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The Morphology, Ultrastructure and Molecular Phylogeny of a New Freshwater Heterolobose Amoeba Parafumarolamoeba Stagnalis N. Sp
diversity Article The Morphology, Ultrastructure and Molecular Phylogeny of a New Freshwater Heterolobose Amoeba Parafumarolamoeba stagnalis n. sp. (Vahlkampfiidae; Heterolobosea) Anastasia S. Borodina 1,2, Alexander P. Mylnikov 1,†, Jan Janouškovec 3 , Patrick J. Keeling 4 and Denis V. Tikhonenkov 1,5,* 1 Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia; [email protected] 2 Department of Zoology and Parasitology, Voronezh State University, Universitetskaya Ploshad 1, 394036 Voronezh, Russia 3 Centre Algatech, Laboratory of Photosynthesis, Institute of Microbiology, Czech Academy of Sciences, Opatovický Mlýn, 37981 Tˇreboˇn,Czech Republic; [email protected] 4 Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T1Z4, Canada; [email protected] 5 AquaBioSafe Laboratory, University of Tyumen, 625003 Tyumen, Russia * Correspondence: [email protected]; Tel.: +7-485-472-4533 † Alexander P. Mylnikov is deceased. http://zoobank.org/References/e543a49a-16c1-4b7c-afdb-0bc56b632ef0 Abstract: Heterolobose amoebae are important members of marine, freshwater, and soil microbial Citation: Borodina, A.S.; Mylnikov, communities, but their diversity remains under-explored. We studied the diversity of Vahlkampfiidae A.P.; Janouškovec, J.; Keeling, P.J.; to improve our understanding of heterolobosean relationships and their representation in aquatic Tikhonenkov, D.V. The Morphology, benthos. Using light and electron microscopy, and molecular phylogenies based on the SSU rRNA Ultrastructure and Molecular and ITS loci, we describe the fine morphology and evolutionary relationships of a new heterolobosean Phylogeny of a New Freshwater Parafumarolamoeba stagnalis n. sp. from a small pond in European Russia. Cells of P. stagnalis possess Heterolobose Amoeba a clearly distinguishable anterior hyaline pseudopodium, eruptive movement, several thin and Parafumarolamoeba stagnalis n. -
The Intestinal Protozoa
The Intestinal Protozoa A. Introduction 1. The Phylum Protozoa is classified into four major subdivisions according to the methods of locomotion and reproduction. a. The amoebae (Superclass Sarcodina, Class Rhizopodea move by means of pseudopodia and reproduce exclusively by asexual binary division. b. The flagellates (Superclass Mastigophora, Class Zoomasitgophorea) typically move by long, whiplike flagella and reproduce by binary fission. c. The ciliates (Subphylum Ciliophora, Class Ciliata) are propelled by rows of cilia that beat with a synchronized wavelike motion. d. The sporozoans (Subphylum Sporozoa) lack specialized organelles of motility but have a unique type of life cycle, alternating between sexual and asexual reproductive cycles (alternation of generations). e. Number of species - there are about 45,000 protozoan species; around 8000 are parasitic, and around 25 species are important to humans. 2. Diagnosis - must learn to differentiate between the harmless and the medically important. This is most often based upon the morphology of respective organisms. 3. Transmission - mostly person-to-person, via fecal-oral route; fecally contaminated food or water important (organisms remain viable for around 30 days in cool moist environment with few bacteria; other means of transmission include sexual, insects, animals (zoonoses). B. Structures 1. trophozoite - the motile vegetative stage; multiplies via binary fission; colonizes host. 2. cyst - the inactive, non-motile, infective stage; survives the environment due to the presence of a cyst wall. 3. nuclear structure - important in the identification of organisms and species differentiation. 4. diagnostic features a. size - helpful in identifying organisms; must have calibrated objectives on the microscope in order to measure accurately. -
Primary Amoebic Meningoencephalitis Due to Naegleria Fowleri
56 Case report Primary amoebic meningoencephalitis due to Naegleria fowleri A. Angrup, L. Chandel, A. Sood, K. Thakur, S. C. Jaryal Department of Microbiology,Dr. Rajendra Prasad Government Medical College, Kangra at Tanda, Himachal Pradesh, Pin Code- 176001, India. Correspondence to: Dr. Archana Angrup, Department of Microbiology, Dr. Rajendra Prasad Government Medical College, Kangra, Tanda, Himachal Pradesh, Pin Code-176001, India. Phone no. 09418119222, Facsimile: 01892-267115 Email: [email protected] Abstract The genus Naegleria comprises of free living ameboflagellates found in soil and fresh water. More than 30 species have been isolated but only N. fowleri has been associated with human disease. N. fowleri causes primary amoebic meningoencephalitis (PAM), an acute, often fulminant infection of CNS. Here we report a rare and first case of PAM in an immunocompetent elderly patient from this part of the country. Amoeboid and flagellate forms of N. fowleri were detected in the direct microscopic examination of CSF and confirmed by flagellation test in distilled water, demonstrating plaques /clear areas on 1.5% non nutrient agar and its survival at 42°C. Keywords: Meningitis, Naegleria fowleri, primary amoebic meningoencephalitis Introduction of our knowledge, in India, only eight cases have been reported so far .1, 5-8 Infection of the central nervous system (CNS) in human We hereby report a rare case of PAM in elderly beings with free living amoebae is uncommon. Among the immunocompetent patient from the hilly state of Himachal many different genera of amoebae, Naegleria spp, Pradesh (H.P) in Northern India. Acanthamoeba spp and Balamuthia spp are primarily pathogenic to the CNS. -
Recent Advances in Trypanosomatid Research: Genome Organization, Expression, Metabolism, Taxonomy and Evolution
Parasitology Recent advances in trypanosomatid research: genome organization, expression, metabolism, cambridge.org/par taxonomy and evolution 1 2 3,4 5,6 Review Dmitri A. Maslov , Fred R. Opperdoes , Alexei Y. Kostygov , Hassan Hashimi , Julius Lukeš5,6 and Vyacheslav Yurchenko3,5,7 Cite this article: Maslov DA, Opperdoes FR, Kostygov AY, Hashimi H, Lukeš J, Yurchenko V 1Department of Molecular, Cell and Systems Biology, University of California – Riverside, Riverside, California, USA; (2018). Recent advances in trypanosomatid 2de Duve Institute, Université Catholique de Louvain, Brussels, Belgium; 3Life Science Research Centre, Faculty of research: genome organization, expression, 4 metabolism, taxonomy and evolution. Science, University of Ostrava, Ostrava, Czech Republic; Zoological Institute of the Russian Academy of Sciences, 5 Parasitology 1–27. https://doi.org/10.1017/ St. Petersburg, Russia; Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice 6 S0031182018000951 (Budweis), Czech Republic; University of South Bohemia, Faculty of Sciences, České Budejovice (Budweis), Czech Republic and 7Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov Received: 30 January 2018 University, Moscow, Russia Revised: 23 April 2018 Accepted: 23 April 2018 Abstract Key words: Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of inverte- Gene exchange; kinetoplast; metabolism; molecular and cell biology; taxonomy; brates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases trypanosomatidae in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental Author for correspondence: conditions, and omnipresence, these protists have major impact on all biotic communities Vyacheslav Yurchenko, E-mail: vyacheslav. -
The Amoeboid Parabasalid Flagellate Gigantomonas Herculeaof
Acta Protozool. (2005) 44: 189 - 199 The Amoeboid Parabasalid Flagellate Gigantomonas herculea of the African Termite Hodotermes mossambicus Reinvestigated Using Immunological and Ultrastructural Techniques Guy BRUGEROLLE Biologie des Protistes, UMR 6023, CNRS and Université Blaise Pascal de Clermont-Ferrand, Aubière Cedex, France Summary. The amoeboid form of Gigantomonas herculea (Dogiel 1916, Kirby 1946), a symbiotic flagellate of the grass-eating subterranean termite Hodotermes mossambicus from East Africa, is observed by light, immunofluorescence and transmission electron microscopy. Amoeboid cells display a hyaline margin and a central granular area containing the nucleus, the internalized flagellar apparatus, and organelles such as Golgi bodies, hydrogenosomes, and food vacuoles with bacteria or wood particles. Immunofluorescence microscopy using monoclonal antibodies raised against Trichomonas vaginalis cytoskeleton, such as the anti-tubulin IG10, reveals the three long anteriorly-directed flagella, and the axostyle folded into the cytoplasm. A second antibody, 4E5, decorates the conspicuous crescent-shaped structure or cresta bordered by the adhering recurrent flagellum. Transmission electron micrographs show a microfibrillar network in the cytoplasmic margin and internal bundles of microfilaments similar to those of lobose amoebae that are indicative of cytoplasmic streaming. They also confirm the internalization of the flagella. The arrangement of basal bodies and fibre appendages, and the axostyle composed of a rolled sheet of microtubules are very close to that of the devescovinids Foaina and Devescovina. The very large microfibrillar cresta supporting an enlarged recurrent flagellum resembles that of Macrotrichomonas. The parabasal apparatus attached to the basal bodies is small in comparison to the cell size; this is probably related to the presence of many Golgi bodies supported by a striated fibre that are spread throughout the central cytoplasm in a similar way to Placojoenia and Mixotricha. -
Large-Scale Phylogenetic Analyses Elucidate the Evolutionary Affiliations of Two Novel Microbial Eukaryotes, Tsukubamonas Globosa and Palipitomonas Bilix
External Review on Center for Computational Sciences, University of Tsukuba Feb. 18-20, 2014 Large-scale phylogenetic analyses elucidate the evolutionary affiliations of two novel microbial eukaryotes, Tsukubamonas globosa and Palipitomonas bilix Yuji Inagaki Graduate School of Life and Environmental Sciences Center for Computational Sciences University of Tsukuba Our goal is A well-resolved global eukaryotic phylogeny Model the evolutions of traits in eukaryotic cells Mitochondria, plastids, other bacterial endosymbionts, translation systems, etc. Novel microbial eukaryotes, which have not been observed (or studied in detail) lots of them in environments Find & isolate Next-generation Cultivate sequencing Characterize Generate large-scale sequence data ‘Phylogenomic’ Determine the phylogenetic position analysis How we find, characterize, and analyze novel eukaryotes Culturing 1 Sampling Microscopic observation 2 Small-scale DNA sequencing Phylogenomic analyses Small subunit Next-generation sequencing rRNA gene 4 3 Large-scale transcriptomic data And/or genome data Two novel eukaryotes Photo by Yabuki Tsukubamonas globosa 1 Photo by N. Yubuki 2 Palpitomonas bilix Adl et al. 2012 J Eukaryot Microbiol 59:429-493 University of Tsukuba: Homo of Tsukubamonas globosa Isolated from Hyoutaro-pond Maintained in UR-YT medium at 20ᵒC since October 2002 Tsukubamonas: How it looks like A fibre Singlet-root associated fibre 10 mm 10 mm 10 mm Right root N, Nucleus; Fv, Food vacuole Singlet root I fibre Posterior basal body B fibre 0.5 mm Posterior Singlet-root basal body associated fibre Backward Posterior Right root Right root basal body Inner right root Mitochondrion Outer Right root B fibre 0.5 mm 2 mm Yabuki et al. -
Genomics of Sorocarpic Amoebae
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1516 Genomics of Sorocarpic Amoebae SANEA SHEIKH ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-554-9913-6 UPPSALA urn:nbn:se:uu:diva-320432 2017 Dissertation presented at Uppsala University to be publicly examined in Lindhalsalen, Norbyvägen 18D, Uppsala, Friday, 9 June 2017 at 09:00 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Assistant professor Matthew W. Brown (Department of Biological Sciences, Mississippi State University, USA). Abstract Sheikh, S. 2017. Genomics of Sorocarpic Amoebae. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1516. 45 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9913-6. Sorocarpy is the aggregation of unicellular organisms to form multicellular fruiting bodies (sorocarps). This thesis is about the two best-known groups of sorocarpic amoebae, Dictyostelids and Acrasids. Paper I describes assembly and analysis of a multigene dataset to identify the root of the dictyostelid tree. Phylogenetic analyses of 213 genes (conserved in all sequenced dictyostelid genomes and an outgroup) place the root between Groups 1+2 and 3+4 (now: Cavenderiaceae + Acytosteliaceae and Raperosteliaceae + Dictyosteliaceae). Resolution of the dictyostelid root made it possible to proceed with a major taxonomic revision of the group. Paper II focuses on the taxonomic revision of Dictyostelia based on molecular phylogeny and SSU ribosomal RNA sequence signatures. The two major divisions were treated at the rank of order as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders were given the rank of family. -
Evolutionary Analyses of Myosin Genes in Trypanosomatids Show A
www.nature.com/scientificreports OPEN Evolutionary analyses of myosin genes in trypanosomatids show a history of expansion, secondary Received: 15 September 2017 Accepted: 18 December 2017 losses and neofunctionalization Published: xx xx xxxx Denise Andréa Silva de Souza1,2, Daniela Parada Pavoni1,2, Marco Aurélio Krieger1,2,3 & Adriana Ludwig1,3 Myosins are motor proteins that comprise a large and diversifed family important for a broad range of functions. Two myosin classes, I and XIII, were previously assigned in Trypanosomatids, based mainly on the studies of Trypanosoma cruzi, T. brucei and Leishmania major, and important human pathogenic species; seven orphan myosins were identifed in T. cruzi. Our results show that the great variety of T. cruzi myosins is also present in some closely related species and in Bodo saltans, a member of an early divergent branch of Kinetoplastida. Therefore, these myosins should no longer be considered “orphans”. We proposed the classifcation of a kinetoplastid-specifc myosin group into a new class, XXXVI. Moreover, our phylogenetic data suggest that a great repertoire of myosin genes was present in the last common ancestor of trypanosomatids and B. saltans, mainly resulting from several gene duplications. These genes have since been predominantly maintained in synteny in some species, and secondary losses explain the current distribution. We also found two interesting genes that were clearly derived from myosin genes, demonstrating that possible redundant or useless genes, instead of simply being lost, can serve as raw material for the evolution of new genes and functions. Myosins are important eukaryotic molecular motor proteins that bind actin flaments and are dependent of ATP hydrolysis1. -
Molecular Identification of Free-Living Amoebae of the Vahlkampfiidae
Protistology Protistology 5 (2/3), 142–145 (2007/8) Molecular identification of free-living amoebae of the Vahlkampfiidae isolated in Mexico Johan F. De Jonckheere 1, Eunice Guzmán Fierros 2 and Fernando Lares Villa2 1 Scientific Institute of Public Health, B-1050 Brussels, Belgium 2 Technological Institute of Sonora, Cd. Obregon, Sonora, 85000, Mexico Summary We performed a search for the presence of the vahlkampfiid amoebae in six different states of Mexico. We obtained five Naegleria isolates belonging to four described species. Two of them, N. indonesiensis and N. byersi, were previously though to have restricted geographic distribu- tion. The four Tetramitus isolates belong to two known species, one of which has recently been described from Arizona. Key words: 5.8S rDNA, internal transcribed spacer, Naegleria, Tetramitus Introduction australiensis and N. lovaniensis, could be iden- tified by this method amongst the isolates from There have been several cases of primary Mexico. However, several Naegleria isolates in amoebic meningoencephalitis (PAM) caused these studies could not be identified, and the only by the free-living amoeba Naegleria fowleri in other member of the Vahlkampfiidae identified is Mexico (Valenzuela et al., 1984, Lopez-Corella et Willaertia magna. Strains of N. fowleri have also al., 1989, Lares-Villa et al., 1993, Vargas-Zepeda et been isolated from the environment and PAM cas- al., 2005). As a result, many investigations on the es in Mexico (Lares-Villa et al., 1993). presence of free-living amoebae in the environ- By sequencing parts of the rDNA it is now pos- ment were performed in Mexico. Identifications sible to identify species and describe new species of the Vahlkampfiidae were conducted mainly amongst isolates of the genus Naegleria and the other on morphological basis (Rivera et al., 1993), but genera of the Vahlkampfiidae (De Jonckheere, 1998; sometimes isoenzymes were used (De Jonckheere De Jonckheere and Brown, 2005). -
Inferring Ancestry
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1176 Inferring Ancestry Mitochondrial Origins and Other Deep Branches in the Eukaryote Tree of Life DING HE ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-554-9031-7 UPPSALA urn:nbn:se:uu:diva-231670 2014 Dissertation presented at Uppsala University to be publicly examined in Fries salen, Evolutionsbiologiskt centrum, Norbyvägen 18, 752 36, Uppsala, Friday, 24 October 2014 at 10:30 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor Andrew Roger (Dalhousie University). Abstract He, D. 2014. Inferring Ancestry. Mitochondrial Origins and Other Deep Branches in the Eukaryote Tree of Life. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1176. 48 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9031-7. There are ~12 supergroups of complex-celled organisms (eukaryotes), but relationships among them (including the root) remain elusive. For Paper I, I developed a dataset of 37 eukaryotic proteins of bacterial origin (euBac), representing the conservative protein core of the proto- mitochondrion. This gives a relatively short distance between ingroup (eukaryotes) and outgroup (mitochondrial progenitor), which is important for accurate rooting. The resulting phylogeny reconstructs three eukaryote megagroups and places one, Discoba (Excavata), as sister group to the other two (neozoa). This rejects the reigning “Unikont-Bikont” root and highlights the evolutionary importance of Excavata. For Paper II, I developed a 150-gene dataset to test relationships in supergroup SAR (Stramenopila, Alveolata, Rhizaria). Analyses of all 150-genes give different trees with different methods, but also reveal artifactual signal due to extremely long rhizarian branches and illegitimate sequences due to horizontal gene transfer (HGT) or contamination. -
Marine Biological Laboratory) Data Are All from EST Analyses
TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878. -
Multi-Gene Phylogenetic Analysis of the Supergroup Excavata
MULTI-GENE PHYLOGENETIC ANALYSIS OF THE SUPERGROUP EXCAVATA By CHRISTINA CASTLEJOHN (Under the Direction of Mark A. Farmer) ABSTRACT The supergroup Excavata, one of six supergroups of eukaryotes, has been a controversial supergroup within the Eukaryotic Tree of Life. Excavata was originally based largely on morphological data and to date has not been well supported by molecular studies. The goals of this research were to test the monophyly of Excavata and to observe relationships among the nine subgroups of excavates included in this study. Several different types of phylogenetic analyses were performed on a data set consisting of sequences from nine reasonably conserved genes. Analyses of this data set recovered monophyly of Excavata with moderate to strong support. Topology tests rejected all but two topologies: one with a monophyletic Excavata and one with Excavata split into two major clades. Simple gap coding, which was performed on the ribosomal DNA alignments, was found to be more useful for species-level analyses than deeper relationships with the eukaryotes. INDEX WORDS: Excavata, excavates, monophyly, phylogenetic analysis, gap coding MULTI-GENE PHYLOGENETIC ANALYSIS OF THE SUPERGROUP EXCAVATA By CHRISTINA CASTLEJOHN B.S., Georgia Institute of Technology, 2002 A Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE ATHENS, GEORGIA 2009 © 2009 Christina Castlejohn All Rights Reserved MULTI-GENE PHYLOGENETIC ANALYSIS OF THE SUPERGROUP EXCAVATA By CHRISTINA CASTLEJOHN Major Professor: Mark A. Farmer Committee: James Leebens-Mack Joseph McHugh Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia August 2009 iv DEDICATION To my family, who have supported me in my journey v ACKNOWLEDGEMENTS I would like to thank Mark Farmer for helping me so much in my pursuit of higher education and my plans for the future.