GENOMICS BASED APPROACHES TO FUNGAL EVOLUTION

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution. In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in maximal growth temperature, with New Mexico isolates being substantially more thermotolerant than isolates from Alaska. Genomic scale comparisons of progeny from crosses between isolates from New Mexico and Alaska indicated that two regions, one on chromosome III and another on chromosome I, are responsible for differences in thermotolerance. Examination of these regions revealed numerous differences between the New Mexico and Alaska isolates at nucleotide and amino-acid levels; and it identified candidate genes for being important for differences in maximal growth temperatures. In a second study, I explored the genomic differences between pathogenic and endophytic isolates in the genus Monosporascus. Culture and sequence-based surveys of root associating fungi at the Sevilleta National Wildlife Refuge (SNWR) revealed the ubiquitous presence of members of this genus. Although M. cannonballus is known as a severe pathogen of melon roots in agricultural settings, all of the host plants associating with Monosporascus species in natural settings appeared to be disease free. Complete genome sequences were obtained from three M. cannonballus isolates, an M. ibericus isolate and six SNWR isolates. Comparative genome analyses revealed that 1) isolates of Monosporascus possess genomes that are more than twice the size of those typical for members of the Sordariomycetes, while having typical numbers of protein-coding genes; 2) isolates from diverse grasses, tree and forbs include lineages closely-related to previously described species including M. cannonballus, in addition to novel lineages; and 3) species of Monosporascus and other Xylariales lack mating-type gene regions typical of other members of the Pezizomycotina

Analysis of EZproxy server logs to visualise research activity in Curtin’s online library

© 2019, Emerald Publishing Limited. Purpose: The purpose of this paper is to develop data visualisation proof of concept prototypes that will enable the Curtin University Library team to explore its users’ information-seeking behaviour and collection use online by analysing the library’s EZproxy logs. Design/methodology/approach: Curtin Library’s EZproxy log file data from 2013 to 2017 is used to develop the data visualisation prototypes using Unity3D software. Findings: Two visualisation prototypes from the EZproxy data set are developed. The first, “Global Visualisation of Curtin Research Activity”, uses a geographical map of the world as a platform to show where each research request comes from, the time each is made and the file size of the request. The second prototype, “Database Usage Visualisation”, shows the use of the library’s various subscription databases by staff and students daily, over a month in April 2017. Research limitations/implications: The paper has following limitations: working to a tight timeline of ten weeks; time taken to cleanse noise data; and requirements for storing and hosting the voluminous data sets. Practical implications: The prototypes provide visual evidence of the use of Curtin Library’s digital resources at any time and from anywhere by its users, demonstrating the demand for the library’s online service offerings. These prototype evidence-based data visualisations empower the library to communicate in a compelling and interesting way how its services and subscriptions support Curtin University’s missions. Originality/value: The paper provides innovative approaches to create immersive 3D data visualisation prototypes to make sense of complex EZproxy data sets

The Broad-Line and Narrow-Line Regions of the LINER NGC 4579

We report the discovery of an extremely broad H-alpha emission line in the LINER nucleus of NGC 4579. From ground-based observations, the galaxy was previously known to contain a Type 1 nucleus with a broad H-alpha line of FWHM = 2300 km/s and FWZI ~ 5000 km/s. New spectra obtained with the Hubble Space Telescope and a 0.2 arcsec-wide slit reveal an H-alpha component with FWZI ~ 18,000 km/s. The line is not obviously double-peaked, but it does possess shoulders on the red and blue sides which resemble the H-alpha profiles of double-peaked emitters such as NGC 4203 and NGC 4450. This similarity suggests that the very broad H-alpha profile in NGC 4579 may represent emission from an accretion disk. Three such objects have been found recently in two HST programs which have targeted a total of 30 galaxies, demonstrating that double-peaked or extremely broad-line emission in LINERs must be much more common than would be inferred from ground-based surveys. The ratio of the narrow [S II] 6716, 6731 lines shows a pronounced gradient indicating a steep rise in density toward the nucleus. The direct detection of a density gradient within the inner arcsecond of the narrow-line region confirms expectations from previous observations of linewidth-critical density correlations in several LINERs.Comment: 8 pages, includes 3 figures. To appear in The Astrophysical Journa

GBM heterogeneity as a function of variable epidermal growth factor receptor variant III activity.

Abnormal activation of the epidermal growth factor receptor (EGFR) due to a deletion of exons 2-7 of EGFR (EGFRvIII) is a common alteration in glioblastoma (GBM). While this alteration can drive gliomagenesis, tumors harboring EGFRvIII are heterogeneous. To investigate the role for EGFRvIII activation in tumor phenotype we used a neural progenitor cell-based murine model of GBM driven by EGFR signaling and generated tumor progenitor cells with high and low EGFRvIII activation, pEGFRHi and pEGFRLo. In vivo, ex vivo, and in vitro studies suggested a direct association between EGFRvIII activity and increased tumor cell proliferation, decreased tumor cell adhesion to the extracellular matrix, and altered progenitor cell phenotype. Time-lapse confocal imaging of tumor cells in brain slice cultures demonstrated blood vessel co-option by tumor cells and highlighted differences in invasive pattern. Inhibition of EGFR signaling in pEGFRHi promoted cell differentiation and increased cell-matrix adhesion. Conversely, increased EGFRvIII activation in pEGFRLo reduced cell-matrix adhesion. Our study using a murine model for GBM driven by a single genetic driver, suggests differences in EGFR activation contribute to tumor heterogeneity and aggressiveness

Salmonid alphavirus infection causes skin dysbiosis in Atlantic salmon (Salmo salar L.) post-smolts

publishedVersio

Interactions Between Moderate- and Long-Period Giant Planets: Scattering Experiments for Systems in Isolation and with Stellar Flybys

The chance that a planetary system will interact with another member of its host star's nascent cluster would be greatly increased if gas giant planets form in situ on wide orbits. In this paper, we explore the outcomes of planet-planet scattering for a distribution of multiplanet systems that all have one of the planets on an initial orbit of 100 AU. The scattering experiments are run with and without stellar flybys. We convolve the outcomes with distributions for protoplanetary disk and stellar cluster sizes to generalize the results where possible. We find that the frequencies of large mutual inclinations and high eccentricities are sensitive to the number of planets in a system, but not strongly to stellar flybys. However, flybys do play a role in changing the low and moderate portions of the mutual inclination distributions, and erase dynamically cold initial conditions on average. Wide-orbit planets can be mixed throughout the planetary system, and in some cases, can potentially become hot Jupiters, which we demonstrate using scattering experiments that include a tidal damping model. If planets form on wide orbits in situ, then there will be discernible differences in the proper motion distributions of a sample of wide-orbit planets compared with a pure scattering formation mechanism. Stellar flybys can enhance the frequency of ejections in planetary systems, but auto-ionization is likely to remain the dominant source of free-floating planets.Comment: Accepted for publication by Ap

Technology ready use of single layer graphene as a transparent electrode for hybrid photovoltaic devices

Graphene has been used recently as a replacement for indium tin oxide (ITO) for the transparent electrode of an organic photovoltaic device. Due to its limited supply, ITO is considered as a limiting factor for the commercialization of organic solar cells. We explored the use of large-area graphene grown on copper by chemical vapor deposition (CVD) and then transferred to a glass substrate as an alternative transparent electrode. The transferred film was shown by scanning Raman spectroscopy measurements to consist of >90% single layer graphene. Optical spectroscopy measurements showed that the layer-transferred graphene has an optical absorbance of 1.23% at a wavelength of 532 nm. We fabricated organic hybrid solar cells utilizing this material as an electrode and compared their performance with ITO devices fabricated using the same procedure. We demonstrated power conversion efficiency up to 3.98%, higher than that of the ITO device (3.86%), showing that layer-transferred graphene promises to be a high quality, low-cost, flexible material for transparent electrodes in solar cell technology.Comment: 6 pages, 3 figure

Realizing spin squeezing with Rydberg interactions in a programmable optical clock

Neutral-atom arrays trapped in optical potentials are a powerful platform for studying quantum physics, combining precise single-particle control and detection with a range of tunable entangling interactions. For example, these capabilities have been leveraged for state-of-the-art frequency metrology as well as microscopic studies of entangled many-particle states. In this work, we combine these applications to realize spin squeezing - a widely studied operation for producing metrologically useful entanglement - in an optical atomic clock based on a programmable array of interacting optical qubits. In this first demonstration of Rydberg-mediated squeezing with a neutral-atom optical clock, we generate states that have almost 4 dB of metrological gain. Additionally, we perform a synchronous frequency comparison between independent squeezed states and observe a fractional frequency stability of $1.087(1)\times 10^{-15}$ at one-second averaging time, which is 1.94(1) dB below the standard quantum limit, and reaches a fractional precision at the $10^{-17}$ level during a half-hour measurement. We further leverage the programmable control afforded by optical tweezer arrays to apply local phase shifts in order to explore spin squeezing in measurements that operate beyond the relative coherence time with the optical local oscillator. The realization of this spin-squeezing protocol in a programmable atom-array clock opens the door to a wide range of quantum-information inspired techniques for optimal phase estimation and Heisenberg-limited optical atomic clocks.Comment: 13 pages, 4 figures; Supplementary Informatio