• Genome sequence analysis reveals evidence of quorum-sensing genes present in Aeromonas hydrophila strain M062, isolated from freshwater

      Chan, K.; Tan, W.; Chang, Chien-Yi; Yin, W.; Mumahad Yunos, N.Y. (2015-03)
      Aeromonas hydrophila has emerged worldwide as a human pathogen. Here, we report the draft whole-genome sequence of a freshwater isolate from Malaysia, A. hydrophila strain M062, and its N-acylhomoserine lactone genes are also reported here.
    • A genome-based species taxonomy of the Lactobacillus genus complex

      Wittouck, S.; Wuyts, S.; Meehan, Conor J.; van Noort, V.; Lebeer, S. (2019-09)
      There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence.
    • Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium

      Tortoli, E.; Meehan, Conor J.; Grottola, A.; Fregni Serpini, J.; Fabio, A.; Trovato, A.; Pecorari, M.; Cirillo, D.M. (2019-11)
      The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and “M. avium subsp. hominissuis”), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections.
    • A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features.

      Adhikari, K.; Fontanil, T.; Cal, S.; Mendoza-Revilla, J.; Fuentes-Guajardo, M.; Chacón-Duque, J-C.; Al-Saadi, F.; Johansson, J.A.; Quinto-Sanchez, M.; Acuña-Alonzo, V.; et al. (2016-03-01)
      We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10−8 to 3 × 10−119), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair.
    • Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.

      Pedersen, J.S.; Valen, E.; Velazquez, A.M.V.; Parker, B.J.; Lindgreen, S.; Lilje, B.; Tobin, Desmond J.; Kelly, T.K.; Vang, S.; Andersson, R.; et al. (2014)
      Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo- Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics.
    • Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum.

      Cuypers, B.; Van den Broeck, F.; Van Reet, N.; Meehan, Conor J.; Cauchard, J.; Wilkes, J.M.; Claes, F.; Goddeeris, B.; Birhanu, H.; Dujardin, J.-C.; et al. (2017-08)
      Trypanosomes cause a variety of diseases in man and domestic animals in Africa, Latin America, and Asia. In the Trypanozoon subgenus, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause human African trypanosomiasis, whereas Trypanosoma brucei brucei, Trypanosoma evansi, and Trypanosoma equiperdum are responsible for nagana, surra, and dourine in domestic animals, respectively. The genetic relationships between T. evansi and T. equiperdum and other Trypanozoon species remain unclear because the majority of phylogenetic analyses has been based on only a few genes. In this study, we have conducted a phylogenetic analysis based on genome-wide SNP analysis comprising 56 genomes from the Trypanozoon subgenus. Our data reveal that T. equiperdum has emerged at least once in Eastern Africa and T. evansi at two independent occasions in Western Africa. The genomes within the T. equiperdum and T. evansi monophyletic clusters show extremely little variation, probably due to the clonal spread linked to the independence from tsetse flies for their transmission.
    • Genomewide expression profiling of the cryptolepine-induced toxicity in Saccharomyces cerevisiae.

      Rojas, M.; Wright, Colin W.; Pina, B.; Portugal, J. (American Chemical Society, 2008)
      We have used the budding yeast Saccharomyces cerevisiae to identify genes that may confer sensitivity in vivo to the antimalarial and cytotoxic agent cryptolepine. Five S. cerevisiae strains, with different genetic backgrounds in cell permeability and DNA damage repair mechanisms, were exposed to several concentrations of cryptolepine. Cryptolepine showed a relatively mild toxicity for wild-type strains, which was augmented by either increasing cell permeability ( erg6 or ISE2 strains) or disrupting DNA damage repair ( rad52 strains). These results are compatible with the ability of cryptolepine to intercalate into DNA and thus promote DNA lesions. The effects of low concentrations of cryptolepine (20% and 40% inhibitory concentrations [IC20 and IC40]) were analyzed by comparing the gene expression profiles of treated and untreated erg6 yeast cells. Significant changes in expression levels were observed for 349 genes (117 upregulated and 232 downregulated). General stress-related genes constituted the only recognizable functional cluster whose expression was increased upon cryptolepine treatment, making up about 20% of upregulated genes. In contrast, analysis of the characteristics of downregulated genes revealed a specific effect of cryptolepine on genes related to iron transport or acid phosphatases, as well as a significant proportion of genes related to cell wall components. The effects of cryptolepine on the transcription of iron transport-related genes were consistent with a loss of function of the iron sensor Aft1p, indicating a possible disruption of iron metabolism in S. cerevisiae. Since the interference of cryptolepine with iron metabolism is considered one of its putative antimalarial targets, this finding supports the utility of S. cerevisiae in drug-developing schemes.
    • A Genomic Approach to Resolving Relapse versus Reinfection among Four Cases of Buruli Ulcer

      Eddyani, M.; Vandelannoote, K.; Meehan, Conor J.; Bhuju, S.; Porter, J.L.; Aguiar, J.; Seemann, T.; Jarek, M.; Singh, M.; Portaels, F.; et al. (2015-11-30)
      Background. Increased availability of Next Generation Sequencing (NGS) techniques allows, for the first time, to distinguish relapses from reinfections in patients with multiple Buruli ulcer (BU) episodes. Methodology. We compared the number and location of single nucleotide polymorphisms (SNPs) identified by genomic screening between four pairs of Mycobacterium ulcerans isolates collected at the time of first diagnosis and at recurrence, derived from a collection of almost 5000 well characterized clinical samples from one BU treatment center in Benin. Principal Findings. The findings suggest that after surgical treatment—without antibiotics—the second episodes were due to relapse rather than reinfection. Since specific antibiotics were introduced for the treatment of BU, the one patient with a culture available from both disease episodes had M. ulcerans isolates with a genomic distance of 20 SNPs, suggesting the patient was most likely reinfected rather than having a relapse. Conclusions. To our knowledge, this study is the first to study recurrences in M. ulcerans using NGS, and to identify exogenous reinfection as causing a recurrence of BU. The occurrence of reinfection highlights the contribution of ongoing exposure to M. ulcerans to disease recurrence, and has implications for vaccine development.
    • Genomic characterization of Nontuberculous Mycobacteria

      Fedrizzi, T.; Meehan, Conor J.; Grottola, A.; Giacobazzi, E.; Fregni Serpini, G.; Tagliazucchi, S.; Fabio, A.; Bettua, C.; Bertorelli, R.; De Sanctis, V.; et al. (2017-03)
      Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species. As a consequence, the taxonomic and phylogenetic structure of the genus remains unsettled and genomic information is lacking to support the identification of these organisms in a clinical setting. In this work, we widen the knowledge of NTMs by reconstructing and analyzing the genomes of 41 previously uncharacterized NTM species. We provide the first comprehensive characterization of the genomic diversity of NTMs and open new venues for the clinical identification of opportunistic pathogens from this genus.
    • Genotoxic Effects in Peripheral Blood and Sperm in Humans in Healthy Individuals and Those with Disease States

      Anderson, Diana; Baumgartner, Adolf; Najafzadeh, Mojgan (2018-05-01)
      The Comet assay is one of the most versatile tools in toxicology today and can be used to measure responses in both diploid (peripheral blood lymphocytes) and haploid (sperm) primary cells in humans. This chapter will discuss how these cells are employed to determine if they have differential responses to chemical and physical agents in healthy and disease-affected individuals and how such information can be of use to man.
    • Genotoxicity and cytotoxicity of zinc oxide and titanium dioxide in HEp-2 cells.

      Osman, Ilham F.; Baumgartner, Adolf; Anderson, Diana; Cemeli, Eduardo; Fletcher, Jonathan N. (2010)
      Aims: The rapidly growing industrial and medical use of nanomaterials, especially zinc oxide and titanium dioxide, has led to growing concerns about their toxicity. Accordingly, the intrinsic genotoxic and cytotoxic potential of these nanoparticles have been evaluated. Materials & methods: Using a HEp-2 cell line, cytotoxicity was tested along with mitochondrial activity and neutral red uptake assays. The genotoxic potential was determined using the Comet and the cytokinesis-blocked micronucleus assays. In addition,tyrosine phosphorylation events were investigated. Results & conclusion: We found concentration- and time-dependent cytotoxicity and an increase in DNA and cytogenetic damage with increasing nanoparticle concentrations. Mainly for zinc oxide, genotoxicity was clearly associated with an increase in tyrosine phosphorylation. Our results suggest that both types of nanoparticles can be genotoxic over a range of concentrations without being cytotoxic.
    • Genotoxicity studies on DNA-interactive telomerase inhibitors with application as anti-cancer agents

      Harrington, Dean J.; Cemeli, Eduardo; Carder, Joanna; Fearnley, Jamie; Estdale, Siân E.; Perry, Philip J.; Jenkins, Terence C.; Anderson, Diana (2003-12)
      Telomerase-targeted strategies have aroused recent interest in anti-cancer chemotherapy, because DNA-binding drugs can interact with high-order tetraplex rather than double-stranded (duplex) DNA targets in tumour cells. However, the protracted cell-drug exposure times necessary for clinical application require that telomerase inhibitory efficacy must be accompanied by both low inherent cytotoxicity and the absence of mutagenicity/genotoxicity. For the first time, the genotoxicity of a number of structurally diverse DNA-interactive telomerase inhibitors is examined in the Ames test using six Salmonella typhimurium bacterial strains (TA1535, TA1537, TA1538, TA98, TA100, and TA102). DNA damage induced by each agent was also assessed using the Comet assay with human lymphocytes. The two assay procedures revealed markedly different genotoxicity profiles that are likely to reflect differences in metabolism and/or DNA repair between bacterial and mammalian cells. The mutational spectrum for a biologically active fluorenone derivative, shown to be mutagenic in the TA100 strain, was characterised using a novel and rapid assay method based upon PCR amplification of a fragment of the hisG46 allele, followed by RFLP analysis. Preliminary analysis indicates that the majority (84%) of mutations induced by this compound are C→A transversions at position 2 of the missense proline codon of the hisG46 allele. However, despite its genotoxic bacterial profile, this fluorenone agent gave a negative response in the Comet assay, and demonstrates how unwanted systemic effects (e.g., cytotoxicity and genotoxicity) can be prevented or ameliorated through suitable molecular fine-tuning of a candidate drug in targeted human tumour cells.
    • Geographical inequalities in uptake of NHS funded eye examinations: Poisson modelling of small-area data for Essex, UK

      Shickle, D.; Farragher, T.M.; Davey, Christopher J.; Slade, S.V.; Syrett, J. (2018-06)
      Background: Small-area analysis of National Health Service (NHS)-funded sight test uptake in Leeds showed significant inequalities in access among people aged <16 or ≥60. Methods: Data were extracted from 604 126 valid General Ophthalmic Services (GOS)1 claim forms for eye examinations for Essex residents between October 2013 and July 2015. Expected GOS1 uptake for each lower super output area was based on England annual uptake. Poisson regression modelling explored associations in GOS1 uptake ratio with deprivation. Results: People aged ≥60 or <16 living in the least deprived quintile were 15% and 26%, respectively, more likely to have an NHS funded eye examination than the most deprived quintile, although all are equally entitled. GOS1 uptake is higher in the more deprived quintiles among 16-59-year old, as means tested social benefits are the main eligibility criteria in this age-group. Inequalities were also observed at local authority level. Conclusions: Inequalities in access among people ≥60 years were not as large as those reported in Leeds, although inequalities in <16-year old were similar. However, demonstrable inequalities in this data set over a longer time period and a larger and more diverse area than Leeds, reinforce the argument that interventions are needed to address eye examination uptake inequalities.
    • Geophysical surveys at King Lobengula's Palace KoBulawayo, Zimbabwe.

      Gaffney, Christopher F.; Hughes, G.; Gater, J.A. (2004)
      This report covers the application of magnetic survey, primarily using a magnetic susceptibility field instrument, at the historically attested site of KoBulawayo, Zimbabwe. The approximate position of the site was known before the geophysical survey took place; it was believed to comprise a Royal Enclosure, a surrounding open space possibly used as a military parade ground and the Commoner/Peripheral Settlement of Lobengula, King of the Ndebele. Occupation at the site was short lived and after only 11 years the capital of the Ndebele state was destroyed by fire in 1881. A pilot survey was undertaken in 1994 to assess the suitability of survey techniques. Consequently, a second, more extensive survey was carried out in late 1996 and early 1997 with the intention of delimiting the Royal Enclosure. Further periods of data collection took place later in 1997 and in 1998. This report describes the methods used and the interpretation of the geophysical results in the context of the understanding and management of this important historical site. Additionally, some of the results of the geophysical work have been tested by excavation and a discussion of the correlation between these data sets is also reported in this article.
    • Geophysical investigation of the neolithic Calanais landscape

      Bates, C.R.; Bates, M.; Gaffney, Christopher F.; Gaffney, Vincent L.; Raub, T.D. (2019-12)
      The northern and western isles of Scotland have proved fertile ground for archaeological investigation over the last 100 years. However, the nature of the landscape with its rugged coastlines and irregular topography, together with rapid peat growth rates, make for challenging surveying. Commonly, an archaeological monument or series of monuments is identified but little is known about the surrounding areas and, in particular, the palaeo-landscapes within which the monuments are located. This situation is exemplified by the standing stones of Calanais in Lewis. Here, surrounding peat bogs have buried a significant portion of the landscape around which the stones were first erected. This project identifies remote sensing geophysical techniques that are effective in mapping the buried (lost) landscape and thus aid better contextualisation of the stone monuments within it. Further, the project demonstrates the most appropriate techniques for prospecting across these buried landscapes for as yet unidentified stone features associated with the lives of the people who constructed the monuments.
    • Geophysical Survey

      Gaffney, Christopher F. (2008)
    • Geophysical Survey and the Emergence of Underground Archaeological Landscapes: The Heart of Neolithic Orkney World Heritage Site.

      Card, N.; Gater, J.A.; Gaffney, Christopher F.; Wood, E. (2007)
      As the essays in this book demonstrate, Prehistoric and Romano-British landscape studies have come a long way since Hoskins, whose work reflected the prevailing 'Celtic' ethnological narrative of Britain before the medieval period. The contributors present a stimulating survey of the subject as it is in the early twenty-first century, and provide some sense of a research frontier where new conceptualisations of 'otherness' and new research techniques are transforming our understanding.
    • Geophysical survey on a southern French oppidum.

      Armit, Ian; Horsley, T.; Marty, F. (2008)
      No Abstract
    • Germ Cell Responses to Doxorubicin Exposure in Vitro

      Habas, Khaled S.A.; Anderson, Diana; Brinkworth, Martin H. (2017-01-04)
      Anthracyclines such as doxorubicin (Dox), widely used to treat various types of tumours, may result in induced testicular toxicity and oxidative stress. The present investigation was designed to determine whether exposure of isolated and purified mouse germ cells to Dox induces DNA damage in the form of strand breaks (presumably) resulting in apoptosis and to investigate the relative sensitivity of specific cell types. DNA damage was assessed using the Comet assay and the presence of apoptosis was determined by TUNEL assay. Isolated mouse germ cells were treated with different concentrations (0.05, 0.5 and 1 mM, respectively) of Dox, and fixed 1 h after treatment. The incidences of both DNA damage shown by single cell gel-electrophoresis and of apoptosis increased significantly in each specific cell type in a concentration-dependent manner. The DNA damage and apoptosis incidences gradually increased with concentration from 0.05 to 1 mM with Dox. Our results indicate that apoptosis plays a vital role in the induction of germ cell phase-specific toxicity caused by Dox with pre-meiotically and meiotically dividing spermatogonia and spermatocytes respectively as highly susceptible target cells.
    • Gerontobiology of the Hair Follicle

      Tobin, Desmond J. (2010)
      The word ¿gerontology¿ is familiar to most of us as a term that captures the study of the social, psychological, and biological aspects of aging. However, its derivative ¿gerontobiology¿ as applied to the hair follicle is more concerned with the latter aspect ¿ the biology of aging in the hair follicle mini-organ. As with any complex multicellular tissue system, the hair follicle is prone to broadly similar underlying processes that determine the functional longevity of organs and tissues. No matter how complex the tissue system is, it will contain cells that eventually lose functionality, reproductive potential and will ultimately die. The hair follicle is somewhat unusual among mammalian tissues in that it is a veritable histologic mélange of multiple cell types (e.g., epithelial, mesenchymal and neuro-ectodermal) that function contemporaneously in all stages of their life histories e.g., stem cells, transit-amplifying cells, and terminally differentiating cells. Some of these interactive cell systems appear to be nonessential for overall hair follicle survival (e.g., melanocytes). However, strikingly graying hair follicles may grow even more vigorously than their pigmented predecessors. Moreover, the hair follicle is unique in the adult mammal in that it follows a tightly regulated script of multiple lifelong cycles of cellular birth, proliferation, differentiation, and death. Powerful evolutionary selection ensures that the hair follicle is, in the main, hardwired against significant aging-related loss of function, even after 12 or more decades of life ¿ although some would argue with this view, if only on purely cosmetic grounds. Processes underlying aging in general, e.g., oxidative damage, telomere shortening, age-relating deficiencies related to nuclear/mitochondrial DNA damage and repair as well as age-related reductions in the cells¿ energy supply, will all impact on whether some follicular cell subpopulations will enter cellular senescence. This chapter will focus on how gerontobiology of the hair follicle may impact on certain aspects of hair fiber phenotype.