DOCSLIB.ORG

Universidad Complutense De Madrid Facultad De Farmacia Departamento De Microbiología Ii

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Universidad Complutense De Madrid Facultad De Farmacia Departamento De Microbiología Ii UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE FARMACIA DEPARTAMENTO DE MICROBIOLOGÍA II ANÁLISIS GENÉTICO Y BIOQUÍMICO DEL CATABOLISMO DEL COLESTEROL EN Mycobacterium smegmatis mc²155 TESIS DOCTORAL IRIA UHÍA CASTRO Madrid, 2010 UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE FARMACIA DEPARTAMENTO DE MICROBIOLOGÍA II ANÁLISIS GENÉTICO Y BIOQUÍMICO DEL CATABOLISMO DEL COLESTEROL EN Mycobacterium smegmatis mc²155 TESIS DOCTORAL IRIA UHÍA CASTRO DIRECTORES: Dra. BEATRIZ GALÁN SICILIA Dr. JOSÉ LUIS GARCÍA LÓPEZ CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS CENTRO DE INVESTIGACIONES BIOLÓGICAS Madrid, 2010 La miro a V. en los ojos, y mis ojos le dicen que soy un pobre buscador en el mundo, que no comprendo nada de mi destino ni del de los demás, que he vivido, y pecado, y creado, y que un día me iré sin haber comprendido nada, en la oscuridad que nos ha parido a todos. J. J. En la Ciencia la única verdad sagrada, es que no hay verdades sagradas. Carl Sagan A mis padres AGRADECIMIENTOS Por si cabe alguna duda, sabed que no se podría entender el trabajo acumulado en estas páginas sin este apartado. Una tesis no son sólo las miles de horas pasadas en el laboratorio intentando que salga ese experimento que no te deja dormir, una tesis es también todo el lado humano que está detrás y que te permite dar lo mejor de ti cada día con ilusión a pesar de los tropiezos. Una tesis es todas las experiencias, buenas y malas, dentro y fuera del laboratorio, acumuladas en estos años, más allá de las pipetas, las electroforesis y los microarrays. No se puede entender lo uno sin lo otro. Por todo eso me es obligatorio dedicar unas líneas a todos los que conformaron el escenario en el que se desarrolló este trabajo, y a todos los que estuvieron entre bastidores. Desde el director hasta el último apuntador, todos son importantes y sin ellos hubiera sido imposible que la obra hubiese empezado y terminado. Es tarea difícil agradecer tantas cosas a tantos en tan poco espacio. Se intentará. Todo sea dicho, os merecéis mucho más. En primer lugar quiero agradecerle al Doctor José Luis García el haberme “engañado” para realizar la tesis doctoral. Ha sido un camino duro, pero ha merecido la pena. Gracias por tus brillantes ideas, por enseñarme a buscar las mías propias, por intentar que diese lo mejor de mi en todo momento, por saber contagiar esa pasión tan grande que tienes por la ciencia y por aparecer (afortunadamente) como por arte de magia cuando tu presencia es imprescindible y ya empezamos a temer que quizás estés en Vladivostock u otro lugar de nombre más impronunciable si cabe. Gracias a la Doctora Beatriz Galán (Bea), mi primera compañera de batalla en el mundo nuevo de las micobacerias; empezamos solas ante el peligro rodeadas de Pseudomonas, Escherichia y Azoarcus, ¡pero al final hemos conseguido hacernos un hueco respetable!. Gracias por tus sabios consejos, por enseñarme a ser práctica cuando tiendo al enrevesamiento, por animarme en los momentos de pesimismo científico, por tu actitud siempre positiva y ante todo por ser, además de una gran codirectora de tesis, una estupenda compañera de laboratorio más. Gracias a todos los miembros de plantilla del grupo de Biotecnología Medioambiental y del grupo de Genética Bacteriana. Creo que uno de los secretos para que un laboratorio funcione a la perfección es que haya entendimiento, cooperatividad y respeto entre los “jefes”; esto siempre influye positivamente en los que estamos más abajo y hace que el ambiente de trabajo sea inmejorable. Felicidades, porque lo habéis conseguido. Gracias al doctor Eduardo Díaz, que nunca deja un cabo suelto, al doctor Manuel Carmona, nuestro experto en evolución, a la doctora Auxiliadora Prieto, maestra de los plásticos, al doctor Rubén López, el patriarca, al doctor Ernesto García, el sentenciador, al doctor Pedro García, eres auténtico, no cambies nunca. A mis compañeros del día a día: en general gracias a todos porque no creo que hubiese mejores personajes con los que compartir alegrías y penas científicas. Sois los mejores. En primer lugar me gustaría recordar a Patricia, Cris F y Pepa; prácticamente nos cruzamos, yo entrando de novata y vosotras saliendo hacia vuestra recién estrenada etapa de post doc. Espero que todo os vaya estupendamente. Gracias a los neumos, tan dispuestos a ayudar en temas científicos como a hacer vídeos al más puro estilo Dogma o a darlo todo con unos abanicos al ritmo de Locomía: Miri, Elisa, José Yuste, Marta, Beatriz, Miriam, Violeta, Susana, Elo. Gracias María del Mar por esas habitaciones rurales compartidas y por tener siempre en la cara esa sonrisa encantadora que ilumina. Gracias Dani, (el más actor de todos los científicos, el más científico de todos los actores) por descubrirme el mundo de la improvisación teatral; aquí tienes una seguidora incondicional. Gracias María por tantas noches imborrables, por el estupendo viaje a Donosti, por todas las historias con un toootal (especialmente aquella de Koldo Matilla), ¡y felicidades por la peque en camino! Ana, Anitaaaaa!!! Muchas gracias por esa alegría y vitalidad que desprendes por cada poro de tu piel y que consigues contagiarnos; gracias por ser la primera en ir a visitarme al 344 cuando aún era territorio recién conquistado y nadie se atrevía a entrar, gracias por tantas y tantas charlas, algunas de camino a casa al borde de la congelación, pero no importa: siempre es un placer hablar contigo. Vales mucho, convéncete de ello. Seguiré por los que me quedan más cerquita, los biodegradadores, y en primer lugar por el primer laboratorio en el que hice escala recién llegada al grupo: el 342. Gracias Irene por ser tan maja y eficiente y ser un apoyo femenino en aquella primera etapa rodeada de testosterona. Gracias Niño; a ti te tocó ejercer de primer papá pato de una Iria totalmente novata; gracias por tu paciencia, por estar siempre dispuesto ayudar, por no quejarte por robarte espacio de poyata y mesa de ordenador, por intentar siempre hacerme reír y conseguirlo, esos primeros meses y los siguientes dos años. Gracias Gonn, el equilibrio perfecto hecho persona, gracias por ponerme bien el cuello de la bata, por estar siempre ahí para lo que haga falta, científico o no, por tomarte la confianza de vacilarme sin ningún pudor, por nonononono, por los conciertos, por tantas y tantas risas. A mis extremeños favoritos: Blas, Blasete, Bleis: gracias por las conversaciones en la campana y fuera de ella, por sorprenderme siempre con nuevas e insospechadas preguntas sobre lo humano y lo divino, por recomendarme buenas series, por tu cruzada pro-cañas los jueves, por tus ji ji ji, por ser tan maligno pero a la vez tan pedazo de pan, por enseñarme tantos consejillos prácticos en el labo y por supuesto por el cloruro de calcio. Ánimo con el postdoc. ¿Para cuándo una quedada rubenil en Las Vegas? Juan: ha sido un privilegio tenerte sentado detrás gran parte de esta tesis. Gracias por tu paciencia infinita todas las veces (que no fueron pocas) que te asalté con dudas, desde cuánto tiempo se dejaba una ligación hasta cómo se hacía un modelo 3D de proteínas. Y sobre todo por los dibujos de colorines sin los que mi mente cuadriculada todavía no entendería la recombinación homóloga. Te debo más pulpos de los que puedas comer en esta vida. Gracias por los momentos grunge (voy a obviar los momentos Sínkope) y gracias sobre todo, ante todo y a pesar de todo por ser un grandísimo amigo. Aunque intentes esconderte detrás de un gruñón a mí no me engañas: eres de las mejores personas que he conocido. Gracias al laboratorio de las niñas, el 343, adonde hacía escapadas cuando ya notaba que me estaba masculinizando en demasía. Gracias Tere por ser el mejor ejemplo a seguir y por luchar contra el caos que nos caracteriza a los biodegradadores; gracias Laura, compañera del metal, por tu mente clara (contado por ti cualquier protocolo parece fácil) y por tu ironía y sarcasmo de los que soy fan número uno, gracias también por salvarme la vida (del ordenador) en un momento de crisis vírica de cuyo nombre no quiero acordarme…Gracias Isa Manso, por esa gracia cordobesa y por no perder tu dulzura e inocencia a pesar que tener que lidiar con los caballeros del 342 durante años. Gracias Merche, mi compañera en la conquista de nuevos territorios, por recordarme que lo más importante en la vida es precisamente eso: vivir y disfrutar de cada momento como si fuera el último; por los cotilleos compartidos y por esa naturalidad tan genial que te caracteriza. A los que llegaron después de mí: Javier, gracias por tu bondad intrínseca e inseparable de tu persona, porque no importa lo apurado que estés, siempre tienes un momento para preguntar ¿qué tal te va? o para ayudar en lo que sea; gracias también por aquel sirtaki sueco y por los momentos Tom Jones a última hora de la tarde. Te deseo toda la suerte del mundo. Gracias Isabel por intentar y lograr el milagro de organizar a los rubenes en tantas ocasiones; después de mi momento de coreógrafa sé lo difícil que es. Gracias junto a Javier por ser los mejores guías posibles en el viaje a León. Gracias Vir por ser un encanto de persona siempre dispuesta a escuchar y a dar cariño, por tus despistes con los que me siento tan identificada, por tus momentos de soprano y por las noches en las que lo dimos todo. Gracias Nina por tu vitalidad incombustible, por las tardes de garrapato y póker y por ser una rubena por derecho propio desde el primer día.
Load more

Recommended publications
  • Relative Genetic Diversity of the Rare and Endangered Agave Shawii Ssp
    Received: 17 July 2020 | Revised: 9 December 2020 | Accepted: 14 December 2020 DOI: 10.1002/ece3.7172 ORIGINAL RESEARCH Relative genetic diversity of the rare and endangered Agave shawii ssp. shawii and associated soil microbes within a southern California ecological preserve Jeanne P. Vu1 | Miguel F. Vasquez1 | Zuying Feng1 | Keith Lombardo2 | Sora Haagensen1,3 | Goran Bozinovic1,4 1Boz Life Science Research and Teaching Institute, San Diego, CA, USA Abstract 2Southern California Research Learning Shaw's Agave (Agave shawii ssp. shawii) is an endangered maritime succulent growing Center, National Park Services, San Diego, along the coast of California and northern Baja California. The population inhabiting CA, USA 3University of California San Diego Point Loma Peninsula has a complicated history of transplantation without documen- Extended Studies, La Jolla, CA, USA tation. The low effective population size in California prompted agave transplanting 4 Biological Sciences, University of California from the U.S. Naval Base site (NB) to Cabrillo National Monument (CNM). Since 2008, San Diego, La Jolla, CA, USA there are no agave sprouts identified on the CNM site, and concerns have been raised Correspondence about the genetic diversity of this population. We sequenced two barcoding loci, rbcL Goran Bozinovic, Boz Life Science Research and Teaching Institute, 3030 Bunker Hill St, and matK, of 27 individual plants from 5 geographically distinct populations, includ- San Diego CA 92109, USA. ing 12 individuals from California (NB and CNM). Phylogenetic analysis revealed the Emails: [email protected]; gbozinovic@ ucsd.edu three US and two Mexican agave populations are closely related and have similar ge- netic variation at the two barcoding regions, suggesting the Point Loma agave popu- Funding information National Park Services (NPS) Pacific West lation is not clonal.
    [Show full text]
  • Development of Bacterial Communities in Biological Soil Crusts Along
    1 Development of bacterial communities in biological soil crusts along 2 a revegetation chronosequence in the Tengger Desert, northwest 3 China 4 5 Author names and affiliations: 6 Lichao Liu1, Yubing Liu1, 2 *, Peng Zhang1, Guang Song1, Rong Hui1, Zengru Wang1, Jin Wang1, 2 7 1Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese 8 Academy of Sciences, Lanzhou, 730000, China 9 2Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Northwest Institute 10 of Eco–Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China 11 12 * Corresponding author: Yubing Liu 13 Address: Donggang West Road 320, Lanzhou 730000, P. R. China. 14 Tel: +86 0931 4967202. 15 E-mail address: [email protected] 16 17 Abstract. Knowledge of structure and function of microbial communities in different 18 successional stages of biological soil crusts (BSCs) is still scarce for desert areas. In this study, 19 Illumina MiSeq sequencing was used to assess the composition changes of bacterial communities 20 in different ages of BSCs in the revegetation of Shapotou in the Tengger Desert. The most dominant 21 phyla of bacterial communities shifted with the changed types of BSCs in the successional stages, 22 from Firmicutes in mobile sand and physical crusts to Actinobacteria and Proteobacteria in BSCs, 23 and the most dominant genera shifted from Bacillus, Enterococcus and Lactococcus to 24 RB41_norank and JG34-KF-361_norank. Alpha diversity and quantitative real-time PCR analysis 25 indicated that bacteria richness and abundance reached their highest levels after 15 years of BSC 26 development.
    [Show full text]
  • Supporting Information
    Supporting Information Fujimura et al. 10.1073/pnas.1310750111 SI Materials and Methods respectively. Photomicrographs were captured using a Zeiss Axio House Dust Collection. Dust from homes with or without dogs was Imager Z1 and AxioVision 4.8 software (Zeiss). collected using a sterile fabric filter sock inserted into a sterile vacuum nozzle immediately before vacuuming a 3′ × 3′ area for mRNA Extraction, Reverse Transcription, and RT-PCR. mRNA was 3 min. The sock was removed from the vacuum, the collected isolated from ground lung tissue using TRIzol reagent (Invi- μ trogen) or the RNeasy Mini kit (Qiagen) according to manu- dust weighed and sieved through a 300- m sieve to remove large ’ μ debris from the sample. Comparable sieved samples have pre- facturer s instructions. A total of 5 g of RNA per sample was reverse transcribed using murine leukemia virus RTase (Applied viously been used successfully to profile microbial communities Biosystems). Expression of relevant genes was analyzed with present in house dust (1, 2). Dust samples were subsequently TaqMan gene expression assays (Applied Biosystems) using an divided into 25- or 6.25-mg fractions for dog (D)- or no-pet ABI Prism 7500 Sequence Detection System (Applied Bio- (NP)-associated houses, respectively, each stored in a sterile − systems). Gene expression was normalized to GAPDH and ex- 5-mL tube at 20 °C until used for murine supplementation. pressed as fold change over expression in control mice. Murine Models. Cockroach allergen model. BALB/c were purchased Culture and Stimulation of Lymph Node Cells. Mediastinal lymph from The Jackson Laboratory.
    [Show full text]
  • Reactor Performance and Microbial Analysis
    www.nature.com/scientificreports OPEN Investigation of foaming causes in three mesophilic food waste digesters: reactor performance and Received: 24 March 2017 Accepted: 9 October 2017 microbial analysis Published: xx xx xxxx Qin He, Lei Li, Xiaofei Zhao, Li Qu, Di Wu & Xuya Peng Foaming negatively afects anaerobic digestion of food waste (FW). To identify the causes of foaming, reactor performance and microbial community dynamics were investigated in three mesophilic digesters treating FW. The digesters were operated under diferent modes, and foaming was induced with several methods. Proliferation of specifc bacteria and accumulation of surface active materials may be the main causes of foaming. Volatile fatty acids (VFAs) and total ammonia nitrogen (TAN) accumulated in these reactors before foaming, which may have contributed to foam formation by decreasing the surface tension of sludge and increasing foam stability. The relative abundance of acid- producing bacteria (Petrimonas, Fastidiosipila, etc.) and ammonia producers (Proteiniphilum, Gelria, Aminobacterium, etc.) signifcantly increased after foaming, which explained the rapid accumulation + of VFAs and NH4 after foaming. In addition, the proportions of microbial genera known to contribute to foam formation and stabilization signifcantly increased in foaming samples, including bacteria containing mycolic acid in cell walls (Actinomyces, Corynebacterium, etc.) and those capable of producing biosurfactants (Corynebacterium, Lactobacillus, 060F05-B-SD-P93, etc.). These fndings improve the understanding of foaming mechanisms in FW digesters and provide a theoretical basis for further research on efective suppression and early warning of foaming. Anaerobic digestion is the most feasible method for treating food waste (FW) and recovering renewable energy due to its high organic and moisture contents and low calorifc value compared with traditional treatments such as incineration or landflls1.
    [Show full text]
  • Piscine Mycobacteriosis
    Piscine Importance The genus Mycobacterium contains more than 150 species, including the obligate Mycobacteriosis pathogens that cause tuberculosis in mammals as well as environmental saprophytes that occasionally cause opportunistic infections. At least 20 species are known to Fish Tuberculosis, cause mycobacteriosis in fish. They include Mycobacterium marinum, some of its close relatives (e.g., M. shottsii, M. pseudoshottsii), common environmental Piscine Tuberculosis, organisms such as M. fortuitum, M. chelonae, M. abscessus and M. gordonae, and Swimming Pool Granuloma, less well characterized species such as M. salmoniphilum and M. haemophilum, Fish Tank Granuloma, among others. Piscine mycobacteriosis, which has a range of outcomes from Fish Handler’s Disease, subclinical infection to death, affects a wide variety of freshwater and marine fish. It Fish Handler’s Nodules has often been reported from aquariums, research laboratories and fish farms, but outbreaks also occur in free-living fish. The same organisms sometimes affect other vertebrates including people. Human infections acquired from fish are most often Last Updated: November 2020 characterized by skin lesions of varying severity, which occasionally spread to underlying joints and tendons. Some lesions may be difficult to cure, especially in those who are immunocompromised. Etiology Mycobacteriosis is caused by members of the genus Mycobacterium, which are Gram-positive, acid fast, pleomorphic rods in the family Mycobacteriaceae and order Actinomycetales. This genus is traditionally divided into two groups: the members of the Mycobacterium tuberculosis complex (e.g., M. tuberculosis, M. bovis, M. caprae, M. pinnipedii), which cause tuberculosis in mammals, and the nontuberculous mycobacteria. The organisms in the latter group include environmental saprophytes, which sometimes cause opportunistic infections, and other species such as M.
    [Show full text]
  • Mycobacterium Kansasii, Strain 824 Catalog No. NR-44269 For
    Product Information Sheet for NR-44269 Mycobacterium kansasii, Strain 824 at -60°C or colder immediately upon arrival. For long-term storage, the vapor phase of a liquid nitrogen freezer is recommended. Freeze-thaw cycles should be avoided. Catalog No. NR-44269 Growth Conditions: For research use only. Not for human use. Media: Middlebrook 7H9 broth with ADC enrichment or equivalent Contributor: Middlebrook 7H10 agar with OADC enrichment or Diane Ordway, Ph.D., Assistant Professor, Department of Lowenstein-Jensen agar or equivalent Microbiology, Immunology and Pathology, Colorado State Incubation: University, Fort Collins, Colorado, USA and National Institute Temperature: 37°C of Allergy and Infectious Diseases (NIAID), National Institutes Atmosphere: Aerobic with 5% CO2 of Health (NIH), Bethesda, Maryland, USA Propagation: 1. Keep vial frozen until ready for use; then thaw. Manufacturer: 2. Transfer the entire thawed aliquot into a single tube of BEI Resources broth. 3. Use several drops of the suspension to inoculate an agar Product Description: slant and/or plate. Bacteria Classification: Mycobacteriaceae, Mycobacterium 4. Incubate the tube, slant and/or plate at 37°C for 1 to 6 Species: Mycobacterium kansasii weeks. Strain: 824 Original Source: Mycobacterium kansasii (M. kansasii), strain Citation: 824 was isolated in 2012 from human sputum at the Acknowledgment for publications should read “The following University of Texas Health Science Center at Tyler, Tyler, reagent was obtained through BEI Resources, NIAID, NIH: 1 Texas, USA. Mycobacterium kansasii, Strain 824, NR-44269.” Comment: M. kansasii, strain 824 is part of the Top Priority Nontuberculous Mycobacteria Whole Genome Sequencing Biosafety Level: 2 Project at the Genomic Sequencing Center for Infectious Appropriate safety procedures should always be used with this Diseases (GSCID) at University of Maryland School of material.
    [Show full text]
  • Wedding Higher Taxonomic Ranks with Metabolic Signatures Coded in Prokaryotic Genomes
    Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes Gregorio Iraola*, Hugo Naya* Corresponding authors: E-mail: [email protected], [email protected] This PDF file includes: Supplementary Table 1 Supplementary Figures 1 to 4 Supplementary Methods SUPPLEMENTARY TABLES Supplementary Tab. 1 Supplementary Tab. 1. Full prediction for the set of 108 external genomes used as test. genome domain phylum class order family genus prediction alphaproteobacterium_LFTY0 Bacteria Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae Unknown candidatus_nasuia_deltocephalinicola_PUNC_CP013211 Bacteria Proteobacteria Gammaproteobacteria Unknown Unknown Unknown candidatus_sulcia_muelleri_PUNC_CP013212 Bacteria Bacteroidetes Flavobacteriia Flavobacteriales NA Candidatus Sulcia deinococcus_grandis_ATCC43672_BCMS0 Bacteria Deinococcus-Thermus Deinococci Deinococcales Deinococcaceae Deinococcus devosia_sp_H5989_CP011300 Bacteria Proteobacteria Unknown Unknown Unknown Unknown micromonospora_RV43_LEKG0 Bacteria Actinobacteria Actinobacteria Micromonosporales Micromonosporaceae Micromonospora nitrosomonas_communis_Nm2_CP011451 Bacteria Proteobacteria Betaproteobacteria Nitrosomonadales Nitrosomonadaceae Unknown nocardia_seriolae_U1_BBYQ0 Bacteria Actinobacteria Actinobacteria Corynebacteriales Nocardiaceae Nocardia nocardiopsis_RV163_LEKI01 Bacteria Actinobacteria Actinobacteria Streptosporangiales Nocardiopsaceae Nocardiopsis oscillatoriales_cyanobacterium_MTP1_LNAA0 Bacteria Cyanobacteria NA Oscillatoriales
    [Show full text]
  • Genomics of Atlantic Forest Mycobacteriaceae Strains Unravels a Mobilome Diversity with a Novel Integrative Conjugative Element and Plasmids Harbouring T7SS
    RESEARCH ARTICLE Morgado and Paulo Vicente, Microbial Genomics 2020;6 DOI 10.1099/mgen.0.000382 Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS Sergio Mascarenhas Morgado* and Ana Carolina Paulo Vicente Abstract Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nev- ertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the Mycobacteriaceae family, focus- ing on strains from Brazilian Atlantic Forest soil. Novel Mycolicibacterium and Mycobacteroides strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type- VII secretion system (T7SS) and mobility- associated genes. In addition, we also identified a T4SS- mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the Mycobacteriaceae mobilome, pro- viding the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS. Data SUMMARY Conjugative elements, such as conjugative plasmids and Genomic data analysed in this work are available in GenBank integrative conjugative elements (ICEs), mediate their own and listed in Tables S1 and S2 (available in the online version transfer to other organisms, often carrying cargo genes.
    [Show full text]
  • (Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
    Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci;
    [Show full text]
  • Mycobacterium Avium Subsp
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Veterinary and Biomedical Sciences, Papers in Veterinary and Biomedical Science Department of July 2001 Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine N. Beth Harris University of Nebraska - Lincoln Raul G. Barletta University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/vetscipapers Part of the Veterinary Medicine Commons Harris, N. Beth and Barletta, Raul G., "Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine" (2001). Papers in Veterinary and Biomedical Science. 5. https://digitalcommons.unl.edu/vetscipapers/5 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. CLINICAL MICROBIOLOGY REVIEWS, July 2001, p. 489–512 Vol. 14, No. 3 0893-8512/01/$04.00ϩ0 DOI: 10.1128/CMR.14.3.489–512.2001 Copyright © 2001, American Society for Microbiology. All Rights Reserved. Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine N. BETH HARRIS AND RAU´ L G. BARLETTA* Department of Veterinary and Biomedical Sciences, University of Nebraska—Lincoln, Lincoln, Nebraska 68583-0905 INTRODUCTION .......................................................................................................................................................489
    [Show full text]
  • Marine Rare Actinomycetes: a Promising Source of Structurally Diverse and Unique Novel Natural Products
    Review Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products Ramesh Subramani 1 and Detmer Sipkema 2,* 1 School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji; [email protected] 2 Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-317-483113 Received: 7 March 2019; Accepted: 23 April 2019; Published: 26 April 2019 Abstract: Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
    [Show full text]
  • Compile.Xlsx
    Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge;
    [Show full text]