A group of short stories.

Thesis (M.A.)--Boston Universit

The Nature of Hypervelocity Stars and the Time between Their Formation and Ejection

We obtain Keck HIRES spectroscopy of HVS5, one of the fastest unbound stars in the Milky Way halo. We show that HVS5 is a 3.62 ± 0.11 M_☉ main-sequence B star at a distance of 50 ± 5 kpc. The difference between its age and its flight time from the Galactic center is 105 ± 18 (stat) ±30 (sys) Myr; flight times from locations elsewhere in the Galactic disk are similar. This 10^8 yr "arrival time" between formation and ejection is difficult to reconcile with any ejection scenario involving massive stars that live for only 10^7 yr. For comparison, we derive arrival times of 10^7 yr for two unbound runaway B stars, consistent with their disk origin where ejection results from a supernova in a binary system or dynamical interactions between massive stars in a dense star cluster. For HVS5, ejection during the first 10^7 yr of its lifetime is ruled out at the 3σ level. Together with the 10^8 yr arrival times inferred for three other well-studied hypervelocity stars (HVSs), these results are consistent with a Galactic center origin for the HVSs. If the HVSs were indeed ejected by the central black hole, then the Galactic center was forming stars ≃200 Myr ago, and the progenitors of the HVSs took ≃100 Myr to enter the black hole's loss cone

Candida albicans Hypha Formation and Mannan Masking of β-Glucan Inhibit Macrophage Phagosome Maturation

Received 28 August 2014 Accepted 28 October 2014 Published 2 December 2014 This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. ACKNOWLEDGMENTS We thank Janet Willment, Aberdeen Fungal Group, University of Aberdeen, for kindly providing the soluble Dectin-1-Fc reporter. All microscopy was performed with the assistance of the University of Aberdeen Core Microscopy & Histology Facility, and we thank the IFCC for their assistance with flow cytometry. We thank the Wellcome Trust for funding (080088, 086827, 075470, 099215, 097377, and 101873). E.R.B. and A.J.P.B. are funded by the European Research Council (ERC-2009-AdG-249793), and J.L. is funded by a Medical Research Council Clinical Training Fellowship.Peer reviewedPublisher PD

Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants

Vampirovibrio chlorellavorus is recognized as a pathogen of commercially-relevant Chlorella species. Algal infection and total loss of productivity (biomass) often occurs when susceptible algal hosts are cultivated in outdoor open pond systems. The pathogenic life cycle of this bacterium has been inferred from laboratory and field observations, and corroborated in part by the genomic analyses for two Arizona isolates recovered from an open algal reactor. V. chlorellavorus predation has been reported to occur in geographically- and environmentally-diverse conditions. Genomic analyses of these and additional field isolates is expected to reveal new information about the extent of ecological diversity and genes involved in host-pathogen interactions. The draft genome sequences for two isolates of the predatory V. chlorellavorus (Cyanobacteria; Ca. Melainabacteria) from an outdoor cultivation system located in the Arizona Sonoran Desert were assembled and annotated. The genomes were sequenced and analyzed to identify genes (proteins) with predicted involvement in predation, infection, and cell death of Chlorella host species prioritized for biofuel production at sites identified as highly suitable for algal production in the southwestern USA. Genomic analyses identified several predicted genes encoding secreted proteins that are potentially involved in pathogenicity, and at least three apparently complete sets of virulence (Vir) genes, characteristic of the VirB-VirD type system encoding the canonical VirB1-11 and VirD4 proteins, respectively. Additional protein functions were predicted suggesting their involvement in quorum sensing and motility. The genomes of two previously uncharacterized V. chlorellavorus isolates reveal nucleotide and protein level divergence between each other, and a previously sequenced V. chlorellavorus genome. This new knowledge will enhance the fundamental understanding of trans-kingdom interactions between a unique cosmopolitan cyanobacterial pathogen and its green microalgal host, of broad interest as a source of harvestable biomass for biofuels or bioproducts.Bioenergy Technology Office within the US Department of Energy Office of Energy Efficiency and Renewable Energy [NL0029949 (WBS 1.3.1.600)]; US Department of Energy [DE-EE0006269]Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Microwave Gaseous Discharges

Contains research objectives and reports on three research projects.Atomic Energy Commission under Contract AT(30-1)184

Phylo‐biogeographical distribution of whitefly Bemisia tabaci (Insecta: Aleyrodidae) mitotypes in Ecuador

Abstract The Bemisia tabaci complex in Ecuador was studied with respect to phylogenetic relationships and eco‐geographical distribution. Whitefly samples were collected from natural and agricultural environments in nine provinces of Ecuador (latitude, 2° N–5° S; longitude, 78°–81° W). Mitotypes were identified based on phylogenetic analysis of the 3′‐mtCOI‐tRNAleu region (832 bp) and corrected pairwise distance analysis. The distribution of mitotypes was modeled using MaxEnt, and their predicted niches were characterized according to environmental gradients. Four B. tabaci mitotypes were identified, of which three are endemic, herein ECU1–3, and the other is the introduced B mitotype. Mitotypes ECU1 (44%), ECU2 (0.74%), and ECU3 (1.47%) grouped in the American Tropics (AMTROP) species and diverged by as much as 10%, which was higher than previous estimates for the AMTROP clade of 7–8.6%. Although haplotypes of ECU1 and ECU2 are known from the American Tropics, this is the first report of the ECU3 mitotype, which may possibly be restricted to southern Ecuador. The distribution of the three ECU‐endemic mitotypes spanned the high‐altitude niches of the western slope of the Andes, rich in microclimates with variable temperature and humidity conditions. The non‐endemic B mitotype (47%) occurred only in the irrigated cropping systems located in hot and/or dry‐tropical ecological niches. Of the endemic mitotypes, ECU1 occupied the most ecological niches. Among variables contributing to ECU1 and B mitotype niche range assignments, the most significant to influence ecological range was rainfall. The B. tabaci endemic to Ecuador were more diverse with respect to mtCOI‐tRNAleu sequence than previously known, and occupied distinct microclimate niches suggestive of ecological resilience

Fungal spore swelling and germination are restricted by the macrophage phagolysosome

Acknowledgements We acknowledge Wellcome support of Senior Investigator (101873/Z/13/Z; 224323/Z/21/Z), Collaborative (200208/A/15/Z) and Strategic Awards (097377/Z11/Z) and the MRC for a programme grant (MR/M026663/2) and the MRC Centre for Medical Mycology (MR/N006364/2). We thank Kevin Mackenzie for help with microscopy. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.Peer reviewedPublisher PD

Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes

Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections. Understanding the evolutionary dynamics of HCMV is essential for the development of effective new drugs and vaccines. By comparing viral genomes from uncultivated or low-passaged clinical samples of diverse origins, we observe evidence of frequent homologous recombination events, both recent and ancient, and no structure of HCMV genetic diversity at the whole-genome scale. Analysis of individual gene-scale loci reveals a striking dichotomy: while most of the genome is highly conserved, recombines essentially freely and has evolved under purifying selection, 21 genes display extreme diversity, structured into distinct genotypes that do not recombine with each other. Most of these hyper-variable genes encode glycoproteins involved in cell entry or escape of host immunity. Evidence that half of them have diverged through episodes of intense positive selection suggests that rapid evolution of hyper-variable loci is likely driven by interactions with host immunity. It appears that this process is enabled by recombination unlinking hyper-variable loci from strongly constrained neighboring sites. It is conceivable that viral mechanisms facilitating super-infection have evolved to promote recombination between diverged genotypes, allowing the virus to continuously diversify at key loci to escape immune detection, while maintaining a genome optimally adapted to its asymptomatic infectious lifecycle

The nature of the fungal cargo induces significantly different temporal programmes of macrophage phagocytosis

Acknowledgements We acknowledge Wellcome support of a Senior Investigator (101873/Z/13/Z), Collaborative (200208/A/15/Z) and Strategic Awards (097377/Z11/Z) and the MRC for a programme grant (MR/M026663/2) and the MRC Centre for Medical Mycology (MR/N006364/2). We thank Kevin Mackenzie for help with microscopy.Peer reviewedPublisher PD

Single base mutations in the nucleocapsid gene of SARS-CoV-2 affects amplification efficiency of sequence variants and may lead to assay failure

Reverse transcriptase quantitative PCR (RT-qPCR) is the main diagnostic assay used to detect SARS-CoV-2 RNA in respiratory samples. RT-qPCR is performed by specifically targeting the viral genome using complementary oligonucleotides called primers and probes. This approach relies on prior knowledge of the genetic sequence of the target. Viral genetic variants with changes to the primer/probe binding region may reduce the performance of PCR assays and have the potential to cause assay failure. In this work we demonstrate how two single nucleotide variants (SNVs) altered the amplification curve of a diagnostic PCR targeting the Nucleocapsid (N) gene and illustrate how threshold setting can lead to false-negative results even where the variant sequence is amplified. We also describe how in silico analysis of SARS-CoV-2 genome sequences available in the COVID-19 Genomics UK Consortium (COG-UK) and GISAID databases was performed to predict the impact of sequence variation on the performance of 22 published PCR assays. The vast majority of published primer and probe sequences contain sequence mismatches with at least one SARS-CoV-2 lineage. We recommend that visual observation of amplification curves is included as part of laboratory quality procedures, even in high throughput settings where thresholds are set automatically and that in silico analysis is used to monitor the potential impact of new variants on established assays. Ideally comprehensive in silico analysis should be applied to guide selection of highly conserved genomic regions to target with future SARS-CoV-2 PCR assays