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  • 1
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    Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-22
    Description: The phenomenon of male sterility in interspecies hybrids has been observed for over a century, however, few genes influencing this recurrent phenotype have been identified. Genetic investigations have been primarily limited to a small number of model organisms, thus limiting our understanding of the underlying molecular basis of this well-documented "rule of speciation." We utilized two interspecies hybrid cat breeds in a genome-wide association study employing the Illumina 63 K single-nucleotide polymorphism array. Collectively, we identified eight autosomal genes/gene regions underlying associations with hybrid male sterility (HMS) involved in the function of the blood-testis barrier, gamete structural development, and transcriptional regulation. We also identified several candidate hybrid sterility regions on the X chromosome, with most residing in close proximity to complex duplicated regions. Differential gene expression analyses revealed significant chromosome-wide upregulation of X chromosome transcripts in testes of sterile hybrids, which were enriched for genes involved in chromatin regulation of gene expression. Our expression results parallel those reported in Mus hybrids, supporting the "Large X-Effect" in mammalian HMS and the potential epigenetic basis for this phenomenon. These results support the value of the interspecies feline model as a powerful tool for comparison to rodent models of HMS, demonstrating unique aspects and potential commonalities that underpin mammalian reproductive isolation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Erratum: Molecular and atomic gas in dust lane early-type galaxies - I. Low star formation efficiencies in minor merger remnants (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-26
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    The JCMT Plane Survey: early results from the {ell} = 30{degrees} field (2015)
    Moore, T. J. T., Plume, R., Thompson, M. A., Parsons, H., Urquhart, J. S., Eden, D. J., Dempsey, J. T., Morgan, L. K., Thomas, H. S., Buckle, J., Brunt, C. M., Butner, H., Carretero, D., Chrysostomou, A., de; Villiers, H. M., Fich, M., Hoare, M. G., Manser, G., Mottram, J. C., Natario, C., Olguin, F., Peretto, N., Polychroni, D., Redman, R. O., Rigby, A. J., Salji, C., Summers, L. J., Berry, D., Currie, M. J., Jenness, T., Pestalozzi, M., Traficante, A., Bastien, P., di; Francesco, J., Davis, C. J., Evans, A., Friberg, P., Fuller, G. A., Gibb, A. G., Gibson, S., Hill, T., Johnstone, D., Joncas, G., Longmore, S. N., Lumsden, S. L., Martin, P. G., Lu'o'ng, Q. N. t., Pineda, J. E., Purcell, C., Richer, J. S., Schieven, G. H., Shipman, R., Spaans, M., Taylor, A. R., Viti, S., Weferling, B., White, G. J., Zhu, M.
    Oxford University Press
    Details
    Publication Date: 2015-09-27
    Description: We present early results from the JCMT (James Clerk Maxwell Telescope) Plane Survey (JPS), which has surveyed the northern inner Galactic plane between longitudes  = 7° and  = 63° in the 850-μm continuum with SCUBA-2 (Submm Common-User Bolometer Array 2), as part of the JCMT Legacy Survey programme. Data from the  = 30° survey region, which contains the massive-star-forming regions W43 and G29.96, are analysed after approximately 40 per cent of the observations had been completed. The pixel-to-pixel noise is found to be 19 mJy beam –1 after a smooth over the beam area, and the projected equivalent noise levels in the final survey are expected to be around 10 mJy beam –1 . An initial extraction of compact sources was performed using the FellWalker method, resulting in the detection of 1029 sources above a 5 surface-brightness threshold. The completeness limits in these data are estimated to be around 0.2 Jy beam –1 (peak flux density) and 0.8 Jy (integrated flux density) and are therefore probably already dominated by source confusion in this relatively crowded section of the survey. The flux densities of extracted compact sources are consistent with those of matching detections in the shallower APEX (Atacama Pathfinder Experiment) Telescope Large Area Survey of the Galaxy (ATLASGAL) survey. We analyse the virial and evolutionary state of the detected clumps in the W43 star-forming complex and find that they appear younger than the Galactic-plane average.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Projection of corn production and stover-harvesting impacts on soil organic carbon dynamics in the U.S. Temperate Prairies (2015)
    Springer Nature
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    Publication Date: 2015-06-02
    Description: Terrestrial carbon sequestration potential is widely considered as a realistic option for mitigating greenhouse gas emissions. However, this potential may be threatened by global changes including climate, land use, and management changes such as increased corn stover harvesting for rising production of cellulosic biofuel. Therefore, it is critical to investigate the dynamics of soil organic carbon (SOC) at regional or global scale. This study simulated the corn production and spatiotemporal changes of SOC in the U.S. Temperate Prairies, which covers over one-third of the U.S. corn acreage, using a biogeochemical model with multiple climate and land-use change projections. The corn production (either grain yield or stover biomass) could reach 88.7–104.7 TgC as of 2050, 70–101% increase when compared to the base year of 2010. A removal of 50% stover at the regional scale could be a reasonable cap in view of maintaining SOC content and soil fertility especially in the beginning years. The projected SOC dynamics indicated that the average carbon sequestration potential across the entire region may vary from 12.7 to 19.6 g C/m2/yr (i.e., 6.6–10.2 g TgC/yr). This study not only helps understand SOC dynamics but also provides decision support for sustainable biofuel development. Scientific Reports 5 doi: 10.1038/srep10830
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 5
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    The HIPASS survey of the Galactic plane in radio recombination lines (2015)
    Oxford University Press
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    Publication Date: 2015-05-02
    Description: We present a Radio Recombination Line (RRL) survey of the Galactic plane from the H i Parkes All-sky Survey and associated Zone of Avoidance survey, which mapped the region l  = 196°–0°–52° and | b | ≤ 5° at 1.4 GHz and 14.4 arcmin resolution. We combine three RRLs, H168α, H167α, and H166α to derive fully sampled maps of the diffuse ionized emission along the inner Galactic plane. The velocity information, at a resolution of 20 km s –1 , allows us to study the spatial distribution of the ionized gas and compare it with that of the molecular gas, as traced by CO. The longitude–velocity diagram shows that the RRL emission is mostly associated with CO gas from the molecular ring and is concentrated within the inner 30° of longitude. A map of the free–free emission in this region of the Galaxy is derived from the line-integrated RRL emission, assuming an electron temperature gradient with Galactocentric radius of 496 ± 100 K kpc –1 . Based on the thermal continuum map, we extracted a catalogue of 317 compact (15 arcmin) sources, with flux densities, sizes, and velocities. We report the first RRL observations of the southern ionized lobe in the Galactic Centre. The line profiles and velocities suggest that this degree-scale structure is in rotation. We also present new evidence of diffuse ionized gas in the 3-kpc arm. Helium and carbon RRLs are detected in this survey. The He line is mostly observed towards H ii regions, whereas the C line is also detected further away from the source of ionization. These data represent the first observations of diffuse C RRLs in the Galactic plane at a frequency of 1.4 GHz.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Topology-function conservation in protein-protein interaction networks (2015)
    Oxford University Press
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    Publication Date: 2015-05-12
    Description: Motivation: Proteins underlay the functioning of a cell and the wiring of proteins in protein–protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN ( topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. Results: To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. Availability and implementation: http://bio-nets.doc.ic.ac.uk/goCCA.zip Contact: natasha@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Tree mortality predicted from drought-induced vascular damage (2015)
    Springer Nature
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    Publication Date: 2015-04-30
    Description: Nature Geoscience 8, 367 (2015). doi:10.1038/ngeo2400 Authors: William R. L. Anderegg, Alan Flint, Cho-ying Huang, Lorraine Flint, Joseph A. Berry, Frank W. Davis, John S. Sperry & Christopher B. Field The projected responses of forest ecosystems to warming and drying associated with twenty-first-century climate change vary widely from resiliency to widespread tree mortality. Current vegetation models lack the ability to account for mortality of overstorey trees during extreme drought owing to uncertainties in mechanisms and thresholds causing mortality. Here we assess the causes of tree mortality, using field measurements of branch hydraulic conductivity during ongoing mortality in Populus tremuloides in the southwestern United States and a detailed plant hydraulics model. We identify a lethal plant water stress threshold that corresponds with a loss of vascular transport capacity from air entry into the xylem. We then use this hydraulic-based threshold to simulate forest dieback during historical drought, and compare predictions against three independent mortality data sets. The hydraulic threshold predicted with 75% accuracy regional patterns of tree mortality as found in field plots and mortality maps derived from Landsat imagery. In a high-emissions scenario, climate models project that drought stress will exceed the observed mortality threshold in the southwestern United States by the 2050s. Our approach provides a powerful and tractable way of incorporating tree mortality into vegetation models to resolve uncertainty over the fate of forest ecosystems in a changing climate.
    Print ISSN: 1752-0894
    Electronic ISSN: 1752-0908
    Topics: Geosciences
    Published by Springer Nature
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  • 8
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    Systematic evaluation of antibody-mediated siRNA delivery using an industrial platform of THIOMAB-siRNA conjugates (2015)
    Oxford University Press
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    Publication Date: 2015-01-24
    Description: Delivery of siRNA is a key hurdle to realizing the therapeutic promise of RNAi. By targeting internalizing cell surface antigens, antibody–siRNA complexes provide a possible solution. However, initial reports of antibody–siRNA complexes relied on non-specific charged interactions and have not been broadly applicable. To assess and improve this delivery method, we built on an industrial platform of therapeutic antibodies called THIOMABs, engineered to enable precise covalent coupling of siRNAs. We report that such coupling generates monomeric antibody–siRNA conjugates (ARCs) that retain antibody and siRNA activities. To broadly assess this technology, we generated a battery of THIOMABs against seven targets that use multiple internalization routes, enabling systematic manipulation of multiple parameters that impact delivery. We identify ARCs that induce targeted silencing in vitro and extend tests to target prostate carcinoma cells following systemic administration in mouse models. However, optimal silencing was restricted to specific conditions and only observed using a subset of ARCs. Trafficking studies point to ARC entrapment in endocytic compartments as a limiting factor, independent of the route of antigen internalization. Our broad characterization of multiple parameters using therapeutic-grade conjugate technology provides a thorough assessment of this delivery technology, highlighting both examples of success as well as remaining challenges.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis (2015)
    Oxford University Press
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    Publication Date: 2015-12-28
    Description: Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions characterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to synthesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. Other pathway differences such as the ability to synthesize siroheme and vitamin B12 point to enhanced metabolic flexibility for P. cangingivalis , which may underlie its prevalence in the canine oral cavity.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Coevolution with Bacteriophages Drives Genome-Wide Host Evolution and Constrains the Acquisition of Abiotic-Beneficial Mutations (2015)
    Oxford University Press
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    Publication Date: 2015-05-30
    Description: Studies of antagonistic coevolution between hosts and parasites typically focus on resistance and infectivity traits. However, coevolution could also have genome-wide effects on the hosts due to pleiotropy, epistasis, or selection for evolvability. Here, we investigate these effects in the bacterium Pseudomonas fluorescens SBW25 during approximately 400 generations of evolution in the presence or absence of bacteriophage (coevolution or evolution treatments, respectively). Coevolution resulted in variable phage resistance, lower competitive fitness in the absence of phages, and greater genome-wide divergence both from the ancestor and between replicates, in part due to the evolution of increased mutation rates. Hosts from coevolution and evolution treatments had different suites of mutations. A high proportion of mutations observed in coevolved hosts were associated with a known phage target binding site, the lipopolysaccharide (LPS), and correlated with altered LPS length and phage resistance. Mutations in evolved bacteria were correlated with higher fitness in the absence of phages. However, the benefits of these growth-promoting mutations were completely lost when these bacteria were subsequently coevolved with phages, indicating that they were not beneficial in the presence of resistance mutations (consistent with negative epistasis). Our results show that in addition to affecting genome-wide evolution in loci not obviously linked to parasite resistance, coevolution can also constrain the acquisition of mutations beneficial for growth in the abiotic environment.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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