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Journal articles on the topic '18S (SSU)'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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1

Eamsobhana, P., P. E. Lim, and H. S. Yong. "Phylogenetics and systematics of Angiostrongylus lungworms and related taxa (Nematoda: Metastrongyloidea) inferred from the nuclear small subunit (SSU) ribosomal DNA sequences." Journal of Helminthology 89, no. 3 (2014): 317–25. http://dx.doi.org/10.1017/s0022149x14000108.

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AbstractThe Angiostrongylus lungworms are of public health and veterinary concern in many countries. At the family level, the Angiostrongylus lungworms have been included in the family Angiostrongylidae or the family Metastrongylidae. The present study was undertaken to determine the usefulness and suitability of the nuclear 18S (small subunit, SSU) rDNA sequences for differentiating various taxa of the genus Angiostrongylus, as well as to determine the systematics and phylogenetic relationship of Angiostrongylus species and other metastrongyloid taxa. This study revealed six 18S (SSU) haploty

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Wehner, Karen A., Jennifer E. G. Gallagher, and Susan J. Baserga. "Components of an Interdependent Unit within the SSU Processome Regulate and Mediate Its Activity." Molecular and Cellular Biology 22, no. 20 (2002): 7258–67. http://dx.doi.org/10.1128/mcb.22.20.7258-7267.2002.

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ABSTRACT The SSU processome is required for production of the small ribosomal subunit RNA, the 18S rRNA. Specifically, the U3 small nucleolar RNA (snoRNA) component of the SSU processome is essential for the formation of the conserved central pseudoknot and for cleavages of the pre-rRNA, both of which are required for 18S maturation. To further elucidate how these events are mediated, we examined the regulatory and mechanistic roles of the U3 specific proteins: Imp3p, Imp4p, and Mpp10p. We found that these proteins demonstrated an interdependence with respect to their stability and to their as

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Bernstein, Kara A., Jennifer E. G. Gallagher, Brianna M. Mitchell, Sander Granneman, and Susan J. Baserga. "The Small-Subunit Processome Is a Ribosome Assembly Intermediate." Eukaryotic Cell 3, no. 6 (2004): 1619–26. http://dx.doi.org/10.1128/ec.3.6.1619-1626.2004.

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ABSTRACT The small-subunit (SSU) processome is a large ribonucleoprotein required for the biogenesis of the 18S rRNA and likely corresponds to the terminal knobs visualized by electron microscopy on the 5′ end of nascent rRNAs. The original purification of the SSU processome of Saccharomyces cerevisiae resulted in the identification of 28 proteins. Here, we characterize 12 additional protein components, including five small-ribosomal-subunit proteins (Rps4, Rps6, Rps7, Rps9, and Rps14) that had previously been copurified. Our multiple criteria for including a component as a bona fide SSU proce

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JENKINS, M. C., J. T. ELLIS, S. LIDDELL, et al. "The relationship of Hammondia hammondi and Sarcocystis mucosa to other heteroxenous cyst-forming coccidia as inferred by phylogenetic analysis of the 18S SSU ribosomal DNA sequence." Parasitology 119, no. 2 (1999): 135–42. http://dx.doi.org/10.1017/s0031182099004618.

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The complete sequence of the 18S small subunit (SSU) ribosomal DNA of Hammondia hammondi and Sarcocystis mucosa was obtained and compared to SSU rDNA sequences of Neospora caninum, Toxoplasma gondii, Besnoitia besnoiti, 2 species of Frenkelia, 3 species of Isospora, and 13 species of Sarcocystis. Analyses showed that H. hammondi and T. gondii are monophyletic and that these taxa shared a common ancestor with N. caninum and B. besnoiti. The weight of evidence shows that S. mucosa, S. neurona, and Frenkelia species form a clade thereby supporting the conclusion that Sarcocystis is paraphyletic.

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Li, Na, Norman F. Neumann, Norma Ruecker, et al. "Development and Evaluation of Three Real-Time PCR Assays for Genotyping and Source Tracking Cryptosporidium spp. in Water." Applied and Environmental Microbiology 81, no. 17 (2015): 5845–54. http://dx.doi.org/10.1128/aem.01699-15.

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ABSTRACTThe occurrence ofCryptosporidiumoocysts in drinking source water can present a serious public health risk. To rapidly and effectively assess the source and human-infective potential ofCryptosporidiumoocysts in water, sensitive detection and correct identification of oocysts to the species level (genotyping) are essential. In this study, we developed three real-time PCR genotyping assays, two targeting the small-subunit (SSU) rRNA gene (18S-LC1 and 18S-LC2 assays) and one targeting the 90-kDa heat shock protein (hsp90) gene (hsp90 assay), and evaluated the sensitivity andCryptosporidium

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Pegova, Anna N., Elena D. Krasnova, and Vladimir V. Aleshin. "Evidence from the small and large ribosomal RNA structure suggests that Anoplostoma rectospiculum Gal'tsova, 1976 (Nematoda: Anoplostomatidae) is a member of the superfamily Enoploidea, not Oncholaimoidea." Nematology 6, no. 3 (2004): 413–21. http://dx.doi.org/10.1163/1568541042360474.

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Abstract Analyses of the primary structure of the 18S rRNA gene and D3 segment of the 28S rRNA, as well as evidence from the secondary structure of the SSU rRNA V7 region, suggest that Anoplostoma rectospiculum (Anoplostomatidae) has closer relationships to the family Enoplidae than to the Oncholaimidae. In phylogenetic trees derived from full length SSU rRNA gene and partial LSU rRNA gene (D3 expansion segment) sequence analyses, A. rectospiculum exhibits long branches. The associated artefacts of long branch attraction (LBA) are circumvented because of the presence of an undoubted molecular

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7

Soltanieh, Sahar, Martin Lapensée, and François Dragon. "Nucleolar proteins Bfr2 and Enp2 interact with DEAD-box RNA helicase Dbp4 in two different complexes." Nucleic Acids Research 42, no. 5 (2013): 3194–206. http://dx.doi.org/10.1093/nar/gkt1293.

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AbstractDifferent pre-ribosomal complexes are formed during ribosome biogenesis, and the composition of these complexes is highly dynamic. Dbp4, a conserved DEAD-box RNA helicase implicated in ribosome biogenesis, interacts with nucleolar proteins Bfr2 and Enp2. We show that, like Dbp4, Bfr2 and Enp2 are required for the early processing steps leading to the production of 18S ribosomal RNA. We also found that Bfr2 and Enp2 associate with the U3 small nucleolar RNA (snoRNA), the U3-specific protein Mpp10 and various pre-18S ribosomal RNA species. Thus, we propose that Bfr2, Dbp4 and Enp2 are co

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8

Peters, Sabine, Stefanie Koschinsky, Frank Schwieger, and Christoph C. Tebbe. "Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes." Applied and Environmental Microbiology 66, no. 3 (2000): 930–36. http://dx.doi.org/10.1128/aem.66.3.930-936.2000.

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ABSTRACT A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4–V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8–V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA m

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Turner, Amy Jane, Andrew Alexander Knox, José-Luis Prieto, Brian McStay, and Nicholas James Watkins. "A Novel Small-Subunit Processome Assembly Intermediate That Contains the U3 snoRNP, Nucleolin, RRP5, and DBP4." Molecular and Cellular Biology 29, no. 11 (2009): 3007–17. http://dx.doi.org/10.1128/mcb.00029-09.

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ABSTRACT Eukaryotic 18S rRNA processing is mediated by the small subunit (SSU) processome, a machine comprised of the U3 small nucleolar RNP (U3 snoRNP), tUTP, bUTP, MPP10, and BMS1/RCL1 subcomplexes. We report that the human SSU processome is a dynamic structure with the recruitment and release of subcomplexes occurring during the early stages of ribosome biogenesis. A novel 50S U3 snoRNP accumulated when either pre-rRNA transcription was blocked or the tUTP proteins were depleted. This complex did not contain the tUTP, bUTP, MPP10, and BMS1/RCL1 subcomplexes but was associated with the RNA-b

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PIERCEY-NORMORE, Michele D., Georg HAUSNER, and Ewan A. GIBB. "Group I intron-like insertions in SSU rDNA of Cladonia gracilis and C. rangiferina." Lichenologist 36, no. 6 (2004): 365–80. http://dx.doi.org/10.1017/s0024282904014501.

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During a study on population genetics of three species of Cladonia using the nuclear ribosomal 18S DNA, two species contained group I intron-like sequences located in positions 788 and 940 with reference to the E. coli 16S rDNA gene. The intron in position 940 was not typical of group I introns and had previously been described only from the Parmeliaceae and Lecanoraceae, but here we report the occurrence of this intron in the Cladoniaceae. The intron in position 788 had characteristics of group I introns and had previously been reported from the Physciaceae. In this paper we provide for the f

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Pereira, Maria das Graças Cabral, Xunde Li, Brenda McCowan, Ralph L. Phillips, and Edward R. Atwill. "Multiple Unique Cryptosporidium Isolates from Three Species of Ground Squirrels (Spermophilus beecheyi, S. beldingi, and S. lateralis) in California." Applied and Environmental Microbiology 76, no. 24 (2010): 8269–76. http://dx.doi.org/10.1128/aem.00687-10.

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ABSTRACT Phylogenetic analyses of the 18S small-subunit (SSU) rRNA and Cryptosporidium oocyst wall protein (COWP) genes indicate that multiple unique Cryptosporidium isolates are shed by separate species of Spermophilus ground squirrels (S. beecheyi, S. beldingi, and S. lateralis) throughout California, despite some squirrel populations' being geographically isolated. The data support our assertion that Spermophilus squirrels shed novel Cryptosporidium species.

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Herr, Roger A., Libero Ajello, John W. Taylor, Sarath N. Arseculeratne, and Leonel Mendoza. "Phylogenetic Analysis of Rhinosporidium seeberi’s 18S Small-Subunit Ribosomal DNA Groups This Pathogen among Members of the Protoctistan Mesomycetozoa Clade." Journal of Clinical Microbiology 37, no. 9 (1999): 2750–54. http://dx.doi.org/10.1128/jcm.37.9.2750-2754.1999.

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For the past 100 years the phylogenetic affinities ofRhinosporidium seeberi have been controversial. Based on its morphological features, it has been classified as a protozoan or as a member of the kingdom Fungi. We have amplified and sequenced nearly a full-length 18S small-subunit (SSU) ribosomal DNA (rDNA) sequence fromR. seeberi. Using phylogenetic analysis, by parsimony and distance methods, of R. seeberi’s 18S SSU rDNA and that of other eukaryotes, we found that this enigmatic pathogen of humans and animals clusters with a novel group of fish parasites referred to as the DRIP clade (Derm

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McDonald, James E., Heather E. Allison, and Alan J. McCarthy. "Composition of the Landfill Microbial Community as Determined by Application of Domain- and Group-Specific 16S and 18S rRNA-Targeted Oligonucleotide Probes." Applied and Environmental Microbiology 76, no. 4 (2009): 1301–6. http://dx.doi.org/10.1128/aem.01783-09.

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ABSTRACT The microbial community composition of colonized cotton and leachate samples from a landfill was quantified using small subunit (SSU) rRNA probes (quantitative rRNA hybridization). Relative quantification of bacteria, eukaryotes, and archaea revealed variations in the landfill microbial community between samples from different areas of the landfill site and indicated the presence of potentially novel archaea. Anaerobic fungi were quantified in rumen fluid samples but were not sufficiently abundant for direct detection in the landfill samples.

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14

Troccoli, Alberto, Monica Oreste, Eustachio Tarasco, Elena Fanelli, and Francesca De Luca. "Mononchoides macrospiculum n. sp. (Nematoda: Neodiplogastridae) and Teratorhabditis synpapillata Sudhaus, 1985 (Nematoda: Rhabditidae): nematode associates of Rhynchophorus ferrugineus (Oliver) (Coleoptera: Curculionidae) in Italy." Nematology 17, no. 8 (2015): 953–66. http://dx.doi.org/10.1163/15685411-00002916.

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Several juvenile and adult nematodes were isolated after dissection of pupae and adults of the red palm weevil,Rhynchophorus ferrugineus, recovered from an infestedPhoenix canariensisChabaud exemplar in Bari, Italy. Two species of nematodes were recovered,Teratorhabditis synpapillataandMononchoides macrospiculumn. sp. which is described herein. The mitochondrial cytochrome oxidase I (COI), the ITS-containing region, the 18S rRNA gene (SSU) and the D2-D3 expansion domains of the 28S rRNA gene (LSU) were amplified and sequenced. The new species,M. macrospiculumn. sp., is described at morphologic

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15

Clerget, Guillaume, Valérie Bourguignon-Igel, Nathalie Marmier-Gourrier, et al. "Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA." Nucleic Acids Research 48, no. 7 (2020): 3848–68. http://dx.doi.org/10.1093/nar/gkaa066.

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Abstract U3 snoRNA and the associated Rrp9/U3-55K protein are essential for 18S rRNA production by the SSU-processome complex. U3 and Rrp9 are required for early pre-rRNA cleavages at sites A0, A1 and A2, but the mechanism remains unclear. Substitution of Arg 289 in Rrp9 to Ala (R289A) specifically reduced cleavage at sites A1 and A2. Surprisingly, R289 is located on the surface of the Rrp9 β-propeller structure opposite to U3 snoRNA. To understand this, we first characterized the protein-protein interaction network of Rrp9 within the SSU-processome. This identified a direct interaction betwee

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16

MANS, BEN J., RONEL PIENAAR, ABDALLA A. LATIF, and FRED T. POTGIETER. "Diversity in the 18S SSU rRNA V4 hyper-variable region ofTheileriaspp. in Cape buffalo (Syncerus caffer) and cattle from southern Africa." Parasitology 138, no. 6 (2011): 766–79. http://dx.doi.org/10.1017/s0031182011000187.

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SUMMARYSequence variation within the 18S SSU rRNA V4 hyper-variable region can affect the accuracy of real-time hybridization probe-based diagnostics for the detection ofTheileriaspp. infections. This is relevant for assays that use non-specific primers, such as the real-time hybridization assay forT. parva(Sibekoet al.2008). To assess the effect of sequence variation on this test, theTheileria18S gene from 62 buffalo and 49 cattle samples was cloned and ∼1000 clones sequenced. Twenty-six genotypes were detected which included known and novel genotypes for theT. buffeli, T. mutans, T. taurotra

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17

Soltanieh, Sahar, Yvonne N. Osheim, Krasimir Spasov, Christian Trahan, Ann L. Beyer, and François Dragon. "DEAD-Box RNA Helicase Dbp4 Is Required for Small-Subunit Processome Formation and Function." Molecular and Cellular Biology 35, no. 5 (2014): 816–30. http://dx.doi.org/10.1128/mcb.01348-14.

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DEAD-box RNA helicase Dbp4 is required for 18S rRNA synthesis: cellular depletion of Dbp4 impairs the early cleavage reactions of the pre-rRNA and causes U14 small nucleolar RNA (snoRNA) to remain associated with pre-rRNA. Immunoprecipitation experiments (IPs) carried out with whole-cell extracts (WCEs) revealed that hemagglutinin (HA)-tagged Dbp4 is associated with U3 snoRNA but not with U14 snoRNA. IPs with WCEs also showed association with the U3-specific protein Mpp10, which suggests that Dbp4 interacts with the functionally active U3 RNP; this particle, called the small-subunit (SSU) proc

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Ortega-Olivares, M. P., and M. García-Varela. "Phylogenetic relationships of the family Gryporhynchidae (Cestoda: Cyclophyllidea) inferred through SSU and LSU rDNA sequences." Journal of Helminthology 93, no. 6 (2018): 763–71. http://dx.doi.org/10.1017/s0022149x18000846.

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AbstractTapeworms of the family Gryporhynchidae are endoparasites of fish-eating birds distributed worldwide. Currently the family contains 16 genera classified on the basis of the morphology of the rostellar apparatus, rostellar hooks and strobilar anatomy. However, the phylogenetic relationships among the genera are still unknown. In this study, sequences of the near complete 18S (SSU) and 28S (LSU) from rDNA of 13 species of gryporhynchids (adult specimens) representing eight genera (Cyclustera, Dendrouterina, Glossocercus, Gryporhynchidae gen. sp., Neovalipora, Paradilepis, Parvitaenia, Va

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Petters, Sebastian, Verena Groß, Andrea Söllinger, et al. "The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?" ISME Journal 15, no. 9 (2021): 2665–75. http://dx.doi.org/10.1038/s41396-021-00958-2.

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AbstractTrophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained

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MORFFE, JANS, NAYLA GARCÍA, KARIN BREUGELMANS, KOICHI HASEGAWA, and ANDREW K. DAVIS. "Morphological and molecular characterization of Lepidonema magnum Morffe & García, 2010 (Nematoda: Oxyuridomorpha: Hystrignathidae) from Passalus interstitialis Eschscholtz, 1829 (Coleoptera: Passalidae) from Cuba and new locality records for the species." Zootaxa 4551, no. 2 (2019): 221. http://dx.doi.org/10.11646/zootaxa.4551.2.6.

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Lepidonema magnum Morffe & García, 2010 (Nematoda: Oxyuridomorpha: Hystrignathidae) is redescribed and illustrated with the aid of SEM. New features of the cephalic end and genital tract of the females were observed. New locality records are given. The phylogenetic position of the species is inferred on the basis of the D2-D3 segment of the 28S LSU rDNA and 18S SSU rDNA. L. magnum forms a monophyletic clade formed by other hystrignathids: Coynema poeyi (Coy, García & Álvarez, 1993), two species of Longior Travassos & Kloss, 1958 and two Hystrignathus Leidy, 1850.

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SATO, H., A. OSANAI, H. KAMIYA, et al. "Characterization of SSU and LSU rRNA genes of threeTrypanosoma (Herpetosoma) grosiisolates maintained in Mongolian jirds." Parasitology 130, no. 2 (2004): 157–67. http://dx.doi.org/10.1017/s0031182004006493.

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Trypanosoma (Herpetosoma) grosi, which naturally parasitizesApodemusspp., can experimentally infect Mongolian jirds (Meriones unguiculatus). Three isolates fromA. agrarius,A. peninsulae, andA. speciosus(named SESUJI, HANTO, and AKHA isolates, respectively) of different geographical origin (AKHA from Japan, and the others from Vladivostok), exhibited different durations of parasitaemia in laboratory jirds (2 weeks for HANTO, and 3 weeks for the others). To assess the genetic background of theseT. grosiisolates, their small (SSU) and large subunit (LSU) ribosomal RNA genes (rDNA) were sequenced

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Khodami, Sahar, Pedro Martinez Arbizu, Sabine Stöhr, and Silke Laakmann. "Molecular Species Delimitation of Icelandic Brittle Stars (Ophiuroidea)." Polish Polar Research 35, no. 2 (2014): 243–60. http://dx.doi.org/10.2478/popore-2014-0011.

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Abstract Brittle stars (Echinodermata: Ophiuroidea) comprise over 2, 000 species, all of which inhabit marine environments and can be abundant in the deep sea. Morphological plasticity in number and shape of skeletal parts, as well as variable colors, can complicate correct species identification. Consequently, DNA sequence analysis can play an important role in species identification. In this study we compared the genetic variability of the mitochondrial cytochrome c subunit I gene (COI) and the nuclear small subunit ribosomal DNA (SSU, 18S rDNA) to morphological identification of 66 specimen

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Kanzaki, Natsumi, and Ryusei Tanaka. "Sheraphelenchus sucus n. sp. (Tylenchina: Aphelenchoididae) isolated from sap flow of Quercus serrata in Japan." Nematology 15, no. 8 (2013): 975–90. http://dx.doi.org/10.1163/15685411-00002736.

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A Sheraphelenchus species was isolated from a sample of sap exuding from a scar on the bark of Quercus serrata. Besides its generic characteristics, i.e., posteriorly located vulva in the female, male spicule with conspicuous dorsal limb and male tail with spike-like projection, the new species is characterised by a short stylet with a small basal swelling. The near-full-length of 18S and D2/D3 expansion segments of ribosomal RNA genes (near-full SSU and D2/D3LSU) were determined as its molecular barcode sequences and the phylogenetic status of the species (= genus Sheraphelenchus) was estimat

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Champion, Erica A., Bennett H. Lane, Meredith E. Jackrel, Lynne Regan, and Susan J. Baserga. "A Direct Interaction between the Utp6 Half-a-Tetratricopeptide Repeat Domain and a Specific Peptide in Utp21 Is Essential for Efficient Pre-rRNA Processing." Molecular and Cellular Biology 28, no. 21 (2008): 6547–56. http://dx.doi.org/10.1128/mcb.00906-08.

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ABSTRACT The small subunit (SSU) processome is a ribosome biogenesis intermediate that assembles from its subcomplexes onto the pre-18S rRNA with yet unknown order and structure. Here, we investigate the architecture of the UtpB subcomplex of the SSU processome, focusing on the interaction between the half-a-tetratricopeptide repeat (HAT) domain of Utp6 and a specific peptide in Utp21. We present a comprehensive map of the interactions within the UtpB subcomplex and further show that the N-terminal domain of Utp6 interacts with Utp18 while the HAT domain interacts with Utp21. Using a panel of

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Armando Sánchez, Juan, Howard R. Lasker, and Derek J. Taylor. "Phylogenetic analyses among octocorals (Cnidaria): mitochondrial and nuclear DNA sequences (lsu-rRNA, 16S and ssu-rRNA, 18S) support two convergent clades of branching gorgonians." Molecular Phylogenetics and Evolution 29, no. 1 (2003): 31–42. http://dx.doi.org/10.1016/s1055-7903(03)00090-3.

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Koohkan, Mina, Ebrahim Shokoohi, and Peter Mullin. "Phylogenetic relationships of three families of the suborder Mononchina Kirjanova & Krall, 1969 inferred from 18S rDNA." Nematology 17, no. 9 (2015): 1113–25. http://dx.doi.org/10.1163/15685411-00002928.

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Mononchida is an order of predatory nematodes and includes the suborders Bathyodontina and Mononchina. In this survey, sequences of the 18S rDNA were amplified and used to reconstruct the phylogeny of the Mononchina. Phylogenetic analyses using Neighbour Joining (NJ) and Maximum Likelihood (ML) were employed with five outgroup taxa and 65 mononch sequences including 14 new sequences from Iran. Both analyses indicated that the Anatonchus is monophyletic. Actus was placed as the sister group of Mylonchulus with weak and strong support, respectively, from the ML and NJ analyses. In both phylogene

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Hoang, Tran, Wen-Tao Peng, Emmanuel Vanrobays, et al. "Esf2p, a U3-Associated Factor Required for Small-Subunit Processome Assembly and Compaction." Molecular and Cellular Biology 25, no. 13 (2005): 5523–34. http://dx.doi.org/10.1128/mcb.25.13.5523-5534.2005.

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ABSTRACT Esf2p is the Saccharomyces cerevisiae homolog of mouse ABT1, a protein previously identified as a putative partner of the TATA-element binding protein. However, large-scale studies have indicated that Esf2p is primarily localized to the nucleolus and that it physically associates with pre-rRNA processing factors. Here, we show that Esf2p-depleted cells are defective for pre-rRNA processing at the early nucleolar cleavage sites A0 through A2 and consequently are inhibited for 18S rRNA synthesis. Esf2p was stably associated with the 5′ external transcribed spacer (ETS) and the box C+D s

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Schmidt, Volker, Linus Klasen, Juliane Schneider, Jens Hübel, and Michael Pees. "Characterization of Metarhizium viride Mycosis in Veiled Chameleons (Chamaeleo calyptratus), Panther Chameleons (Furcifer pardalis), and Inland Bearded Dragons (Pogona vitticeps)." Journal of Clinical Microbiology 55, no. 3 (2016): 832–43. http://dx.doi.org/10.1128/jcm.02206-16.

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ABSTRACT Metarhizium viride has been associated with fatal systemic mycoses in chameleons, but subsequent data on mycoses caused by this fungus in reptiles are lacking. The aim of this investigation was therefore to obtain information on the presence of M. viride in reptiles kept as pets in captivity and its association with clinical signs and pathological findings as well as improvement of diagnostic procedures. Beside 18S ribosomal DNA (rDNA) (small subunit [SSU]) and internal transcribed spacer region 1 (ITS-1), a fragment of the large subunit (LSU) of 28S rDNA, including domain 1 (D1) and

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Wedin, Mats, Heidi Döring, Anders Nordin, and Leif Tibell. "Small subunit rDNA phylogeny shows the lichen families Caliciaceae and Physciaceae (Lecanorales, Ascomycotina) to form a monophyletic group." Canadian Journal of Botany 78, no. 2 (2000): 246–54. http://dx.doi.org/10.1139/b99-185.

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A phylogenetic analysis based on small subunit (SSU) rDNA sequences shows the lecanoralean lichen families Caliciaceae and Physciaceae form a well-supported monophyletic group within the order Lecanorales (Ascomycotina). Support for this relationship is present from anatomical data, in particular data from spore ontogeny, where close similarities between the pattern of development of spore surface structures in the two families are pointed out. The Caliciaceae-Physciaceae group is characterized by having thick-walled, pigmented spores, often with a distinctive ornamentation which is usually fo

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Couto, MCM, AP Sudre, MF Lima, and TCB Bomfim. "Comparison of techniques for DNA extraction and agarose gel staining of DNA fragments using samples of Cryptosporidium." Veterinární Medicína 58, No. 10 (2013): 535–42. http://dx.doi.org/10.17221/7085-vetmed.

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Differentiating between the Cryptosporidium species and their subtypes using only microscopy is impossible. Therefore, molecular tools are indispensable for accurate species and subtype diagnosis. However, if these tools are to be used correctly and accurately, the techniques used must be standardised. In the present study, two molecular techniques for diagnosing Cryptosporidium infection in cows were compared to determine the optimal methods. For each technique, we tested two DNA extraction methods, several annealing temperatures for nested PCR reactions targeting the 18S, SSU rRNA (small sub

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Okada, Gen, Keith A. Seifert, Akiko Takematsu, Yuichi Yamaoka, Satoru Miyazaki, and Keisuke Tubaki. "A molecular phylogenetic reappraisal of theGraphiumcomplex based on 18S rDNA sequences." Canadian Journal of Botany 76, no. 9 (1998): 1495–506. http://dx.doi.org/10.1139/b98-089.

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Based on nuclear encoded small subunit (18S) rDNA sequences, a taxonomic reappraisal of Graphium (anamorphic fungi) was undertaken using neighbour-joining (NJ) and fast DNA maximum likelihood (fastDNAml) methods and compared with traditional classifications. In common with Graphium putredinis, Graphium penicillioides (the lectotype species) was found to be related to the Microascales, not the Ophiostomatales as previously believed. Both species might be heterogenous and should be treated as species aggregates. The representative mode of conidiogenesis for these two species was nodular-annellid

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Sekhavati, Mohammad Hadi, Mohammad Reza Nassiry, Mohsen Danesh Mesgaran, Amir Mohammadi, Ali Javadmanesh, and Hossein Esmaeilzadeh. "Microscopic Studies and Molecular Identification of Ruminal Zygomycetes Fungi in Sheep." Proceedings of the British Society of Animal Science 2007 (April 2007): 222. http://dx.doi.org/10.1017/s1752756200021256.

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Rumen is an area with high potential for growing of diverse living organisms including anaerobic fungi. The most studies on rumen fungi focused on anaerobic fungi classified asChytridiomycetes, familyNeocallimasticaceas, while few studies have done on determination ofZygomycetesthat can be native in the rumen. The most fungi within the subkingdomZygomycotinabelong to the classZygomycetes. Fungi in this class possess some distinctive properties that contain rapid growth, nonseptate mycelium, reproduction by sporangiospores (Pittet al., 1985) and production of some hydrolytic enzymes (Vinogradov

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Simdyanov, Timur G., Laure Guillou, Andrei Y. Diakin, Kirill V. Mikhailov, Joseph Schrével, and Vladimir V. Aleoshin. "A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)." PeerJ 5 (May 30, 2017): e3354. http://dx.doi.org/10.7717/peerj.3354.

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Background Gregarines are a group of early branching Apicomplexa parasitizing invertebrate animals. Despite their wide distribution and relevance to the understanding the phylogenesis of apicomplexans, gregarines remain understudied: light microscopy data are insufficient for classification, and electron microscopy and molecular data are fragmentary and overlap only partially. Methods Scanning and transmission electron microscopy, PCR, DNA cloning and sequencing (Sanger and NGS), molecular phylogenetic analyses using ribosomal RNA genes (18S (SSU), 5.8S, and 28S (LSU) ribosomal DNAs (rDNAs)).

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Osheim, Yvonne N., Sarah L. French, Kristin M. Keck, et al. "Pre-18S Ribosomal RNA Is Structurally Compacted into the SSU Processome Prior to Being Cleaved from Nascent Transcripts in Saccharomyces cerevisiae." Molecular Cell 16, no. 6 (2004): 943–54. http://dx.doi.org/10.1016/j.molcel.2004.11.031.

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Romanova, E. V., L. S. Kravtsova, L. A. Izhboldina, I. V. Khanaev, and D. Yu Sherbakov. "Identification of filamentous green algae from an area of local biogenic pollution of Lake Baikal (Listvennichnyi Bay) using SSU 18S rDNA." Russian Journal of Genetics: Applied Research 5, no. 2 (2015): 118–25. http://dx.doi.org/10.1134/s2079059715020082.

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Cohen, Bernard L., and Maria Aleksandra Bitner. "Molecular phylogeny of rhynchonellide articulate brachiopods (Brachiopoda, Rhynchonellida)." Journal of Paleontology 87, no. 2 (2013): 211–16. http://dx.doi.org/10.1666/12-100r.1.

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We present here the first report based on phylogenetic analyses of small subunit (SSU/18S) and large subunit (LSU/28S) ribosomal DNA (rDNA) sequences from a wider-than-token sample of rhynchonellide articulate brachiopods, with data from 11 of ∼20 extant genera (12 species) belonging to all four extant superfamilies. Data exploration by network and saturation analyses shows that the molecular sequence data are free from major aberrations and are suitable for phylogenetic reconstruction despite the presence of large deletions in four SSU rDNA sequences. Although molecular sequence analyses cann

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ZHAO, ZENG QI, and THOMAS R. BUCKLEY. "Phylogenetic analysis of nematode nuclear 18S rDNA sequences indicates the genus Tripylina Brzeski, 1963 (Nematoda: Tripylidae de Man, 1876) should be placed in Enoplida." Zootaxa 2238, no. 1 (2009): 25–32. http://dx.doi.org/10.11646/zootaxa.2238.1.2.

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We have made an extensive study of New Zealand representatives of nematodes from the family Tripylidae de Man, 1876. Based on SSU DNA sequence data and phylogenetic analysis, the genera Tripylina Brzeski, 1964 and Trischistoma Cobb, 1913 are not closely related to Tripyla Bastian, 1865, the type genus of the family Tripylidae de Man 1876. The genus Tripylina is sister to Trischistoma and Trefusia de Man, 1893 and is more closely related to Enoplida than to Triplonchida. Our phylogenetic results indicate that Tripylina should be placed in Enoplida.

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Vos, Timothy John, and Ute Kothe. "snR30/U17 Small Nucleolar Ribonucleoprotein: A Critical Player during Ribosome Biogenesis." Cells 9, no. 10 (2020): 2195. http://dx.doi.org/10.3390/cells9102195.

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The small nucleolar RNA snR30 (U17 in humans) plays a unique role during ribosome synthesis. Unlike most members of the H/ACA class of guide RNAs, the small nucleolar ribonucleoprotein (snoRNP) complex assembled on snR30 does not direct pseudouridylation of ribosomal RNA (rRNA), but instead snR30 is critical for 18S rRNA processing during formation of the small subunit (SSU) of the ribosome. Specifically, snR30 is essential for three pre-rRNA cleavages at the A0/01, A1/1, and A2/2a sites in yeast and humans, respectively. Accordingly, snR30 is the only essential H/ACA guide RNA in yeast. Here,

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ORSINI, MARÍA NOÉ DAMBROSI, NATALIA CUELLAR, JUAN C. RONDAN DUEÑAS, CRISTINA N. GARDENAL, MARCELO E. DOUCET, and PAOLA LAX. "Thelastoma vanwaerebekei n. sp. (Oxyurida: Thelastomatidae) a parasite of Gymnetis litigiosa (Coleoptera: Scarabaeidae) from Uruguay." Zootaxa 4375, no. 1 (2018): 75. http://dx.doi.org/10.11646/zootaxa.4375.1.3.

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Thelastoma vanwaerebekei n. sp. was extracted from the hindgut of Gymnetis litigiosa. The new species is included in the group of species with females having the excretory pore at the same level as the pharyngeal basal bulb (or slightly anteriorly), long tail length (approximately 30% of total body length) and males without spicules. Females of T. vanwaerebekei n. sp. differ from those of T. madecassum in tail shape (filiform and conical, respectively). They differ from T. basiri, T. imphalensis and T. dessetae in the morphology of the anterior region. In females, pharyngeal length is shorter

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Hassan, Zuber I. "Prevalence and Phylogenetic Analysis of Babesia ovis Isolated from Sheep and Goats in Erbil Province, Kurdistan Region- Iraq." Polytechnic Journal 10, no. 2 (2020): 98–104. http://dx.doi.org/10.25156/ptj.v10n2y2020.pp98-104.

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A total of 143 blood smears were obtained from sheep and goats (n = 98) and (n = 45), respectively, by jugular venipuncture between February 2019 and December 2019. Samples were examined for parasite occurrences. Results reveal that the prevalence of infection by the parasite was 12.24% and 11.11%, respectively (microscopically), while 20.41% sheep and 17.78% goats (molecular-based identification using 18S SSU rRNA sequence). Both methods revealed the specificity and sensitivity of the diagnostic assays. Phylogenetic analysis of Babesia ovis (MN309736-MN309745) displays that the pathogens iden

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Hestetun, Jon T., Anders Lanzén, and Thomas G. Dahlgren. "Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding." PeerJ 9 (June 21, 2021): e11619. http://dx.doi.org/10.7717/peerj.11619.

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Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples

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Romanova, Elena Vladimirovna, Lyubov Sergeevna Kravtsova, Lyudmila Aleksandrovna Izhboldina, Igor Veniaminovich Khanaev, and Dmitriy Yuryevich Sherbakov. "Identification of filamentous green algae from an area of local biogenic pollution of Lake Baikal (Listvennichnyy bay) using SSU 18S rDNA molecular marker." Ecological genetics 11, no. 4 (2013): 23. http://dx.doi.org/10.17816/ecogen11423-33.

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Kenmotsu, Harutaro, Masahiro Ishikawa, Tomokazu Nitta, Yuu Hirose, and Toshihiko Eki. "Distinct community structures of soil nematodes from three ecologically different sites revealed by high-throughput amplicon sequencing of four 18S ribosomal RNA gene regions." PLOS ONE 16, no. 4 (2021): e0249571. http://dx.doi.org/10.1371/journal.pone.0249571.

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Quantitative taxonomic compositions of nematode communities help to assess soil environments due to their rich abundance and various feeding habitats. DNA metabarcoding by the 18S ribosomal RNA gene (SSU) regions were preferentially used for analyses of soil nematode communities, but the optimal regions for high-throughput amplicon sequencing have not previously been well investigated. In this work, we performed Illumina-based amplicon sequencing of four SSU regions (regions 1–4) to identify suitable regions for nematode metabarcoding using the taxonomic structures of nematodes from uncultivat

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Tandingan De Ley, Irma, Rory D. McDonnell, Sandy Lopez, Timothy D. Paine, and Paul De Ley. "Phasmarhabditis hermaphrodita (Nematoda: Rhabditidae), a potential biocontrol agent isolated for the first time from invasive slugs in North America." Nematology 16, no. 10 (2014): 1129–38. http://dx.doi.org/10.1163/15685411-00002838.

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Phasmarhabditis hermaphroditais reported for the first time in North America from cadavers of the invasive slug speciesDeroceras reticulatum,D. laeveandLehmannia valentianacollected from three different locations in California, USA. Four isolates were identified using combined morphology, morphometrics and molecular sequence data for complete internal transcribed spacer (ITS-1, 5.8S, ITS-2), D2-D3 expansion segments of the large subunit (LSU or 28S) and nearly complete small subunit (SSU or 18S) ribosomal DNA. Extremely low sequence variations in the COI gene of the mitochondria were observed

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Liu, Yueteng, Hui He, Liang Fu, Qian Liu, Zuosheng Yang, and Yu Zhen. "Environmental DNA Sequencing Reveals a Highly Complex Eukaryote Community in Sansha Yongle Blue Hole, Xisha, South China Sea." Microorganisms 7, no. 12 (2019): 624. http://dx.doi.org/10.3390/microorganisms7120624.

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We report an Illumina high-throughput sequencing protocol of eukaryotic microbes in the world’s deepest marine blue hole, Sansha Yongle Blue Hole, Xisha, South China Sea. The variable V9 region of small subunit (SSU) rDNA, was sequenced using this approach from the waters of blue hole and outer reef slope. 917,771 unique eukaryotic 18S rRNA gene sequences and 6093 operational taxonomic units (OTUs) were identified. Significant differences in the eukaryotic composition were observed between the blue hole and outer reef slope, and the richness in the blue hole was much higher than that in the ou

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Ishaq, Suzanne L., and André-Denis G. Wright. "Design and Validation of Four New Primers for Next-Generation Sequencing To Target the 18S rRNA Genes of Gastrointestinal Ciliate Protozoa." Applied and Environmental Microbiology 80, no. 17 (2014): 5515–21. http://dx.doi.org/10.1128/aem.01644-14.

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ABSTRACTFour new primers and one published primer were used to PCR amplify hypervariable regions within the protozoal 18S rRNA gene to determine which primer pair provided the best identification and statistical analysis. PCR amplicons of 394 to 498 bases were generated from three primer sets, sequenced using Roche 454 pyrosequencing with Titanium, and analyzed using the BLAST database (NCBI) and MOTHUR version 1.29. The protozoal diversity of rumen contents from moose in Alaska was assessed. In the present study, primer set 1, P-SSU-316F and GIC758R (amplicon of 482 bases), gave the best repr

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Hu, Xiaozhong, Yangbo Fan, and Alan Warren. "New record of Apoholosticha sinica (Ciliophora, Urostylida) from the UK: morphology, 18S rRNA gene phylogeny and notes on morphogenesis." International Journal of Systematic and Evolutionary Microbiology 65, Pt_8 (2015): 2549–61. http://dx.doi.org/10.1099/ijs.0.000301.

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The benthic urostylid ciliate Apoholosticha sinica Fan et al., 2014 was isolated from a salt marsh at Blakeney, UK, and reinvestigated using light microscopy and small-subunit rRNA gene sequencing. Morphologically, it corresponds well with the original description. Several stages of divisional morphogenesis and physiological reorganization were also observed from which the following could be deduced: (i) the oral apparatus is completely newly built in the proter; (ii) frontal-ventral-transverse cirral anlage II does not produce a buccal cirrus; (iii) each of the posteriormost three or four anl

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Borquez-Román, Manuel Alejandro, Luis Fernando Lares-Jiménez, Libia Zulema Rodriguez-Anaya, et al. "Stenamoeba dejonckheerei sp. nov., a Free-Living Amoeba Isolated from a Thermal Spring." Pathogens 9, no. 7 (2020): 586. http://dx.doi.org/10.3390/pathogens9070586.

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Two amoeboid organisms were obtained from water samples taken from a thermal spring, "Agua Caliente", in Northwestern Mexico. The isolates were obtained when samples were cultivated at 37 °C on non-nutrient agar coated with Escherichia coli. The initial identification of the isolates was performed morphologically using light microscopy. The samples were found to have trophozoite morphology consistent with members of the genus Stenamoeba, a genus derived in 2007 from within the abolished polyphyletic genus Platyamoeba. Further analysis was performed by sequencing PCR products obtained using uni

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Pinto, R., L. Ludueña, S. Anzuay, T. Taurian, and J. Angelini. "Cambio en la diversidad de hongos micorrícicos arbusculares asociados a la planta del maní (Arachis hypogaea L.) luego de la aplicación de Agroquímicos." Agrotecnia, no. 25 (November 30, 2017): 9. http://dx.doi.org/10.30972/agr.0252397.

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Actualmente se ha podido demostrar que los hongos micorrícicos arbusculares (HMA) están presentes formando parte de simbiosis con más del 80% de las plantas terrestres. El estudio de diversidad de especies en las comunidades de los HMA presenta serias dificultades debido a que no se conocen estadios de reproducción sexual, sus células ser multinucleadas y ser simbiontes obligados, por lo que en los estudios de biodiversidad es necesario llevar a cabo análisis basados en criterios morfológicos como el recuento e identificación de esporas, porcentaje de colonización, y criterios genéticos a trav

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KONDO, TAKUMASA, NATE HARDY, LYN COOK, and PENNY GULLAN. "Description of two new genera and species of Eriococcidae (Hemiptera: Coccoidea) from southern South America." Zootaxa 1349, no. 1 (2006): 19. http://dx.doi.org/10.11646/zootaxa.1349.1.2.

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Two new genera of Eriococcidae, Intecticoccus Kondo and Orafortis Hardy, each with a new species (I. viridis Kondo and O. luma Hardy), are described and illustrated based on the adult females. I. viridis was collected on Nothofagus antarctica (Nothofagaceae) in Argentina and Chile, and O. luma was collected in Chile on Amomyrtus luma (Myrtaceae). Based on a phylogenetic analysis of SSU rDNA (18S) sequence data, I. viridis and O. luma are placed within the Gondwanan group of eriococcids (sensu Cook & Gullan 2004), which also includes other Nothofagus-feeding genera such as Chilechiton Hodgs

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