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Omar HM, Fahmy M, Abuowarda M. Hand palm sparganosis: morphologically and genetically confirmed Spirometra erinaceieuropaei in a fourteen-year-old girl, Egypt. J Parasit Dis 2023; 47:859-864. [PMID: 38009142 PMCID: PMC10667186 DOI: 10.1007/s12639-023-01623-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/28/2023] [Indexed: 11/28/2023] Open
Abstract
Two spargana of 5 and 7 cm long were removed from the right-hand palm of 14-year-old girl at the General Hospital, Qalyubia, Egypt. Sparganum is the 2nd larval stage (pleurocercoid) of Diphyllobothrid cestode species develops in the vertebrate second intermediate host through ingestion of the crustacean first intermediate host.Dogs and cats are the final hosts get infected through predation of the second vertebrate host.Human attracts infection through drinking water contaminated with the infected crustacean host or consumption of the flesh of of vertebrate hosts such as frogs and reptilian species. The surgically removed specimens were parsitologically identified as a non-proliferative metacestodes of a spirometran species that then on molecular analysis proved to be Spirometra erinaceieuropaei. The present report has allocated Egypt on the world sparganosis map.Molecular characterization of 28 S rRNA of S. erinaceieuropae and correlation to other Spirometra spp. from the Nile countries, particularly Ethiopia and Lake Victoria countries where the Nile waters originate, and from China were dealt with. Drinking of contaminated fresh water is the only proposed mode of infection in Egypt.
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Affiliation(s)
- Hussein M. Omar
- Department of Parasitology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211 Egypt
| | - Magdy Fahmy
- Department of Parasitology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211 Egypt
| | - Mai Abuowarda
- Department of Parasitology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211 Egypt
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About the Analysis of 18S rDNA Sequence Data from Trypanosomes in Barcoding and Phylogenetics: Tracing a Continuation Error Occurring in the Literature. BIOLOGY 2022; 11:biology11111612. [DOI: 10.3390/biology11111612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
The variable regions (V1–V9) of the 18S rDNA are routinely used in barcoding and phylogenetics. In handling these data for trypanosomes, we have noticed a misunderstanding that has apparently taken a life of its own in the literature over the years. In particular, in recent years, when studying the phylogenetic relationship of trypanosomes, the use of V7/V8 was systematically established. However, considering the current numbering system for all other organisms (including other Euglenozoa), V7/V8 was never used. In Maia da Silva et al. [Parasitology 2004, 129, 549–561], V7/V8 was promoted for the first time for trypanosome phylogenetics, and since then, more than 70 publications have replicated this nomenclature and even discussed the benefits of the use of this region in comparison to V4. However, the primers used to amplify the variable region of trypanosomes have actually amplified V4 (concerning the current 18S rDNA numbering system).
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Sheir D, Elnahas M, Amer O, El Hagrassi A. Gas chromatography-mass spectrometry and scanning electron microscopy with energy-dispersive radiograph analysis of biodeteriorative metabolites produced by Aspergillus species. EGYPTIAN PHARMACEUTICAL JOURNAL 2022. [DOI: 10.4103/epj.epj_86_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kim T, Lee Y, Kil HJ, Park JK. The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda). PeerJ 2020; 8:e9108. [PMID: 32440374 PMCID: PMC7229770 DOI: 10.7717/peerj.9108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.
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Affiliation(s)
- Taeho Kim
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Yucheol Lee
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Hyun-Jong Kil
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
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Conter CC, Mota CA, Dos Santos BA, de Souza Braga L, de Souza Terron M, Navasconi TR, Fernandes ACBS, Demarchi IG, de Castro KRR, Aristides SMA, Lonardoni MVC, Teixeira JJV, Silveira TGV. PCR primers designed for new world Leishmania: A systematic review. Exp Parasitol 2019; 207:107773. [PMID: 31605671 DOI: 10.1016/j.exppara.2019.107773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 01/03/2023]
Abstract
Studies of the primers that were designed to detect New World Leishmania were systematically reviewed to report the characteristics of each target, detection limit, specificity of the primers designed and diagnostic sensibility. The papers identified in the databases PubMed and Web of Science involved 50 studies. Minicircle is the most applied target in molecular research for diagnosis, due to its high sensitivity in detecting Leishmania in different clinical samples, a characteristic that can be partially attributed to the higher number of copies of the minicircle per cell. The other molecular targets shown in this review were less sensitive to diagnostic use because of the lower number of copies of the target gene per cell, but more specific for identification of the subgenus and/or species. The choice of the best target is an important step towards the result of the research. The target allows the design of primers that are specific to the genus, subgenus or a particular species and also imparts sensitivity to the method for diagnosis. The findings of this systematic review provide the advantages and disadvantages of the main molecular targets and primers designed for New World Leishmania, offering information so that the researcher can choose the PCR system best suited to their research need. This is a timely and extremely thorough review of the primers designed for New World Leishmania.
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Affiliation(s)
- Carolina Cella Conter
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | - Camila Alves Mota
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Laís de Souza Braga
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Taísa Rocha Navasconi
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Izabel Galhardo Demarchi
- Department of Clinical Analyses and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
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Peterson SW, Logrieco A. Ribosomal Rna Sequence Variation Among Interfertile Strains of SomeGibberellaSpecies. Mycologia 2018. [DOI: 10.1080/00275514.1991.12026028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Stephen W. Peterson
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, Illinois 61604
| | - Antonio Logrieco
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, Illinois 61604
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Shibata F, Hizume M, Ohashi H, Furukawa S. An Event Preceding Genome Differentiation in the A Genome Populations of <i>Scilla scilloides</i>. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Fukashi Shibata
- Faculty of Education, Ehime University
- Institute of Small World
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Shibata F, Hizume M, Ohashi H, Furukawa S. Multiple Origin of Amphidiploids in the Complex Species of Scilla scilloides, Asparagaceae. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Fukashi Shibata
- Faculty of Education, Ehime University
- Institute of Small World
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Kim T, Kim J, Nadler SA, Park JK. The complete mitochondrial genome of Koerneria sudhausi (Diplogasteromorpha: Nematoda) supports monophyly of Diplogasteromorpha within Rhabditomorpha. Curr Genet 2015; 62:391-403. [PMID: 26581631 DOI: 10.1007/s00294-015-0536-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 11/29/2022]
Abstract
Testing hypotheses of monophyly for different nematode groups in the context of broad representation of nematode diversity is central to understanding the patterns and processes of nematode evolution. Herein sequence information from mitochondrial genomes is used to test the monophyly of diplogasterids, which includes an important nematode model organism. The complete mitochondrial genome sequence of Koerneria sudhausi, a representative of Diplogasteromorpha, was determined and used for phylogenetic analyses along with 60 other nematode species. The mtDNA of K. sudhausi is comprised of 16,005 bp that includes 36 genes (12 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) encoded in the same direction. Phylogenetic trees inferred from amino acid and nucleotide sequence data for the 12 protein-coding genes strongly supported the sister relationship of K. sudhausi with Pristionchus pacificus, supporting Diplogasteromorpha. The gene order of K. sudhausi is identical to that most commonly found in members of the Rhabditomorpha + Ascaridomorpha + Diplogasteromorpha clade, with an exception of some tRNA translocations. Both the gene order pattern and sequence-based phylogenetic analyses support a close relationship between the diplogasterid species and Rhabditomorpha. The nesting of the two diplogasteromorph species within Rhabditomorpha is consistent with most molecular phylogenies for the group, but inconsistent with certain morphology-based hypotheses that asserted phylogenetic affinity between diplogasteromorphs and tylenchomorphs. Phylogenetic analysis of mitochondrial genome sequences strongly supports monophyly of the diplogasteromorpha.
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Affiliation(s)
- Taeho Kim
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
| | - Jiyeon Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Republic of Korea
| | - Steven A Nadler
- Department of Entomology and Nematology, University of California, Davis, CA, 95616, USA
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Republic of Korea.
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Wei F, Fan R, Dong H, Shang W, Xu X, Zhu H, Yang J, Hu X. Threshold microsclerotial inoculum for cotton verticillium wilt determined through wet-sieving and real-time quantitative PCR. PHYTOPATHOLOGY 2015; 105:220-229. [PMID: 25098492 DOI: 10.1016/b978-0-12-372180-8.50042-1] [Citation(s) in RCA: 6641] [Impact Index Per Article: 737.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quantification of Verticillium dahliae microsclerotia is an important component of wilt management on a range of crops. Estimation of microsclerotia by dry or wet sieving and plating of soil samples on semiselective medium is a commonly used technique but this method is resource-intensive. We developed a new molecular quantification method based on Synergy Brands (SYBR) Green real-time quantitative polymerase chain reaction of wet-sieving samples (wet-sieving qPCR). This method can detect V. dahliae microsclerotia as low as 0.5 CFU g(-1) of soil. There was a high correlation (r=0.98) between the estimates of conventional plating analysis and the new wet-sieving qPCR method for 40 soil samples. To estimate the inoculum threshold for cotton wilt, >400 soil samples were taken from the rhizosphere of individual plants with or without visual wilt symptoms in experimental and commercial cotton fields at the boll-forming stage. Wilt inoculum was estimated using the wet-sieving qPCR method and related to wilt development. The estimated inoculum threshold varied with cultivar, ranging from 4.0 and 7.0 CFU g(-1) of soil for susceptible and resistant cultivars, respectively. In addition, there was an overall relationship of wilt incidence with inoculum density across 31 commercial fields where a single composite soil sample was taken at each field, with an estimated inoculum threshold of 11 CFU g(-1) of soil. These results suggest that wilt risk can be predicted from the estimated soil inoculum density using the new wet-sieving qPCR method. We recommend the use of 4.0 and 7.0 CFU g(-1) as an inoculum threshold on susceptible and resistant cultivars, respectively, in practical risk prediction schemes.
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Zhao YE, Wang ZH, Xu Y, Wu LP, Hu L. Secondary structure prediction for complete rDNA sequences (18S, 5.8S, and 28S rDNA) of Demodex folliculorum, and comparison of divergent domains structures across Acari. Exp Parasitol 2013; 135:370-81. [DOI: 10.1016/j.exppara.2013.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 05/06/2013] [Accepted: 07/31/2013] [Indexed: 11/24/2022]
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Hanshew AS, Mason CJ, Raffa KF, Currie CR. Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities. J Microbiol Methods 2013; 95:149-55. [PMID: 23968645 DOI: 10.1016/j.mimet.2013.08.007] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/07/2013] [Accepted: 08/11/2013] [Indexed: 11/25/2022]
Abstract
Chloroplast sequence contamination in 16S ribosomal RNA gene (16S) analyses can be particularly problematic when sampling microbial communities in plants and folivorous arthropods. We previously encountered high levels of plastid contamination in herbivorous insect samples when we used the predominant 454 pyrosequencing 16S methodologies described in the literature. 799F, a primer previously found to exclude chloroplast sequences, was modified to enhance its efficacy, and we describe, in detail, our methodology throughout amplicon pyrosequencing. Thirteen versions of 799F were assessed for the exclusion of chloroplast sequences from our samples. We found that a shift in the mismatch between 799F and chloroplast 16S resulted in significant reduction of chloroplast reads. Our results also indicate that amplifying sequences from environmental samples in a two-step PCR process, with the addition of the multiplex identifiers and 454 adapters in a second round of PCR, further improved primer specificity. Primers that included 3' phosphorothioate bonds, which were designed to block primer degradation, did not amplify consistently across samples. The different forward primers do not appear to bias the bacterial communities detected. We provide a methodological framework for reducing chloroplast reads in high-throughput sequencing data sets that can be applied to a number of environmental samples and sequencing techniques.
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Affiliation(s)
- Alissa S Hanshew
- Department of Bacteriology, 6145 Microbial Sciences Building, 1550 Linden Dr, University of Wisconsin-Madison, Madison, WI 53706, United States.
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Ramesh A, Small ST, Kloos ZA, Kazura JW, Nutman TB, Serre D, Zimmerman PA. The complete mitochondrial genome sequence of the filarial nematode Wuchereria bancrofti from three geographic isolates provides evidence of complex demographic history. Mol Biochem Parasitol 2012; 183:32-41. [PMID: 22326389 PMCID: PMC3725818 DOI: 10.1016/j.molbiopara.2012.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 01/18/2012] [Accepted: 01/18/2012] [Indexed: 11/26/2022]
Abstract
Mitochondrial (mt) genome sequences have enabled comparison of population genetics and evolution for numerous free-living and parasitic nematodes. Here we define the complete mt genome of Wuchereria bancrofti through analysis of isolates from Papua New Guinea, India and West Africa. Sequences were assembled for each isolate and annotated with reference to the mt genome sequence for Brugia malayi. The length of the W. bancrofti mt genome is approximately 13,637 nucleotides, contains 2 ribosomal RNAs (rrns), 22 transfer RNAs (trns), 12 protein-coding genes, and is characterized by a 74.6% AT content. The W. bancrofti mt gene order is identical to that reported for Onchocerca volvulus, Dirofilaria immitis, Setaria digitata and B. malayi. In addition to using translational start codons identified previously in the mt protein-coding genes of other filarial nematodes, W. bancrofti appears to be unique in using TGT as a translational start codon. Similarly, use of incomplete stop codons in mt protein-coding genes appears to be more common in W. bancrofti than in other human filarial parasites. The complete mt genome sequence reported here provides new genetic markers for investigating phylogenetic and geographic relationships between isolates, and assessing population diversity within endemic regions. The sequence polymorphism enables new strategies to monitor the progress of public health interventions to control and eliminate this important human parasite. We illustrate the utility of this sequence and single nucleotide polymorphisms by inferring the divergence times between the three W. bancrofti isolates, suggesting predictions into their origin and migration.
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Affiliation(s)
- Akshaya Ramesh
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106-4983, USA
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Sequence‐Based Identification and Characterization of Mycobacteria. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Molecular cloning and sequence analysis of an inulinase gene from an Aspergillus sp. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0683-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kim JY, Kim HJ, Oh JH, Lee I. Characteristics of Monascus sp. isolated from Monascus fermentation products. Food Sci Biotechnol 2010. [DOI: 10.1007/s10068-010-0164-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Hoffmann M, Brown EW, Feng PCH, Keys CE, Fischer M, Monday SR. PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species. BMC Microbiol 2010; 10:90. [PMID: 20331883 PMCID: PMC2856557 DOI: 10.1186/1471-2180-10-90] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 03/23/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Vibrio is a diverse group of Gram-negative bacteria comprised of 74 species. Furthermore, the genus has and is expected to continue expanding with the addition of several new species annually. Consequently, it is of paramount importance to have a method which is able to reliably and efficiently differentiate the numerous Vibrio species. RESULTS In this study, a novel and rapid polymerase chain reaction (PCR)-based intergenic spacer (IGS)-typing system for vibrios was developed that is based on the well-known IGS regions located between the 16S and 23S rRNA genes on the bacterial chromosome. The system was optimized to resolve heteroduplex formation as well as to take advantage of capillary gel electrophoresis technology such that reproducible analyses could be achieved in a rapid manner. System validation was achieved through testing of 69 archetypal Vibrio strains, representing 48 Vibrio species, from which an 'IGS-type' profile database was generated. These data, presented here in several cluster analyses, demonstrated successful differentiation of the 69 type strains showing that this PCR-based fingerprinting method easily discriminates bacterial strains at the species level among Vibrio. Furthermore, testing 36 strains each of V. parahaemolyticus and V. vulnificus, important food borne pathogens, isolated from a variety of geographical locations with the IGS-typing method demonstrated distinct IGS-typing patterns indicative of subspecies divergence in both populations making this technique equally useful for intraspecies differentiation, as well. CONCLUSION This rapid, reliable and efficient IGS-typing system, especially in combination with 16S rRNA gene sequencing, has the capacity to not only discern and identify vibrios at the species level but, in some cases, at the sub-species level, as well. This procedure is particularly well-suited for preliminary species identification and, lends itself nicely to epidemiological investigations providing information more quickly than other time-honoured methods traditionally used in these types of analyses.
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Affiliation(s)
- Maria Hoffmann
- Division of Microbiology, Office of Regulatory Science Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD 20740, USA.
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Winnepenninckx B, Backeljau T. 18S rRNA alignments derived from different secondary structure models can produce alternative phylogenies. J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.1996.tb00819.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Jex AR, Waeschenbach A, Littlewood DTJ, Hu M, Gasser RB. The mitochondrial genome of Toxocara canis. PLoS Negl Trop Dis 2008; 2:e273. [PMID: 18682828 PMCID: PMC2483351 DOI: 10.1371/journal.pntd.0000273] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 07/10/2008] [Indexed: 11/25/2022] Open
Abstract
Toxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secementean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts.
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Affiliation(s)
- Aaron R. Jex
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | | | | | - Min Hu
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Robin B. Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
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Hilszczańska D, Sierota Z, Palenzona M. New tuber species found in Poland. MYCORRHIZA 2008; 18:223-226. [PMID: 18414906 DOI: 10.1007/s00572-008-0175-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Accepted: 03/20/2008] [Indexed: 05/22/2023]
Abstract
New information from a survey of truffles carried out in southern part of Poland in September 2007 is presented. The fruit bodies of Tuber aestivum, T. excavatum, T. rufum and one unidentified Tuber sp. were found. The soil chemistry of the five T. aestivum sites was analysed. Our inventory showed that T. aestivum prefers the mixed forest with host-trees such as: Quercus robur, Corylus avellana, Carpinus betulus, Fagus silvaticus and Tilia cordata. Selection of local inocula of T. aestivum for the propagation of truffles production could be an alternative to the Mediterranean truffles orchards in times when demand for the fungi will be increasing. Fruit bodies of truffles are conserved in the collection of biological material in the Forest Research Institute in Sekocin Stary.
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Affiliation(s)
- Dorota Hilszczańska
- Department of Forest Pathology, Forest Research Institute, Braci Leśnej 3, Sękocin Stary, 05-090, Raszyn, Poland.
| | - Zbigniew Sierota
- Department of Forest Pathology, Forest Research Institute, Braci Leśnej 3, Sękocin Stary, 05-090, Raszyn, Poland
| | - Mario Palenzona
- Forestry and Environment Institute, Corso Casale 473, 10132, Torino, Italy
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Jex AR, Hu M, Littlewood DTJ, Waeschenbach A, Gasser RB. Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda). BMC Genomics 2008; 9:11. [PMID: 18190685 PMCID: PMC2254599 DOI: 10.1186/1471-2164-9-11] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Accepted: 01/11/2008] [Indexed: 11/17/2022] Open
Abstract
Background Mitochondrial (mt) genomes represent a rich source of molecular markers for a range of applications, including population genetics, systematics, epidemiology and ecology. In the present study, we used 454 technology (or the GS20, massively parallel picolitre reactor platform) to determine the complete mt genome of Haemonchus contortus (Nematoda: Trichostrongylidae), a parasite of substantial agricultural, veterinary and economic significance. We validate this approach by comparison with mt sequences from publicly available expressed sequence tag (EST) and genomic survey sequence (GSS) data sets. Results The complete mt genome of Haemonchus contortus was sequenced directly from long-PCR amplified template utilizing genomic DNA (~20–40 ng) from a single adult male using 454 technology. A single contig was assembled and compared against mt sequences mined from publicly available EST (NemBLAST) and GSS datasets. The comparison demonstrated that the 454 technology platform is reliable for the sequencing of AT-rich mt genomes from nematodes. The mt genome sequenced for Haemonchus contortus was 14,055 bp in length and was highly AT-rich (78.1%). In accordance with other chromadorean nematodes studied to date, the mt genome of H. contortus contained 36 genes (12 protein coding, 22 tRNAs, rrnL and rrnS) and was similar in structure, size and gene arrangement to those characterized previously for members of the Strongylida. Conclusion The present study demonstrates the utility of 454 technology for the rapid determination of mt genome sequences from tiny amounts of DNA and reveals a wealth of mt genomic data in current databases available for mining. This approach provides a novel platform for high-throughput sequencing of mt genomes from nematodes and other organisms.
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Affiliation(s)
- Aaron R Jex
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia.
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23
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Wang XW, Zhang L, Jin LQ, Jin M, Shen ZQ, An S, Chao FH, Li JW. Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens. Appl Microbiol Biotechnol 2007; 76:225-33. [PMID: 17492283 DOI: 10.1007/s00253-007-0993-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2007] [Revised: 04/10/2007] [Accepted: 04/11/2007] [Indexed: 01/10/2023]
Abstract
The rapid and accurate detection and identification of food-borne pathogenic bacteria is critical for food safety. In this paper, we describe a rapid (<4 h) high-throughput detection and identification system that uses universal polymerase chain reaction (PCR) primers to amplify a variable region of bacterial the 16S rRNA gene, followed by reverse hybridization of the products to species-specific oligonucleotide probes on a chip. This procedure was successful in discriminating 204 strains of bacteria from pure culture belonging to 13 genera of bacteria. When this method was applied directly to 115 strains of bacteria isolated from foods, 112/115 (97.4%) were correctly identified; two strains were indistinguishable due to weak signal, while one failed to produce a PCR product. The array was used to detect and successfully identify two strains of bacteria from food poisoning outbreak samples, giving results through hybridization that were identical to those obtained by traditional methods. The sensitivity of the microarray assay was 10(2) CFU of bacteria. Thus, the oligonucleotide microarray is a powerful tool for the detection and identification of pathogens from foods.
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Affiliation(s)
- Xin-Wei Wang
- Institute of Environment and Health, No. 1, Dali Road, Tianjin, 300050, People's Republic of China
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Abstract
Understanding patterns of rRNA evolution is critical for a number of fields, including structure prediction and phylogeny. The standard model of RNA evolution is that compensatory mutations in stems make up the bulk of the changes between homologous sequences, while unpaired regions are relatively homogeneous. We show that considerable heterogeneity exists in the relative rates of evolution of different secondary structure categories (stems, loops, bulges, etc.) within the rRNA, and that in eukaryotes, loops actually evolve much faster than stems. Both rates of evolution and abundance of different structural categories vary with distance from functionally important parts of the ribosome such as the tRNA path and the peptidyl transferase center. For example, fast-evolving residues are mainly found at the surface; stems are enriched at the subunit interface, and junctions near the peptidyl transferase center. However, different secondary structure categories evolve at different rates even when these effects are accounted for. The results demonstrate that relative rates and patterns of evolution are lineage specific, suggesting that phylogenetically and structurally specific models will improve evolutionary and structural predictions.
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Affiliation(s)
| | | | - R. Knight
- *To whom correspondence should be addressed. Tel: 303-492-1984; Fax: 303-492-7744;
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Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. INSECT MOLECULAR BIOLOGY 2006; 15:657-86. [PMID: 17069639 PMCID: PMC2048585 DOI: 10.1111/j.1365-2583.2006.00689.x] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/28/2006] [Indexed: 05/12/2023]
Abstract
As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.
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Affiliation(s)
- J J Gillespie
- Department of Entomology, Texas A & M University, College Station, TX, USA.
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Jin LQ, Li JW, Wang SQ, Chao FH, Wang XW, Yuan ZQ. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays. World J Gastroenterol 2006; 11:7615-9. [PMID: 16437687 PMCID: PMC4727218 DOI: 10.3748/wjg.v11.i48.7615] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To detect the common intestinal pathogenic bacteria quickly and accurately. METHODS A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays. RESULTS One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified. CONCLUSION Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, Proteus sp., Bacillus cereus, Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range, and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost.
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Affiliation(s)
- Lian-Qun Jin
- Tianjin Institute of Hygiene and Environmental Medicine 1, Da Li Road, Tianjin 300050, China.
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27
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Johnson AM, Baverstock PR. Rapid ribosomal RNA sequencing and the phylogenetic analysis of protists. ACTA ACUST UNITED AC 2005; 5:102-5. [PMID: 15463187 DOI: 10.1016/0169-4758(89)90046-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A newly described technique for rapidly obtaining the partial nucleotide sequence of ribosomal RNA is being applied to investigate phylogenetic relationships among living organisms. Alan Johnson and Peter Boverstock describe the importance of this method to parasitology in providing new information on the phylogenetic relationships of parasitic organisms previously placed in groups of convenience. The phylum Apicomplexo in particular, has been the object of much study using this technique, but the technology is likely to extend soon to the restructuring of the phylogenetic trees of many groups of parasites.
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Affiliation(s)
- A M Johnson
- Department of Clinical Microbiology, Flinders Medical Centre, Bedford Park, South Australia, 5042 Australia
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Richert K, Brambilla E, Stackebrandt E. Development of PCR primers specific for the amplification and direct sequencing of gyrB genes from microbacteria, order Actinomycetales. J Microbiol Methods 2005; 60:115-23. [PMID: 15567231 DOI: 10.1016/j.mimet.2004.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Revised: 08/09/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
PCR primer sets were developed for the specific amplification and sequence analyses encoding the gyrase subunit B (gyrB) of members of the family Microbacteriaceae, class Actinobacteria. The family contains species highly related by 16S rRNA gene sequence analyses. In order to test if the gene sequence analysis of gyrB is appropriate to discriminate between closely related species, we evaluate the 16S rRNA gene phylogeny of its members. As the published universal primer set for gyrB failed to amplify the responding gene of the majority of the 80 type strains of the family, three new primer sets were identified that generated fragments with a composite sequence length of about 900 nt. However, the amplification of all three fragments was successful only in 25% of the 80 type strains. In this study, the substitution frequencies in genes encoding gyrase and 16S rDNA were compared for 10 strains of nine genera. The frequency of gyrB nucleotide substitution is significantly higher than that of the 16S rDNA, and no linear correlation exists between the similarities of both molecules among members of the Microbacteriaceae. The phylogenetic analyses using the gyrB sequences provide higher resolution than using 16S rDNA sequences and seem able to discriminate between closely related species.
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Affiliation(s)
- Kathrin Richert
- DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany.
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Glaeser J, Overmann J. Biogeography, evolution, and diversity of epibionts in phototrophic consortia. Appl Environ Microbiol 2004; 70:4821-30. [PMID: 15294820 PMCID: PMC492462 DOI: 10.1128/aem.70.8.4821-4830.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Motile phototrophic consortia are highly regular associations in which numerous cells of green sulfur bacteria surround a flagellated colorless beta-proteobacterium in the center. To date, seven different morphological types of such consortia have been described. In addition, two immotile associations involving green sulfur bacteria are known. By employing a culture-independent approach, different types of phototrophic consortia were mechanically isolated by micromanipulation from 14 freshwater environments, and partial 16S rRNA gene sequences of the green sulfur bacterial epibionts were determined. In the majority of the lakes investigated, different types of phototrophic consortia were found to co-occur. In all cases, phototrophic consortia with the same morphology from the same habitat contained only a single epibiont phylotype. However, morphologically indistinguishable phototrophic consortia collected from different lakes contained different epibionts. Overall, 19 different types of epibionts were detected in the present study. Whereas the epibionts within one geographic region were very similar (Dice coefficient, 0.582), only two types of epibionts were found to occur on both the European and North American continents (Dice coefficient, 0.190). None of the epibiont 16S rRNA gene sequences have been detected so far in free-living green sulfur bacteria, suggesting that the interaction between epibionts and chemotrophic bacteria in the phototrophic consortia is an obligate interaction. Based on our phylogenetic analysis, the epibiont sequences are not monophyletic. Thus, the ability to form symbiotic associations either arose independently from different ancestors or was present in a common ancestor prior to the radiation of green sulfur bacteria and the transition to the free-living state in independent lineages. The present study thus demonstrates that there is great diversity and nonrandom geographical distribution of phototrophic consortia in the natural environment.
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Affiliation(s)
- Jens Glaeser
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Maria-Ward-Strasse 1a, D-80638 Munich, Germany
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Santos SR, Kinzie RA, Sakai K, Coffroth MA. Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta). J Eukaryot Microbiol 2004; 50:417-21. [PMID: 14733432 DOI: 10.1111/j.1550-7408.2003.tb00264.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the dinoflagellates, an important group of single-cell protists, some nuclear rDNA phylogenetic studies have reported the discovery of rDNA pseudogenes. However, it is unknown if these aberrant molecules are confined to free-living taxa or occur in other members of the group. We have cultured a strain of symbiotic dinoflagellate, belonging to the genus Symbiodinium, which produces three distinct amplicons following PCR for nuclear small subunit (18S) rDNA genes. These amplicons contribute to a unique restriction fragment length polymorphism pattern diagnostic for this particular strain. Sequence analyses revealed that the largest amplicon was the expected region of 18S-rDNA, while the two smaller amplicons are Symbiodinium nuclear 18S-rDNA genes that contain single long tracts of nucleotide deletions. Reverse transcription (RT)-PCR experiments did not detect RNA transcripts of these latter genes, suggesting that these molecules represent the first report of nuclear 18S-rDNA pseudogenes from the genome of Symbiodinium. As in the free-living dinoflagellates, nuclear rDNA pseudogenes are effective indicators of unique Symbiodinium strains. Furthermore, the evolutionary pattern of dinoflagellate nuclear rDNA pseudogenes appears to be unique among organisms studied to date, and future studies of these unusual molecules will provide insight on the cellular biology and genomic evolution of these protists.
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Affiliation(s)
- Scott R Santos
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York 14260-1300, USA
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Alkorta I, Amezaga I, Albizu I, Aizpurua A, Onaindia M, Buchner V, Garbisu C. Molecular microbial biodiversity assessment: a biological indicator of soil health. REVIEWS ON ENVIRONMENTAL HEALTH 2003; 18:131-151. [PMID: 14531477 DOI: 10.1515/reveh.2003.18.2.131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The soil performs a variety of key functions: (i) provides the food, fuel, and fiber needs of the world's population, (ii) regulates the quality of the air and water, (iii) decomposes organic wastes, (iv) recycles nutrients, and (v) acts as a sink for pollutants (including global gases). Soil degradation is increasingly recognized as an urgent environmental issue and a crucial need exists for the capacity to evaluate soil health. After all, soil health is a key component in sustaining the different world's ecosystems and the myriad of natural and socioeconomic systems they support. In this respect, soil health has been defined as the "continued capacity of a specific kind of soil to function as a vital living system, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, to maintain or enhance the quality of air and water environments, and to support human health and habitation". A biological indicator is an organism, a part of an organism, or a community of organisms, used to obtain information about environmental quality. The assessment of microbial biodiversity has the potential to provide useful insight into the health and functioning of soil. Our inability to culture most microorganisms that are present in soils has, until recently, impaired studying the relationships between the structure and the function of soil microbial communities. This shortcoming has been recently overcome by using several molecular techniques that allow the detection, enumeration, and characterization of soil microorganisms without cultivation.
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Affiliation(s)
- Itziar Alkorta
- Unidad de Biofísica, Centro Mixto CSIC/UPV, Apdo. 644, Bilbao, Spain
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Suhara H, Sakai K, Kondo R, Maekawa N, Kubayashi T. Identification of the basidiomycetous fungus isolated from butt rot of the Japanese cypress. MYCOSCIENCE 2002. [DOI: 10.1007/s102670200070] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Ciarmela P, Potenza L, Cucchiarini L, Zeppa S, Stocchi V. PCR amplification and polymorphism analysis of the intergenic spacer region of ribosomal DNA in Tuber borchii. Microbiol Res 2002; 157:69-74. [PMID: 11911615 DOI: 10.1078/0944-5013-00132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PCR amplification of the complete intergenic spacer region (IGS) of the Tuber borchii nuclear ribosomal repeat was obtained using universal primers CNL 12 and NS1rev. In order to improve amplification yield a specific primer, T1, was selected from a partial sequence of the IGS product. IGS diversity was characterized both at the intraindividual and intraspecific level. The results obtained at the intraindividual level showed 10% varying repeats on ten screened colonies, while at the intraspecific level the IGS polymorphism was evident as difference in length amplification between mycelial strains and fruit bodies: 3.5 kb and 2 kb respectively.
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Affiliation(s)
- Pasquapina Ciarmela
- Istituto di Chimica Biologica Giorgio Fornaini, Università degli Studi di Urbino, PU, Italy
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Fukushima M, Kakinuma K, Kawaguchi R. Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 2002; 40:2779-85. [PMID: 12149329 PMCID: PMC120687 DOI: 10.1128/jcm.40.8.2779-2785.2002] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic analysis of about 200 strains of Salmonella, Shigella, and Escherichia coli was carried out using the nucleotide sequence of the gene for DNA gyrase B (gyrB), which was determined by directly sequencing PCR fragments. The results establish a new phylogenetic tree for the classification of Salmonella, Shigella, and Escherichia coli in which Salmonella forms a cluster separate from but closely related to Shigella and E. coli. In comparison with 16S rRNA analysis, the gyrB sequences indicated a greater evolutionary divergence for the bacteria. Thus, in screening for the presence of bacteria, the gyrB gene might be a useful tool for differentiating between closely related species of bacteria such as Shigella spp. and E. coli. At present, 16S rRNA sequence analysis is an accurate and rapid method for identifying most unknown bacteria to the genus level because the highly conserved 16S rRNA region is easy to amplify; however, analysis of the more variable gyrB sequence region can identify unknown bacteria to the species level. In summary, we have shown that gyrB sequence analysis is a useful alternative to 16S rRNA analysis for constructing the phylogenetic relationships of bacteria, in particular for the classification of closely related bacterial species.
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Affiliation(s)
- Masao Fukushima
- Genomics Research Institute, SRL, Inc., 5-6-50 Shinmachi, Hino-shi, Tokyo 191-0002, Japan
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35
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Vallorani L, Polidori E, Sacconi C, Agostini D, Pierleoni R, Piccoli G, Zeppa S, Stocchi V. Biochemical and molecular characterization of NADP-glutamate dehydrogenase from the ectomycorrhizal fungus Tuber borchii. THE NEW PHYTOLOGIST 2002; 154:779-790. [PMID: 33873467 DOI: 10.1046/j.1469-8137.2002.00409.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• NADP-glutamate dehydrogenase (NADP-GDH) from Tuber borchii was purified and the corresponding gene was cloned in order to elucidate the physiological role of the enzyme in this ectomycorrhizal fungus. • NADP-GDH was purified using an anion-exchange column followed by affinity chromatography. The complete gene was cloned from a 30-d-old-mycelium cDNA library and characterized. • T. borchii NADP-GDH appears to be physically and kinetically similar to those from other fungi and the deduced amino acid sequence of the gdh gene showed a significant similarity to other fungal NADP-dependent GDHs. Biochemical and Northern blotting analyses carried out with mycelia grown on different nitrogen sources clearly showed that the regulation of T. borchii NADP-GDH in response to different nitrogen sources was markedly different from the responses of the NADP-GDHs of other ascomycetes. Northern blotting analyses highlighted that the gdh gene was also expressed in the symbiotic phase. • The biochemical and molecular data suggest that the fungal NADP-GDH contributes to the primary nitrogen metabolism in the ectomycorrhizal tissues.
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Affiliation(s)
- Luciana Vallorani
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Emanuela Polidori
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Cinzia Sacconi
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Deborah Agostini
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Raffaella Pierleoni
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Giovanni Piccoli
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Sabrina Zeppa
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Vilberto Stocchi
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
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Ciarmela P, Potenza L, Zeppa S, Cucchiarini L, Stocchi V. Structural analysis of the rDNA intergenic spacer of Tuber borchii. J Biomol Struct Dyn 2002; 19:701-8. [PMID: 11843631 DOI: 10.1080/07391102.2002.10506776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The sequence and characterisation of the entire nuclear rDNA intergenic spacer (IGS) for the genus Tuber are presented. Sequence analyses showed that the organisation of the Tuber borchii rDNA IGS is typical of rDNA spacers, consisting of a central repetitive region and flanking unique sequences on either side. Direct repeats, symmetry elements, tandem repeats and possible areas of recombination were found. The putative ends of the 25S and 17S rDNA were identified. The presence of 5S rDNA in the IGS region was excluded.
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Affiliation(s)
- Pasquapina Ciarmela
- Istituto di Chimica Biologica Giorgio Fornaini, Universit degli Studi di Urbino, Via A. Saffi 2, 61029 Urbino (PU), Italy
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Hendrickson ER, Payne JA, Young RM, Starr MG, Perry MP, Fahnestock S, Ellis DE, Ebersole RC. Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Appl Environ Microbiol 2002; 68:485-95. [PMID: 11823182 PMCID: PMC126671 DOI: 10.1128/aem.68.2.485-495.2002] [Citation(s) in RCA: 352] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The environmental distribution of Dehalococcoides group organisms and their association with chloroethene-contaminated sites were examined. Samples from 24 chloroethene-dechlorinating sites scattered throughout North America and Europe were tested for the presence of members of the Dehalococcoides group by using a PCR assay developed to detect Dehalococcoides 16S rRNA gene (rDNA) sequences. Sequences identified by sequence analysis as sequences of members of the Dehalococcoides group were detected at 21 sites. Full dechlorination of chloroethenes to ethene occurred at these sites. Dehalococcoides sequences were not detected in samples from three sites at which partial dechlorination of chloroethenes occurred, where dechlorination appeared to stop at 1,2-cis-dichloroethene. Phylogenetic analysis of the 16S rDNA amplicons confirmed that Dehalococcoides sequences formed a unique 16S rDNA group. These 16S rDNA sequences were divided into three subgroups based on specific base substitution patterns in variable regions 2 and 6 of the Dehalococcoides 16S rDNA sequence. Analyses also demonstrated that specific base substitution patterns were signature patterns. The specific base substitutions distinguished the three sequence subgroups phylogenetically. These results demonstrated that members of the Dehalococcoides group are widely distributed in nature and can be found in a variety of geological formations and in different climatic zones. Furthermore, the association of these organisms with full dechlorination of chloroethenes suggests that they are promising candidates for engineered bioremediation and may be important contributors to natural attenuation of chloroethenes.
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MESH Headings
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/isolation & purification
- Bacteria, Anaerobic/metabolism
- Base Sequence
- Biodegradation, Environmental
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- Environmental Pollutants/metabolism
- Europe
- Molecular Sequence Data
- North America
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
- Soil Pollutants
- Tetrachloroethylene/metabolism
- Trichloroethylene/metabolism
- Water Microbiology
- Water Pollution, Chemical
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Affiliation(s)
- Edwin R Hendrickson
- Corporate Center for Engineering Research, Central Research and Development, E. I. Du Pont de Nemours & Co., Glasgow Site 300/318, Newark, DE 19714, USA.
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Hu M, Chilton NB, Gasser RB. The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). Int J Parasitol 2002; 32:145-58. [PMID: 11812491 DOI: 10.1016/s0020-7519(01)00316-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complete mitochondrial genome sequences were determined for two species of human hookworms, Ancylostoma duodenale (13,721 bp) and Necator americanus (13,604 bp). The circular hookworm genomes are amongst the smallest reported to date for any metazoan organism. Their relatively small size relates mainly to a reduced length in the AT-rich region. Both hookworm genomes encode 12 protein, two ribosomal RNA and 22 transfer RNA genes, but lack the ATP synthetase subunit 8 gene, which is consistent with three other species of Secernentea studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T, but low in G and C. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. For both hookworm species, genes were arranged in the same order as for Caenorhabditis elegans, except for the presence of a non-coding region between genes nad3 and nad5. In A. duodenale, this non-coding region is predicted to form a stem-and-loop structure which is not present in N. americanus. The mitochondrial genome structure for both hookworms differs from Ascaris suum only in the location of the AT-rich region, whereas there are substantial differences when compared with Onchocerca volvulus, including four gene or gene-block translocations and the positions of some transfer RNA genes and the AT-rich region. Based on genome organisation and amino acid sequence identity, A. duodenale and N. americanus were more closely related to C. elegans than to A. suum or O. volvulus (all secernentean nematodes), consistent with a previous phylogenetic study using ribosomal DNA sequence data. Determination of the complete mitochondrial genome sequences for two human hookworms (the first members of the order Strongylida ever sequenced) provides a foundation for studying the systematics, population genetics and ecology of these and other nematodes of socio-economic importance.
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Affiliation(s)
- Min Hu
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Victoria 3030, Werribee, Australia
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MacKenzie S, Cutler CP, Hazon N, Cramb G. The effects of dietary sodium loading on the activity and expression of Na, K-ATPase in the rectal gland of the European dogfish (Scyliorhinus canicula). Comp Biochem Physiol B Biochem Mol Biol 2002; 131:185-200. [PMID: 11818240 DOI: 10.1016/s1096-4959(01)00493-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
cDNA fragments of both the alpha- and beta-subunits of the Na, K-ATPase and a cDNA fragment of the secretory form of Na-K-Cl cotransporter from the European dogfish (Scyliorhinus canicula) were amplified and cloned using degenerate primers in RT-PCR. These clones were used along with a sCFTR cDNA from the related dogfish shark, Squalus acanthias to characterise the expression of mRNAs for these ion transporters in the dogfish rectal gland subsequent to an acute feeding episode. Following a single feeding event where starved dogfish were fed squid portions (20 g squid/kg fish), there was a delayed and transient 40-fold increase in the activity of Na, K-ATPase in crude rectal gland homogenates. Increases in enzyme activity were apparent 3 h after the feeding event and peaked at 9 h before returning to control values within 24 h. These increases in activity were accompanied by small and transient decreases in plasma sodium and chloride concentrations lasting up to 3 days. Significant increases in the expression of mRNAs for alpha- and beta-subunits of the Na, K-ATPase, the Na-K-Cl cotransporter and CFTR chloride channel were detected but not until 1-2 days after the feeding event. It is concluded that the transient increase in Na, K-ATPase activity is not attributable to increases in the abundance of alpha- and beta-subunit mRNAs but must be associated with some, as yet unknown, post-transcriptional activation mechanism.
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Affiliation(s)
- S MacKenzie
- Unitat de Fisiologia Animal, Dept. de Biol. Cellular, Fisiologia i d'lmmunologia Facultat de Ciències. Edifici C. Universitat Autonoma de Barcelona 08913 Bellaterra, (Barcelona), Spain
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40
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Ruf M, Kössel H. Occurrence and spacing of ribosome recognition sites in mRNAs of chloroplasts from higher plants. FEBS Lett 2001. [DOI: 10.1016/0014-5793(88)80336-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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May LA, Smiley B, Schmidt MG. Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage. Can J Microbiol 2001; 47:829-41. [PMID: 11683465 DOI: 10.1139/w01-086] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Significant portions of grain produced for livestock consumption are convened into ensiled forage. Silage producers have long recognized the positive effects of using an inoculant to insure the proper transformation of forage into a palatable and digestible feedstuff. When silage is fed from a storage structure, exposure to air stimulates the growth of epiphytic aerobes that may result in the loss of up to 50% of the dry matter. Moreover, fungi have been found to be associated with ensiled forage, but their growth is normally suppressed by the anaerobic conditions. However, the introduction of oxygen results in a fungal bloom, and the fungi and the associated metabolites may result in lost productivity in the livestock consuming the contaminated forage. In this study, we report on the diversity of the fungal community associated with whole plant corn silage during the ensiling process, and the effect of two different bacterial inoculants as compared with the uninoculated natural epiphytic fermentation on the distribution of the fungi associated with the silage. The fungal community from duplicate mini-silo packages of the same treatment was analyzed by denaturing gradient gel electrophoresis and direct sequencing of the resulting operational taxonomic units. This method proved useful in analyzing the complex microbial communities associated with the forage in that it was possible to determine that one inoculant dramatically influenced the fungal community associated with whole plant corn silage.
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Affiliation(s)
- L A May
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston 29425-0504, USA
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42
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Kuroda H, Maliga P. Complementarity of the 16S rRNA penultimate stem with sequences downstream of the AUG destabilizes the plastid mRNAs. Nucleic Acids Res 2001; 29:970-5. [PMID: 11160930 PMCID: PMC29611 DOI: 10.1093/nar/29.4.970] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2000] [Revised: 12/13/2000] [Accepted: 12/13/2000] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein accumulation without a significant affect on mRNA stability. The objective of this study was to test whether enhancing the complementarity of plastid mRNAs downstream of the AUG (downstream sequence or DS) with the 16S rRNA penultimate stem (anti-DS or ADS region) enhances protein accumulation. The test system was the tobacco plastid rRNA operon promoter fused with the E.coli phage T7 gene 10 (T7g10) 5'-untranslated region (5'-UTR) and DB region. Translation efficiency was tested by measuring neomycin phosphotransferase (NPTII) accumulation in tobacco chloroplasts. We report here that the phage T7g10 5'-UTR and DB region promotes accumulation of NPTII up to approximately 16% of total soluble leaf protein (TSP). Enhanced mRNA stability and an improved NPTII yield ( approximately 23% of TSP) was obtained from a construct in which the T7g10 5'-UTR was linked with the NPTII coding region via a NheI site. However, replacing the T7g10 DB region with the plastid DS sequence reduced NPTII and mRNA levels to 0.16 and 28%, respectively. Reduced NPTII accumulation is in part due to accelerated mRNA turnover.
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MESH Headings
- Bacteriophage T7/genetics
- Base Pairing
- Base Sequence
- Codon/genetics
- Codon, Initiator/genetics
- Escherichia coli/genetics
- Genes, Bacterial/genetics
- Genes, Plant/genetics
- Genes, Reporter/genetics
- Genes, rRNA/genetics
- Molecular Sequence Data
- Plant Leaves/cytology
- Plant Leaves/genetics
- Plants, Genetically Modified
- Plants, Toxic
- Plastids/genetics
- Promoter Regions, Genetic/genetics
- Protein Biosynthesis/genetics
- RNA Stability/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Nicotiana/cytology
- Nicotiana/genetics
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Affiliation(s)
- H Kuroda
- Waksman Institute, Rutgers-The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
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Amicucci A, Zambonelli A, Guidi C, Stocchi V. Morphological and molecular characterisation of Pulvinula constellatio ectomycorrhizae. FEMS Microbiol Lett 2001; 194:121-5. [PMID: 11164295 DOI: 10.1111/j.1574-6968.2001.tb09456.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The ascomycete Pulvinula constellatio was found to form competing ectomycorrhizal relationships with plants that had been inoculated with Tuber spp. and other edible ectomycorrhizal fungi. In order to be able to distinguish P. constellatio mycorrhizae from those of the Tuber spp., we determined the morphological and bio-molecular characteristics of P. constellatio. The complete sequence of the ITS regions was determined, in order to select specific primers. The ITS region was also studied using restriction fragment length polymorphism analyses with several restriction enzymes that allowed an unambiguous identification of the species.
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Affiliation(s)
- A Amicucci
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, Italy
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Nath K, Chen X, Ahn KS, Chen S. Characterization of the 16S rRNA gene V2 region and the rrn operons of Gardnerella vaginalis. Res Microbiol 2000; 151:747-54. [PMID: 11130865 DOI: 10.1016/s0923-2508(00)01140-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomal RNA (rRNA) gene polymorphism was apparent when Gardnerella vaginalis DNA restriction profiles were hybridized with nonradioactively labeled total rRNA isolated from this bacterium. In contrast, use of a polymerase chain reaction (PCR)-based 16S rRNA gene V2 region resulted in a 118-bp V2-PCR amplicon that was specific and common in all 30 tested G. vaginalis isolates. In addition to providing a G. vaginalis-specific fingerprint, when the V2-PCR amplicon along with total rRNA were utilized as probes, a partial rRNA gene restriction map could be constructed. G. vaginalis contains two rrn operons with an EcoRI fragment of 1.6 kb common to both.
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Affiliation(s)
- K Nath
- Long Island University, Department of Biology, Brookville, NY 11548-1300, USA.
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Sawada S, Kokeguchi S, Takashiba S, Murayama Y. Development of 16S rDNA-based PCR assay for detecting centipeda periodontii and selenomonas sputigena. Lett Appl Microbiol 2000; 30:423-6. [PMID: 10849269 DOI: 10.1046/j.1472-765x.2000.00735.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To detect oral motile bacteria directly from dental plaque, specific PCR primers for Centipeda periodontii and Selenomonas sputigena were designed based on the sequence analysis of their 16S rDNA. The primers were specific and sensitive enough to amplify DNA fragments from the available oral bacteria. The detection limit was fewer than 10 bacterial cells per sample. It was also possible to detect these bacteria in dental plaque. The prevalence of these bacteria varied in each sample. The specific primers designed in this study may clarify the epidemiology of periodontal disease.
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Affiliation(s)
- S Sawada
- Department of Periodontology and Endodontology, Okayama University Dental School, Okayama, Japan
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46
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Identification, purification and gene cloning of a protein from Tuber dryophilum fruitbodies homologous to TBF-1 protein. ACTA ACUST UNITED AC 2000. [DOI: 10.1017/s0953756299001951] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Zahler M, Rinder H, Schein E, Gothe R. Detection of a new pathogenic Babesia microti-like species in dogs. Vet Parasitol 2000; 89:241-8. [PMID: 10760414 DOI: 10.1016/s0304-4017(00)00202-8] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small babesiae in dogs are generally considered to belong to Babesia gibsoni. Here we describe the genotypic characterisation of small piroplasms found in the blood of a dog which suffered from clinical babesiosis. Pairwise identities as well as distance, parsimony and maximum likelihood analyses of the 18S rDNA clearly demonstrated that this isolate was only distantly related to the other canine piroplasms characterised genetically so far, including B. gibsoni. It was more closely related to B. microti, B. rodhaini, and Theileria equi. It is concluded that the small canine piroplasms described in this study represent a hitherto unknown species and that the fauna of piroplasms occurring in dogs is more diverse than assumed so far.
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Affiliation(s)
- M Zahler
- Institute for Comparative Tropical Medicine and Parasitology, University of Munich, Leopoldstr. 5, D-80802, Munich, Germany.
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48
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Duga S, Asselta R, Malcovati M, Tenchini ML, Ronchi S, Simonic T. The intron-containing L3 ribosomal protein gene (RPL3): sequence analysis and identification of U43 and of two novel intronic small nucleolar RNAs. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1490:225-36. [PMID: 10684968 DOI: 10.1016/s0167-4781(99)00237-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Isolation and sequencing of bovine and human intron-containing L3 ribosomal protein genes are here reported. They exhibit very similar organisation, both comprising 10 exons and nine introns. A polymorphic locus, involving a 19-bp deletion, was found in intron 6 of the human gene. The frequency of the two alleles has been estimated in 200 haploid genomes. In bovine and human genes intron sequences are rather different, except for limited regions, located in corresponding positions, which show a surprisingly high degree of identity. All these regions contain conserved features defining the box C/D class of small nucleolar RNAs. Demonstration is given that U43 small nucleolar RNA is encoded within the first intron of both bovine and human genes. Single nucleotide sequences, encoding two novel species of small nucleolar RNAs (U82, U83a and U83b), are located in introns 3, 5 and 7. Their expression has been investigated and a possible role of these molecules in 2'-O-ribose methylation of rRNAs is discussed.
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Affiliation(s)
- S Duga
- Istituto di Fisiologia Veterinaria e Biochimica, Università di Milano, Via Celoria 10, 20133, Milan, Italy
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49
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Norén F, Moestrup Ø, Rehnstam-Holm AS. Parvilucifera infectans norén et moestrup gen. et sp. nov. (perkinsozoa phylum nov.): a parasitic flagellate capable of killing toxic microalgae. Eur J Protistol 1999. [DOI: 10.1016/s0932-4739(99)80001-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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50
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Abstract
Studies of the budding yeast Saccharomyces cerevisiae have greatly advanced our understanding of the posttranscriptional steps of eukaryotic gene expression. Given the wide range of experimental tools applicable to S. cerevisiae and the recent determination of its complete genomic sequence, many of the key challenges of the posttranscriptional control field can be tackled particularly effectively by using this organism. This article reviews the current knowledge of the cellular components and mechanisms related to translation and mRNA decay, with the emphasis on the molecular basis for rate control and gene regulation. Recent progress in characterizing translation factors and their protein-protein and RNA-protein interactions has been rapid. Against the background of a growing body of structural information, the review discusses the thermodynamic and kinetic principles that govern the translation process. As in prokaryotic systems, translational initiation is a key point of control. Modulation of the activities of translational initiation factors imposes global regulation in the cell, while structural features of particular 5' untranslated regions, such as upstream open reading frames and effector binding sites, allow for gene-specific regulation. Recent data have revealed many new details of the molecular mechanisms involved while providing insight into the functional overlaps and molecular networking that are apparently a key feature of evolving cellular systems. An overall picture of the mechanisms governing mRNA decay has only very recently begun to develop. The latest work has revealed new information about the mRNA decay pathways, the components of the mRNA degradation machinery, and the way in which these might relate to the translation apparatus. Overall, major challenges still to be addressed include the task of relating principles of posttranscriptional control to cellular compartmentalization and polysome structure and the role of molecular channelling in these highly complex expression systems.
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Affiliation(s)
- J E McCarthy
- Posttranscriptional Control Group, Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology (UMIST), Manchester M60 1QD, United Kingdom.
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