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UDORA is the institutional repository of research produced by staff at the University of Derby, and an archive of our completed doctoral theses.

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  • On some results concerning the polygonal polynomials.

    Andrica, Dorin; Bagdasar, Ovidiu; Babeș-Bolyai University; University of Derby (Technical University of Cluj-Napoca., 2019-02-13)
    In this paper we define the $n$th polygonal polynomial $P_n(z) = (z-1)(z^2-1)\cdots(z^n-1)$ and we investigate recurrence relations and exact integral formulae for the coefficients of $P_n(z)$ and for those of the Mahonian polynomials $Q_n(z)=(z+1)(z^2+z+1)\cdots(z^{n-1}+\cdots+z+1)$. We also explore numerical properties of these coefficients, unraveling new meanings for old sequences and generating novel entries to the Online Encyclopedia of Integer Sequences (OEIS). Some open questions are also formulated.
  • Endemicity and climatic niche differentiation in three marine ciliated protists

    Williams, Richard, A.J.; Owens, Hannah, L; Clamp, John; Peterson, A Townsend; Warren, Alan; Martin-Cereceda, Mercedes; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82, Kalmar, Sweden; Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA; Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, 28040, Madrid, Spain; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK; Department of Genetics, Physiology and Microbiology, Universidad Complutense de Madrid, 28040, Madrid, Spain (Association for the Sciences of Limnology and Oceanography (ASLO), 2018-07-18)
    The biogeographic pattern of single‐celled eukaryotes (protists), including ciliates, is poorly understood. Most marine species are believed to have a relatively high dispersal potential, such that both globally distributed and geographically isolated taxa exist. Primary occurrence data for three large, easily identified ciliate species, Parafavella gigantea, Schmidingerella serrata, and Zoothamnium pelagicum, and environmental data drawn from the National Oceanic and Atmospheric Administration's World Ocean Atlas were used to estimate each species’ spatial and environmental distributions using Maxent v3.3.3k. The predictive power of the models was tested with a series of spatial stratification studies, which were evaluated using partial receiver operating characteristic (ROC) statistics. Differences between niches occupied by each taxon were evaluated using background similarity tests. All predictions showed significant ability to anticipate test points. The null hypotheses of niche similarity were rejected in all background similarity tests comparing the niches among the three species. This article provides the first quantitative assessment of environmental conditions associated with three species of ciliates and a first estimate of their spatial distributions in the North Atlantic, which can serve as a benchmark against which to document distributional shifts. These species follow consistent, predictable patterns related to climate and environmental biochemistry; the importance of climatic conditions as regards protist distributions is noteworthy considering the effects of global climate change.
  • Molecular identification of papillomavirus in ducks

    Williams, Richard, A.J.; Tolf, Conny; Waldenström, Jonas; Linnaeus University (Nature Research, 2018-06-14)
    Papillomaviruses infect many vertebrates, including birds. Persistent infections by some strains can cause malignant proliferation of cells (i.e. cancer), though more typically infections cause benign tumours, or may be completely subclinical. Sometimes extensive, persistent tumours are recorded– notably in chaffinches and humans. In 2016, a novel papillomavirus genotype was characterized from a duck faecal microbiome, in Bhopal, India; the sixth papillomavirus genotype from birds. Prompted by this finding, we screened 160 cloacal swabs and 968 faecal samples collected from 299 ducks sampled at Ottenby Bird Observatory, Sweden in 2015, using a newly designed real-time PCR. Twenty one samples (1.9%) from six individuals (2%) were positive. Eighteen sequences were identical to the published genotype, duck papillomavirus 1. One additional novel genotype was recovered from three samples. Both genotypes were recovered from a wild strain domestic mallard that was infected for more than 60 days with each genotype. All positive individuals were adult (P = 0.004). Significantly more positive samples were detected from swabs than faecal samples (P < 0.0001). Sample type data suggests transmission may be via direct contact, and only infrequently, via the oral-faecal route. Infection in only adult birds supports the hypothesis that this virus is sexually transmitted, though more work is required to verify this.
  • A century of Shope Papillomavirus in museum rabbit specimens

    Duch, Clara Esucdero; Williams, Richard, A.J.; Timm, Robert M; Perez-Tris, Javier; Benitez, Laura; Department of Microbiology III, Faculty of Biological Sciences, Universidad Complutense de Madrid,; Department of Zoology and Physical Anthropology, Faculty of Biological Sciences, Universidad Complutense de Madrid; Natural Sciences, Saint Louis University, Madrid,; Department of Ecology and Evolutionary Biology & Natural History Museum, University of Kansas (Public Library of Science, 2015-07-06)
    Sylvilagus floridanus Papillomavirus (SfPV) causes growth of large horn-like tumors on rabbits. SfPV was described in cottontail rabbits (probably Sylvilagus floridanus) from Kansa and Iowa by Richard Shope in 1933, and detected in S. audubonii in 2011. It is known almost exclusively from the US Midwest. We explored the University of Kansas Natural History Museum for historical museum specimens infected with SfPV, using molecular techniques, to assess if additional wild species host SfPV, and whether SfPV occurs throughout the host range, or just in the Midwest. Secondary aims were to detect distinct strains, and evidence for strain spatio-temporal specificity. We found 20 of 1395 rabbits in the KU collection SfPV symptomatic. Three of 17 lagomorph species (S. nuttallii, and the two known hosts) were symptomatic, while Brachylagus, Lepus and eight additional Sylvilagus species were not. 13 symptomatic individuals were positive by molecular testing, including the first S. nuttallii detection. Prevalence of symptomatic individuals was significantly higher in Sylvilagus (1.8%) than Lepus. Half of these specimens came from Kansas, though new molecular detections were obtained from Jalisco—Mexico’s first—and Nebraska, Nevada, New Mexico, and Texas, USA. We document the oldest lab-confirmed case (Kansas, 1915), predating Shope’s first case. SfPV amplification was possible from 63.2% of symptomatic museum specimens. Using multiple methodologies, rolling circle amplification and, multiple isothermal displacement amplification in addition to PCR, greatly improved detection rates. Short sequences were obtained from six individuals for two genes. L1 gene sequences were identical to all previously detected sequences; E7 gene sequences, were more variable, yielding five distinct SfPV1 strains that differing by less than 2% from strains circulating in the Midwest and Mexico, between 1915 and 2005. Our results do not clarify whether strains are host species specific, though they are consistent with SfPV specificity to genus Sylvilagus.
  • Spatio-temporal dynamics and aetiology of proliferative leg skin lesions in wild British finches

    Lawson, Becki; Robinson, Robert A.; Fernandez, Julia Rodriguez-Ramos; John, Shinto K.; Benitez, Laura; Tolf, Conny; Risely, Kate; Toms, Mike P.; Cunningham, Andrew A.; Williams, Richard, A.J.; Institute of Zoology, Zoological Society of London, Regent’s Park, London, NW1 4RY, UK.; British Trust for Ornithology, The Nunnery, Thetford, Norfolk, IP24 2PU, UK.; IDEXX Laboratories Limited, Grange House, Sandbeck Way, Wetherby, West Yorkshire, LS22 7DN, UK.; Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain.; Zoonotic Ecology and Epidemiology, EEMiS, Linnaeus University, Kalmar, 391 82, Sweden; Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain (Nature Publiching Group, 2018-10-10)
    Proliferative leg skin lesions have been described in wild finches in Europe although there have been no large-scale studies of their aetiology or epizootiology to date. Firstly, disease surveillance, utilising public reporting of observations of live wild finches was conducted in Great Britain (GB) and showed proliferative leg skin lesions in chaffinches (Fringilla coelebs) to be widespread. Seasonal variation was observed, with a peak during the winter months. Secondly, pathological investigations were performed on a sample of 39 chaffinches, four bullfinches (Pyrrhula pyrrhula), one greenfinch (Chloris chloris) and one goldfinch (Carduelis carduelis) with proliferative leg skin lesions and detected Cnemidocoptes sp. mites in 91% (41/45) of affected finches and from all species examined. Fringilla coelebs papillomavirus (FcPV1) PCR was positive in 74% (23/31) of birds tested: a 394 base pair sequence was derived from 20 of these birds, from all examined species, with 100% identity to reference genomes. Both mites and FcPV1 DNA were detected in 71% (20/28) of birds tested for both pathogens. Histopathological examination of lesions did not discriminate the relative importance of mite or FcPV1 infection as their cause. Development of techniques to localise FcPV1 within lesions is required to elucidate the pathological significance of FcPV1 DNA detection.

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