DPCP was impaired by 120MI (skinfold thickness -67% vs CON; P < 0.05). However, immune induction was unaffected by 30MI and 30HI despite elevated circulating catecholamines (30HI vs pre: P < 0.01) and greater circulating cortisol post 30HI (vs CON; P < 0.01). There was no effect of 120MI on skin irritant responses to CO.Conclusions: Prolonged moderate-intensity exercise, but not short-lasting high- or short-lasting moderate-intensity exercise, decreases the induction of in vivo immunity. No effect of prolonged moderate-intensity exercise on the skin's response to irritant challenge points toward a suppression of cell-mediated immunity in the observed decrease in CHS. Diphenylcyclopropenone provides an attractive tool to assess the effect of exercise on in vivo immunity.
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| 8. |
- Falster, Daniel, et al.
(author)
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AusTraits, a curated plant trait database for the Australian flora
- 2021
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In: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Journal article (peer-reviewed)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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| 9. |
- Hanstock, Helen, 1989-, et al.
(author)
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Potential of tear fluid antimicrobial proteins to evaluate risk of upper respiratory illness
- 2017
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In: 13th ISEI Symposium.
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Conference paper (other academic/artistic)abstract
- Transmission of upper respiratory tract infections (URTI) has been demonstrated at the ocular surface (Bischoff et al., 2011). Thus, the immunological profile of the tear fluid likely plays an important role in host defence against URTI, and moreover provides a non-invasive medium for assessment of immune status. We recently demonstrated that tear secretory IgA (SIgA) has potential as a biomarker of URTI risk (Hanstock et al., 2016). It is likely that several other antimicrobial proteins abundant in tears such as lactoferrin (Lf) and lysozyme (Lys) contribute to host defence at the ocular surface (McDermott, 2013). PURPOSE: To explore the potential of tear Lf and Lys to evaluate risk of subsequent URTI independently and in combination with tear SIgA data from the same subjects presented in Hanstock et al., (2016). METHODS: Forty healthy, physically active subjects were recruited during the common-cold season. Subjects reported upper respiratory symptoms (URS) daily and provided weekly tear samples for 4 weeks. If URS were reported for ≥ 48h, subjects provided a nasopharyngeal swab for identification of common-cold pathogens using RT-PCR and a tear sample. Following an episode of URS, subjects reported daily URS until they had been symptom-free for 4 weeks at which time a ‘Recovery’ tear sample was collected. Tear Lf and Lys concentration was determined using ELISA. RESULTS: Eleven students reported episodes of URS; nine returned positive virology tests for human rhinovirus (URTI). Twenty-two students remained symptom-free during the monitoring period (Healthy) and seven were excluded due to non-compliance. Tear Lys concentration (Lys-C) and secretion rate (Lys-SR) were lower in URTI vs. Healthy (p<0.01 and p<0.05 respectively) but there was no difference in Lf-C and Lf-SR. The potential of Lf and Lys to assess URS risk was determined by comparing Lf and Lys the week before URS with Recovery samples. Tear Lf-C, Lf-SR and Lys-C were not altered before URS, whereas Lys-SR tended to be reduced in the week before URS (p<0.1). A binary logistic regression incorporating tear flow rate, Lys-C, Lf-C and SIgA-C as predictors was able to correctly identify subjects at risk of URS in the next week with 70% accuracy (95% CI: 54 – 85%) but only 27% sensitivity. CONCLUSION: Although tear Lys was decreased during URTI, the new model including tear Lys and Lf was not able to improve upon the utility of tear SIgA alone to assess URS risk in this small cohort. Larger datasets will be required to evaluate and optimise model performance for models based on tear SIgA, possibly in combination with other biomarkers, to predict URTI.
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| 10. |
- Hanstock, Helen, 1989-, et al.
(author)
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Tear Fluid SIgA as a Noninvasive Biomarker of Mucosal Immunity and Common Cold Risk
- 2016
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In: Medicine & Science in Sports & Exercise. - 0195-9131 .- 1530-0315. ; 48:3, s. 569-577
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Journal article (peer-reviewed)abstract
- Purpose: Research has not convincingly demonstrated the utility of saliva secretory Immunoglobulin-A (SIgA) as a biomarker of upper-respiratory-tract-infection (URTI) risk and disagreement exists about the influence of heavy exercise ('open-window-theory') and dehydration on saliva SIgA. Prompted by the search for viable alternatives, we compared the utility of tear and saliva SIgA to predict URTI prospectively (study-one) and assessed the influence of exercise (study-two) and dehydration (study-three) using a repeated-measures-crossover design.Methods: In study-one, forty subjects were recruited during the common-cold season. Subjects provided tear and saliva samples weekly and recorded upper-respiratory-symptoms (URS) daily for 3-weeks. RT-PCR confirmed common-cold pathogens in 9 of 11 subjects reporting URS (82%). Predictive utility of tear and saliva SIgA was explored by comparing healthy samples with those collected the week pre-URS. In study-two, thirteen subjects performed a 2-hour run at 65% VO2peak. In study-three, thirteen subjects performed exercise-heat-stress to 3% body-mass-loss followed by overnight fluid restriction.Results: Tear SIgA concentration and secretion rate were 48% and 51% lower respectively during URTI and 34% and 46% lower the week pre-URS (P<0.05) but saliva SIgA remained unchanged. URS risk the following week increased 9-fold (95% CI: 1.7 to 48) when tear SIgA secretion rate <5.5 μg[BULLET OPERATOR]min and 6-fold (95% CI: 1.2 to 29) when tear SIgA secretion rate decreased >30%. Tear SIgA secretion rate >5.5 μg[BULLET OPERATOR]min or no decrease >30% predicted subjects free of URS in >80% of cases. Tear SIgA concentration decreased post-exercise (-57%: P<0.05) in line with the 'open-window-theory' but was unaffected by dehydration. Saliva flow rate decreased and saliva SIgA concentration increased post-exercise and during dehydration (P<0.05).Conclusion: Tear SIgA has utility as a non-invasive biomarker of mucosal immunity and common-cold risk.
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