List of Microbes Present in New Zealand
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Biofilm Formation by Moraxella Catarrhalis
BIOFILM FORMATION BY MORAXELLA CATARRHALIS APPROVED BY SUPERVISORY COMMITTEE Eric J. Hansen, Ph.D. ___________________________ Kevin S. McIver, Ph.D. ___________________________ Michael V. Norgard, Ph.D. ___________________________ Philip J. Thomas, Ph.D. ___________________________ Nicolai S.C. van Oers, Ph.D. ___________________________ BIOFILM FORMATION BY MORAXELLA CATARRHALIS by MELANIE MICHELLE PEARSON DISSERTATION Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY The University of Texas Southwestern Medical Center at Dallas Dallas, Texas March, 2004 Copyright by Melanie Michelle Pearson 2004 All Rights Reserved Acknowledgements As with any grand endeavor, there was a large supporting cast who guided me through the completion of my Ph.D. First and foremost, I would like to thank my mentor, Dr. Eric Hansen, for granting me the independence to pursue my ideas while helping me shape my work into a coherent story. I have seen that the time involved in supervising a graduate student is tremendous, and I am grateful for his advice and support. The members of my graduate committee (Drs. Michael Norgard, Kevin McIver, Phil Thomas, and Nicolai van Oers) have likewise given me a considerable investment of time and intellect. Many of the faculty, postdocs, students and staff of the Microbiology department have added to my education and made my experience here positive. Many members of the Hansen laboratory contributed to my work. Dr. Eric Lafontaine gave me my first introduction to M. catarrhalis. I hope I have learned from his example of patience, good nature, and hard work. -
New Zealand's Genetic Diversity
1.13 NEW ZEALAND’S GENETIC DIVERSITY NEW ZEALAND’S GENETIC DIVERSITY Dennis P. Gordon National Institute of Water and Atmospheric Research, Private Bag 14901, Kilbirnie, Wellington 6022, New Zealand ABSTRACT: The known genetic diversity represented by the New Zealand biota is reviewed and summarised, largely based on a recently published New Zealand inventory of biodiversity. All kingdoms and eukaryote phyla are covered, updated to refl ect the latest phylogenetic view of Eukaryota. The total known biota comprises a nominal 57 406 species (c. 48 640 described). Subtraction of the 4889 naturalised-alien species gives a biota of 52 517 native species. A minimum (the status of a number of the unnamed species is uncertain) of 27 380 (52%) of these species are endemic (cf. 26% for Fungi, 38% for all marine species, 46% for marine Animalia, 68% for all Animalia, 78% for vascular plants and 91% for terrestrial Animalia). In passing, examples are given both of the roles of the major taxa in providing ecosystem services and of the use of genetic resources in the New Zealand economy. Key words: Animalia, Chromista, freshwater, Fungi, genetic diversity, marine, New Zealand, Prokaryota, Protozoa, terrestrial. INTRODUCTION Article 10b of the CBD calls for signatories to ‘Adopt The original brief for this chapter was to review New Zealand’s measures relating to the use of biological resources [i.e. genetic genetic resources. The OECD defi nition of genetic resources resources] to avoid or minimize adverse impacts on biological is ‘genetic material of plants, animals or micro-organisms of diversity [e.g. genetic diversity]’ (my parentheses). -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
Neisseria Acinetobacter, Moraxella ? and Kingella Based on Partial 16S Ribosomal DNA Sequence Analysis4
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1994, p. 387-391 Vol. 44, No. 3 0020-7713/94/$04.00 + 0 Copyright 0 1994, International Union of Microbiological Societies Phylogenetic Relationships between Some Members of the Genera Neisseria Acinetobacter, Moraxella ? and Kingella Based on Partial 16s Ribosomal DNA Sequence Analysis4. M. C. ENRIGHT,” P. E. CARTER, I. A. MACLEAN,AND H. McKENZIE Department of Medical Microbiology, Faculty of Medicine, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB9 220 We obtained 16s ribosomal DNA (rDNA) sequence data for strains belonging to 11 species of Proteobacteria, including the type strains of Kingella kingae, Neisseria lactamica, Neisseria meningitidis, Moraxella lacunata subsp. lacunata, [Neisseria] ovis, Moraxella catarrhalis, Moraxella osloensis, [Moraxella] phenylpyruvica, and Acineto- bacter lwo$i, as well as strains of Neisseria subflava and Acinetobacter calcoaceticus. The data in a distance matrix constructed by comparing the sequences supported the proposal that the genera Acinetobacter and Moraxella and [N.] ovis should be excluded from the family Neisseriaceae. Our results are consistent with hybridization data which suggest that these excluded taxa should be part of a new family, the Moraxellaceae. The strains that we studied can be divided into the following five groups: (i) M. lacunata subsp. lacunata, [N.] ovis, and M. catarrhalis; (ii) M. osloensis; (iii) [M.]phenylpyruvica; (iv) A. calcoaceticus and A. lwofii; and (v) N. meningitidis, N. subflava, N. lactamica, and K. kingae. We agree with the previous proposal that [N.] ovis should be renamed Moraxella ovis, as this organism is closely related to Moraxella species and not to Neisseria species. The generically misnamed taxon [M.] phenylpyruvica belongs to the proposed family Moraxellaceae, but it is sufficiently different to warrant exclusion from the genus Moraxella. -
Cave-73-02-Fullr.Pdf
EDITORIAL Production Changes for Future Publication of the Journal of Cave and Karst Studies SCOTT ENGEL Production Editor The Journal of Cave and Karst Studies has experienced December 2011 issue, printed copies of the Journal will be budget shortfalls for the last several years for a multitude automatically distributed to paid subscribers, institutions, of reasons that include, but are not limited to, increased and only those NSS members with active Life and cost of paper, increased costs of shipping through the Sustaining level memberships. The remainder of the NSS United State Postal Service, increased submissions, and membership will be able to view the Journal electronically stagnant funding from the National Speleological Society online but will not automatically receive a printed copy. Full (NSS). The cost to produce the Journal has increased 5 to content of each issue of the Journal will be available for 20 percent per year for the last five years, yet the budget for viewing and downloading in PDF format at no cost from the the Journal has remained unchanged. To offset rising costs, Journal website www.caves.org/pub/journal. the Journal has implemented numerous changes over recent Anyone wishing to receive a printed copy of the Journal years to streamline the production and printing process. will be able to subscribe for an additional cost separate However, the increasing production costs, combined with from normal NSS dues. The cost and subscription process the increasing rate of good-quality submissions, has were still being determined at the time of this printing. resulted in the number of accepted manuscripts by the Once determined, the subscription information will be Journal growing faster than the acquisition of funding to posted on the Journal website. -
Moraxella Species: Infectious Microbes Identified by Use of Time-Of
Japanese Journal of Ophthalmology (2019) 63:328–336 https://doi.org/10.1007/s10384-019-00669-4 CLINICAL INVESTIGATION Moraxella species: infectious microbes identifed by use of time‑of‑fight mass spectrometry Shunsuke Takahashi1 · Kazuhiro Murata1 · Kenji Ozawa1 · Hiroki Yamada2 · Hideaki Kawakami3 · Asami Nakayama4 · Yuko Asano5 · Kiyofumi Mochizuki1 · Hiroshige Mikamo6 Received: 14 August 2018 / Accepted: 2 April 2019 / Published online: 4 July 2019 © Japanese Ophthalmological Society 2019 Abstract Purpose To report the clinical manifestations, identifcation, antimicrobial susceptibilities, and treatment outcomes of ocular infections caused by Moraxella species. Study design Retrospective study. Patients and methods The medical records of all patients treated at the Departments of Ophthalmology of the Ogaki Munici- pal Hospital and the Gifu University Graduate School of Medicine for ocular infections caused by Moraxella species between January 2011 and June 2017 were examined. The stored Moraxella species isolated from ocular samples were identifed by matrix-assisted laser desorption/ionization time-of-fight mass spectrometry (MALDI-TOF MS), molecular identifcation, and the biochemical properties. Results Sixteen eyes of 16 patients were treated for Moraxella ocular infections. The patients’ median age was 72 years. A predisposing systemic or ocular condition was identifed in 15 of the patients. Nine of the patients developed keratitis; four, conjunctivitis; and three, blebitis. M lacunata (6 eyes), M catarrhalis (6), M nonliquefaciens (3), and M osloensis (1) were identifed by MALDI-TOF MS. All isolates were sensitive to levofoxacin, tobramycin, ceftazidime, ceftriaxone, and cefa- zolin. Twelve patients with keratitis or blebitis were treated with various topical antimicrobial combinations, and systemic antibiotics were used in 10 of the 12 patients. -
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. -
Moraxella Bacteremia in Cancer Patients
Open Access Case Report DOI: 10.7759/cureus.15316 Moraxella Bacteremia in Cancer Patients Shamra Zaman 1 , John Greene 2 1. Medicine, University of South Florida, Tampa, USA 2. Internal Medicine, Moffitt Cancer Center, Tampa, USA Corresponding author: John Greene, [email protected] Abstract Moraxella is a gram-negative bacterium part of the Moraxellaceae family. It is a pathogen that is commonly found in the upper respiratory tract of humans. It is a rare cause of community-acquired pneumonia and can be found in immunocompromised individuals, especially those with impaired humoral immunity such as hypogammaglobulinemia and those with lung diseases. We present three cases of Moraxella infections at the Moffitt Cancer Center between the years 2011 and 2017. We performed a literature review of Moraxella bacteremia in cancer patients and included three patients, two with a history of multiple myeloma and one undergoing radiation therapy for non-small cell lung carcinoma. None of the patients died as a result of the infection. Moraxella infections can result in a range of severity with increasing resistance to antibiotic therapy. Categories: Infectious Disease, Oncology Keywords: moraxella, myeloma, respiratory tract, pneumonia, immunocompromised patient Introduction Moraxella is a gram-negative bacterium that has a coccobacillus shape [1]. Originally considered normal flora in the human respiratory system, it can cause respiratory tract infections [2]. It primarily affects adults with prior chronic lung disease and the immunosuppressed. The most common immunodeficiency is hypogammaglobulinemia, which is found in patients with multiple myeloma and chronic lymphocytic leukemia (CLL). Invasive infections include meningitis, pneumonia, and endocarditis [3,4]. We present the cases of three cancer patients with Moraxella infections that illustrate the most common risk factors that predispose to this infection. -
Culturing and Environmental DNA Sequencing Uncover Hidden Kinetoplastid Biodiversity and a Major Marine Clade Within Ancestrally Freshwater Neobodo Designis
International Journal of Systematic and Evolutionary Microbiology (2005), 55, 2605–2621 DOI 10.1099/ijs.0.63606-0 Culturing and environmental DNA sequencing uncover hidden kinetoplastid biodiversity and a major marine clade within ancestrally freshwater Neobodo designis Sophie von der Heyden3 and Thomas Cavalier-Smith Correspondence Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK Thomas Cavalier-Smith [email protected] Bodonid flagellates (class Kinetoplastea) are abundant, free-living protozoa in freshwater, soil and marine habitats, with undersampled global biodiversity. To investigate overall bodonid diversity, kinetoplastid-specific PCR primers were used to amplify and sequence 18S rRNA genes from DNA extracted from 16 diverse environmental samples; of 39 different kinetoplastid sequences, 35 belong to the subclass Metakinetoplastina, where most group with the genus Neobodo or the species Bodo saltans, whilst four group with the subclass Prokinetoplastina (Ichthyobodo). To study divergence between freshwater and marine members of the genus Neobodo, 26 new Neobodo designis strains were cultured and their 18S rRNA genes were sequenced. It is shown that the morphospecies N. designis is a remarkably ancient species complex with a major marine clade nested among older freshwater clades, suggesting that these lineages were constrained physiologically from moving between these environments for most of their long history. Other major bodonid clades show less-deep separation between marine and freshwater strains, but have extensive genetic diversity within all lineages and an apparently biogeographically distinct distribution of B. saltans subclades. Clade-specific 18S rRNA gene primers were used for two N. designis subclades to test their global distribution and genetic diversity. -
Heme Pathway Evolution in Kinetoplastid Protists Ugo Cenci1,2, Daniel Moog1,2, Bruce A
Cenci et al. BMC Evolutionary Biology (2016) 16:109 DOI 10.1186/s12862-016-0664-6 RESEARCH ARTICLE Open Access Heme pathway evolution in kinetoplastid protists Ugo Cenci1,2, Daniel Moog1,2, Bruce A. Curtis1,2, Goro Tanifuji3, Laura Eme1,2, Julius Lukeš4,5 and John M. Archibald1,2,5* Abstract Background: Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetoplastids have emerged from free-living, non-pathogenic ancestors on multiple occasions during the evolutionary history of the group. Interestingly, in both parasitic and free-living kinetoplastids, the heme pathway—a core metabolic pathway in a wide range of organisms—is incomplete or entirely absent. Indeed, Kinetoplastea investigated thus far seem to bypass the need for heme biosynthesis by acquiring heme or intermediate metabolites directly from their environment. Results: Here we report the existence of a near-complete heme biosynthetic pathway in Perkinsela spp., kinetoplastids that live as obligate endosymbionts inside amoebozoans belonging to the genus Paramoeba/Neoparamoeba.Wealso use phylogenetic analysis to infer the evolution of the heme pathway in Kinetoplastea. Conclusion: We show that Perkinsela spp. is a deep-branching kinetoplastid lineage, and that lateral gene transfer has played a role in the evolution of heme biosynthesis in Perkinsela spp. and other Kinetoplastea. We also discuss the significance of the presence of seven of eight heme pathway genes in the Perkinsela genome as it relates to its endosymbiotic relationship with Paramoeba. Keywords: Heme, Kinetoplastea, Paramoeba pemaquidensis, Perkinsela, Evolution, Endosymbiosis, Prokinetoplastina, Lateral gene transfer Background are poorly understood and the evolutionary relationship Kinetoplastea is a diverse group of unicellular flagellated amongst bodonids is still debated [8, 10, 12]. -
Large-Scale Patterns in Biodiversity of Microbial Eukaryotes from the Abyssal Sea floor
Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor Frank Scheckenbacha,1, Klaus Hausmannb, Claudia Wylezicha,c, Markus Weiterea, and Hartmut Arndta aDepartment of General Ecology and Limnology, Institute for Zoology, Biocenter, University of Cologne, Cologne, Germany; bDivision of Protozoology, Institute of Biology/Zoology, Free University of Berlin, Berlin, Germany; and cDepartment of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved November 4, 2009 (received for review August 6, 2009) Eukaryotic microbial life at abyssal depths remains “uncharted ter- role of microbial eukaryotic communities is essential to under- ritory” in eukaryotic microbiology. No phylogenetic surveys have standing global biogeochemical cycles (18). focused on the largest benthic environment on this planet, the The perceived homogeneity of abyssal environments, with abyssal plains. Moreover, knowledge of the spatial patterns of little environmental variation, has led to the assumption that deep-sea community structure is scanty, and what little is known species have broad distribution ranges. This is in fact supported originates primarily from morphology-based studies of foramini- by studies of foraminiferans, which in some cases have ranges ferans. Here we report on the great phylogenetic diversity of mi- encompassing entire abyssal plains (19). But environmental crobial eukaryotic communities of all 3 abyssal plains of the gradients do shape the deep-sea community structure, especially southeastern Atlantic Ocean—the Angola, Cape, and Guinea Abys- in benthic environments (20). Except for the studies by Count- sal Plains—from depths of 5,000 m. A high percentage of retrieved way et al. -
Component Causes of Infectious Bovine Keratoconjunctivitis - the Role of Moraxella Species in the Epidemiology of Infectious Bovine Keratoconjunctivitis
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Veterinary and Biomedical Sciences, Papers in Veterinary and Biomedical Science Department of 5-2021 Component Causes of Infectious Bovine Keratoconjunctivitis - The Role of Moraxella Species in the Epidemiology of Infectious Bovine Keratoconjunctivitis John Dustin Loy Matthew Hille Gabriele Maier Michael L. Clawson Follow this and additional works at: https://digitalcommons.unl.edu/vetscipapers Part of the Biochemistry, Biophysics, and Structural Biology Commons, Cell and Developmental Biology Commons, Immunology and Infectious Disease Commons, Medical Sciences Commons, Veterinary Microbiology and Immunobiology Commons, and the Veterinary Pathology and Pathobiology Commons This Article is brought to you for free and open access by the Veterinary and Biomedical Sciences, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Papers in Veterinary and Biomedical Science by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Component Causes of Infectious Bovine Keratoconjunctivitis - The Role of Moraxella Species in the Epidemiology of Infectious Bovine Keratoconjunctivitis a, a John Dustin Loy, DVM, PhD, DACVM *, Matthew Hille, DVM , b c Gabriele Maier, DVM, MPVM, PhD, DACVPM , Michael L. Clawson, PhD KEYWORDS Infectious bovine keratoconjunctivitis Moraxella bovis Moraxella bovoculi Moraxella ovis MALDI-TOF MS Genomics Pathogenesis KEY POINTS Moraxella bovis can cause infectious bovine keratoconjunctivitis (IBK). The role of M bovoculi in IBK is not fully understood. M bovis and M bovoculi appear to undergo genetic recombination with each other or other members of the Moraxellaceae. Recombination complicates their classification and potential role(s) in IBK pathogenesis. MALDI-TOF MS is used to identify M bovis, 2 major strains or genotypes of M bovoculi, M ovis, and other members of the Moraxellaceae.