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Journal articles on the topic 'Nuclear rDNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Muscarella, D. E., and V. M. Vogt. "A mobile group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 2 (1993): 1023–33. http://dx.doi.org/10.1128/mcb.13.2.1023.

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Pp LSU3 is a mobile group I intron in the extrachromosomal nuclear ribosomal DNA (rDNA) of Physarum polycephalum. As found for other mobile introns, Pp LSU3 encodes a site-specific endonuclease, I-Ppo, which mediates "homing" to unoccupied target sites in Physarum rDNA. The recognition sequence for this enzyme is conserved in all eucaryotic nuclear rDNAs. We have introduced this intron into a heterologous species, Saccharomyces cerevisiae, in which nuclear group I introns have not been detected. The expression of Pp LSU3, under control of the inducible GAL10 promoter, was found to be lethal as

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2

Muscarella, D. E., and V. M. Vogt. "A mobile group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 2 (1993): 1023–33. http://dx.doi.org/10.1128/mcb.13.2.1023-1033.1993.

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Pp LSU3 is a mobile group I intron in the extrachromosomal nuclear ribosomal DNA (rDNA) of Physarum polycephalum. As found for other mobile introns, Pp LSU3 encodes a site-specific endonuclease, I-Ppo, which mediates "homing" to unoccupied target sites in Physarum rDNA. The recognition sequence for this enzyme is conserved in all eucaryotic nuclear rDNAs. We have introduced this intron into a heterologous species, Saccharomyces cerevisiae, in which nuclear group I introns have not been detected. The expression of Pp LSU3, under control of the inducible GAL10 promoter, was found to be lethal as

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3

Holst-Jensen, Arne, Linda M. Kohn, and Trond Schumacher. "Nuclear rDNA Phylogeny of the Sclerotiniaceae." Mycologia 89, no. 6 (1997): 885. http://dx.doi.org/10.2307/3761109.

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4

Ravel-Chapuis, Patrick, Paul Nicolas, Victor Nigon, Odile Neyret, and Georges Freyssinet. "Extrachromosomal circular nuclear rDNA inEuglena gracilis." Nucleic Acids Research 13, no. 20 (1985): 7529–37. http://dx.doi.org/10.1093/nar/13.20.7529.

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5

Holst-Jensen, Arne, Linda M. Kohn, and Trond Schumacher. "Nuclear rDNA phylogeny of the Sclerotiniaceae." Mycologia 89, no. 6 (1997): 885–99. http://dx.doi.org/10.1080/00275514.1997.12026859.

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6

Horton, J. Stephen, and Paul A. Horgen. "Polymorphisms in the nuclear DNA of Achlya species: some taxonomic implications." Canadian Journal of Microbiology 35, no. 12 (1989): 1146–55. http://dx.doi.org/10.1139/m89-190.

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Within the genus Achyla, which belongs to the class of fungi known as the Oomycetes, taxonomic judgments have traditionally been made using a variety of sexual criteria. We have used restriction fragment length polymorphisms as a new taxonomic character to examine intra- and inter-specific variation within this genus. Using a cDNA clone coding for the Achlya 18S rRNA gene as a hybridization probe, a 10-kb fragment of ribosomal DNA (rDNA) from Achlya ambisexualis strain E87 was cloned and then mapped for selected restriction enzyme sites. In Southern blot hybridizations, both this rDNA fragment

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7

Yu, G. L., and E. H. Blackburn. "Amplification of tandemly repeated origin control sequences confers a replication advantage on rDNA replicons in Tetrahymena thermophila." Molecular and Cellular Biology 10, no. 5 (1990): 2070–80. http://dx.doi.org/10.1128/mcb.10.5.2070.

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The macronuclear rRNA genes (rDNA) in the ciliate Tetrahymena thermophila are normally palindromic linear replicons, containing two copies of the replication origin region in inverted orientation. A circular plasmid containing a single Tetrahymena rRNA gene (one half palindrome) joined to a tandem repeat of a 1.9-kilobase (kb) rDNA segment encompassing the rDNA replication origin and known replication control elements was used to transform Tetrahymena macronuclei by microinjection. This plasmid was shown previously to have a replication advantage over the rDNA allele of the recipient cell stra

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Yu, G. L., and E. H. Blackburn. "Amplification of tandemly repeated origin control sequences confers a replication advantage on rDNA replicons in Tetrahymena thermophila." Molecular and Cellular Biology 10, no. 5 (1990): 2070–80. http://dx.doi.org/10.1128/mcb.10.5.2070-2080.1990.

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The macronuclear rRNA genes (rDNA) in the ciliate Tetrahymena thermophila are normally palindromic linear replicons, containing two copies of the replication origin region in inverted orientation. A circular plasmid containing a single Tetrahymena rRNA gene (one half palindrome) joined to a tandem repeat of a 1.9-kilobase (kb) rDNA segment encompassing the rDNA replication origin and known replication control elements was used to transform Tetrahymena macronuclei by microinjection. This plasmid was shown previously to have a replication advantage over the rDNA allele of the recipient cell stra

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9

Panigrahi, Sunil K., Gagan Deep Jhingan, Indrani Som, Alok Bhattacharya, William A. Petri, and Sudha Bhattacharya. "Promoter Analysis of Palindromic Transcription Units in the Ribosomal DNA Circle of Entamoeba histolytica." Eukaryotic Cell 8, no. 1 (2008): 69–76. http://dx.doi.org/10.1128/ec.00254-08.

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ABSTRACT rRNA genes of Entamoeba histolytica are organized as palindromic ribosomal DNA (rDNA) units (I and II) in a 24.5-kb circle. Although the two rDNAs are identical in sequence, their upstream spacers are completely different. Since the intergenic sequences (IGS) of all rDNA copies in other organisms are conserved and contain transcription regulatory sequences, the lack of sequence conservation in the IGS prompted the question of whether both rDNAs are indeed transcriptionally active. We mapped the transcriptional start points (tsp's) and promoters of the two rDNAs. A 51-bp sequence immed

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10

Zheng, Xu, Qiao-Cheng Chang, Yan Zhang, et al. "Characterization of the Complete Nuclear Ribosomal DNA Sequences ofParamphistomum cervi." Scientific World Journal 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/751907.

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Sequences of the complete nuclear ribosomal DNA (rDNA) gene from five individualParamphistomum cerviwere determined for the first time. The five complete rDNA sequences, which included the 18S rDNA, the internal transcribed spacer 1 (ITS1), the 5.8S rDNA, the internal transcribed spacer 2 (ITS2), the 28S rDNA, and the intergenic spacer (IGS) regions, had a length range of 8,493–10,221 bp. The lengths of the investigated 18S, ITS1, 5.8S, ITS2, and 28S rDNA sequences, which were 1,994 bp, 1,293 bp, 157 bp, 286 bp, and 4,186 bp, respectively, did not vary. However, the IGS rDNA sequences had a le

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11

Su, X., Y. Zhang, X. Zheng, et al. "Characterization of the complete nuclear ribosomal DNA sequences of Eurytrema pancreaticum." Journal of Helminthology 92, no. 4 (2017): 484–90. http://dx.doi.org/10.1017/s0022149x17000554.

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AbstractEurytrema pancreaticum is one of the most common trematodes of cattle and sheep, and also infects humans occasionally, causing great economic losses and medical costs. In this study, the sequences of the complete nuclear ribosomal DNA (rDNA) repeat units of five E. pancreaticum individuals were determined for the first time. They were 8306–8310 bp in length, including the small subunit (18S) rDNA, internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), large subunit (28S) rDNA and intergenic spacer (IGS). There were no length variations in any of the inve

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12

Cameron, Kenneth, and Chengxin Fu. "A Nuclear rDNA Phylogeny of Smilax (Smilacaceae)." Aliso 22, no. 1 (2006): 598–605. http://dx.doi.org/10.5642/aliso.20062201.47.

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13

O’Sullivan, Justin M., Dave A. Pai, Andrew G. Cridge, David R. Engelke, and Austen R. D. Ganley. "The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?" BioMolecular Concepts 4, no. 3 (2013): 277–86. http://dx.doi.org/10.1515/bmc-2012-0043.

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AbstractThe nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfill the cellular demand for rRNA, the ribosomal RNA (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review, we address the questio

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14

Symonová, Radka. "Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome." Genes 10, no. 5 (2019): 345. http://dx.doi.org/10.3390/genes10050345.

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Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copie

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15

Mostofa, Md Golam, Muhammad Arifur Rahman, Naoki Koike, et al. "CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy." Journal of Cell Biology 217, no. 8 (2018): 2675–90. http://dx.doi.org/10.1083/jcb.201706164.

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Nutrient starvation or inactivation of target of rapamycin complex 1 (TORC1) in budding yeast induces nucleophagy, a selective autophagy process that preferentially degrades nucleolar components. DNA, including ribosomal DNA (rDNA), is not degraded by nucleophagy, even though rDNA is embedded in the nucleolus. Here, we show that TORC1 inactivation promotes relocalization of nucleolar proteins and rDNA to different sites. Nucleolar proteins move to sites proximal to the nuclear–vacuolar junction (NVJ), where micronucleophagy (or piecemeal microautophagy of the nucleus) occurs, whereas rDNA diss

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16

Liu, G. H., W. Zhou, A. J. Nisbet, et al. "Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA." Journal of Helminthology 88, no. 1 (2012): 64–68. http://dx.doi.org/10.1017/s0022149x12000740.

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AbstractTrichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representati

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17

Nakazawa, Norihiko, Takahiro Nakamura, Aya Kokubu, Masahiro Ebe, Koji Nagao, and Mitsuhiro Yanagida. "Dissection of the essential steps for condensin accumulation at kinetochores and rDNAs during fission yeast mitosis." Journal of Cell Biology 180, no. 6 (2008): 1115–31. http://dx.doi.org/10.1083/jcb.200708170.

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The condensin complex has a fundamental role in chromosome dynamics. In this study, we report that accumulation of Schizosaccharomyces pombe condensin at mitotic kinetochores and ribosomal DNAs (rDNAs) occurs in multiple steps and is necessary for normal segregation of the sister kinetochores and rDNAs. Nuclear entry of condensin at the onset of mitosis requires Cut15/importin α and Cdc2 phosphorylation. Ark1/aurora and Cut17/Bir1/survivin are needed to dock the condensin at both the kinetochores and rDNAs. Furthermore, proteins that are necessary to form the chromatin architecture of the kine

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18

Oakes, M., J. P. Aris, J. S. Brockenbrough, H. Wai, L. Vu, and M. Nomura. "Mutational Analysis of the Structure and Localization of the Nucleolus in the Yeast Saccharomyces cerevisiae." Journal of Cell Biology 143, no. 1 (1998): 23–34. http://dx.doi.org/10.1083/jcb.143.1.23.

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The nucleolus in Saccharomyces cerevisiae is a crescent-shaped structure that makes extensive contact with the nuclear envelope. In different chromosomal rDNA deletion mutants that we have analyzed, the nucleolus is not organized into a crescent structure, as determined by immunofluorescence microscopy, fluorescence in situ hybridization, and electron microscopy. A strain carrying a plasmid with a single rDNA repeat transcribed by RNA polymerase I (Pol I) contained a fragmented nucleolus distributed throughout the nucleus, primarily localized at the nuclear periphery. A strain carrying a plasm

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19

Imperador, Carlos Henrique L., Vanessa B. Bardella, Eli Heber M. dos Anjos, Vera L. C. C. Rodrigues, Diogo C. Cabral-de-Mello, and Maria Luiza S. Mello. "Spatial Distribution of Heterochromatin Bodies in the Nuclei of Triatoma infestans (Klug)." Microscopy and Microanalysis 26, no. 3 (2020): 567–74. http://dx.doi.org/10.1017/s143192762000149x.

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AbstractConstitutive heterochromatin typically exhibits low gene density and is commonly found adjacent or close to the nuclear periphery, in contrast to transcriptionally active genes concentrated in the innermost nuclear region. In Triatoma infestans cells, conspicuous constitutive heterochromatin forms deeply stained structures named chromocenters. However, to the best of our knowledge, no information exists regarding whether these chromocenters acquire a precise topology in the cell nuclei or whether their 18S rDNA, which is important for ribosome function, faces the nuclear center prefere

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20

Moore, Thomas C. "Tailor-Surgeon, Soviet and Silovik : Russian Nuclear Strategy." Revue Défense Nationale N° 801, no. 6 (2017): 42–50. http://dx.doi.org/10.3917/rdna.801.0042.

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21

Maitre, Emmanuelle. "La Nuclear Posture Review vue d’Europe." Revue Défense Nationale N° 810, no. 5 (2018): 105–10. http://dx.doi.org/10.3917/rdna.810.0105.

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22

Mahelka, Václav, Karol Krak, David Kopecký, et al. "Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages." Proceedings of the National Academy of Sciences 114, no. 7 (2017): 1726–31. http://dx.doi.org/10.1073/pnas.1613375114.

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The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some cur

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23

Zhao, G. H., B. Hu, J. K. Song, et al. "Characterization of Oesophagostomum asperum and O. columbianum by internal transcribed spacers of nuclear ribosomal DNA." Journal of Helminthology 88, no. 1 (2012): 74–81. http://dx.doi.org/10.1017/s0022149x12000764.

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AbstractIn the present study, the internal transcribed spacers (ITS) of ribosomal DNA (rDNA) of Oesophagostomum asperum and O. columbianum were amplified and sequenced. The ITS-1, 5.8S and ITS-2 rDNA sequences of O. asperum were 374 bp, 153 bp and 259 bp in length, respectively, and the corresponding sequences of O. columbianum were 259, 153 and 218 bp in length, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA between the two Oesophagostomum species were 9.5–10.2% and 12.7–13.9%, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA among members of the genus Oesophagos

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Zietara, Marek S., Allan Arndt, Aldegonda Geets, Bart Hellemans, and Filip A. M. Volckaert. "THE NUCLEAR rDNA REGION OFGYRODACTYLUS ARCUATUSANDG. BRANCHICUS(MONOGENEA: GYRODACTYLIDAE)." Journal of Parasitology 86, no. 6 (2000): 1368–73. http://dx.doi.org/10.1645/0022-3395(2000)086[1368:tnrrog]2.0.co;2.

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Dumoulin, André. "La nouvelle Nuclear Posture Review : évolution ou révolution ?" Revue Défense Nationale N° 810, no. 5 (2018): 111–15. http://dx.doi.org/10.3917/rdna.810.0111.

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26

Sakhanokho, Hamidou F., and Nurul Islam-Faridi. "Nuclear DNA Content, Base Composition, and Cytogenetic Characterization of Christia obcordata." Journal of the American Society for Horticultural Science 138, no. 3 (2013): 205–9. http://dx.doi.org/10.21273/jashs.138.3.205.

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Christia obcordata is an intriguing small-sized house plant with unusual and attractive features such as its striped leaves. Because very little is known about the plant, we conducted an investigation of its genome and chromosomes. The number of chromosomes was determined using a protoplast technique to prepare root tip chromosome spread and was found to be 2n = 2x = 20. Flow cytometry was used to determine nuclear DNA content (1C = 0.65 pg = 634.4 Mb) for C. obcordata and AT/GC composition was shown to be AT% = 62.8% ± 0.0% and GC% = 37.2% ± 0.0%. Finally, fluorescent in situ hybridization wa

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27

Pillay, Michael. "Variation of nuclear ribosomal RNA genes in Eragrostis tef (Zucc.) Trotter." Genome 40, no. 6 (1997): 815–21. http://dx.doi.org/10.1139/g97-805.

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Variation in the ribosomal RNA genes (rDNA) was examined to assess the genetic variability among 314 plants representing 28 accessions of Eragrostis tef, an important food crop. A restriction site map was constructed for the species by localization of the BamHI, BglII, DraI, EcoRI, EcoRV, NdeI, SacI, SpeI, XbaI, and XhoI sites. A comparison of this map with those of other grasses showed conservation of sites, especially in the coding region. However, a unique EcoRI site combined with a BamHI site in the 18S region may be of diagnostic value for the species. A BamHI fragment that spans the inte

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28

Lloyd, A. D., C. H. A. Little, E. J. Mellerowicz, and R. T. Riding. "Changes in nuclear genome size and relative ribosomal RNA gene content in cambial region cells of Abies balsamea shoots during the development of dormancy." Canadian Journal of Botany 74, no. 2 (1996): 290–98. http://dx.doi.org/10.1139/b96-035.

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The relationship between nuclear genome size, measured cytophotometrically, and relative ribosomal RNA gene (rDNA) content, determined as the ratio of the hybridization signals from a 25S rRNA gene probe and a randomly labelled total genomic DNA probe, was investigated in cambial region cells of balsam fir (Abies balsamea (L.) Mill.) shoots during the onset of dormancy and the transition between the dormancy stages of rest and quiescence. The dormancy status was manipulated by exposing potted trees for 13 weeks, starting August 14 when the cambium was still active, to one of the following envi

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Hannan, Katherine M., Lawrence I. Rothblum, and Leonard S. Jefferson. "Regulation of ribosomal DNA transcription by insulin." American Journal of Physiology-Cell Physiology 275, no. 1 (1998): C130—C138. http://dx.doi.org/10.1152/ajpcell.1998.275.1.c130.

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The experiments reported here used 3T6-Swiss albino mouse fibroblasts and H4-II-E-C3 rat hepatoma cells as model systems to examine the mechanism(s) through which insulin regulates rDNA transcription. Serum starvation of 3T6 cells for 72 h resulted in a marked reduction in rDNA transcription. Treatment of serum-deprived cells with insulin was sufficient to restore rDNA transcription to control values. In addition, treatment of exponentially growing H4-II-E-C3 with insulin stimulated rDNA transcription. However, for both cell types, the stimulation of rDNA transcription in response to insulin w

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Wang, Yurui, Yaohan Jiang, Yongqiang Liu, et al. "Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research." Microorganisms 8, no. 3 (2020): 316. http://dx.doi.org/10.3390/microorganisms8030316.

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While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy

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31

Small, Randall L., Richard C. Cronn, and Jonathan F. Wendel. "Use of nuclear genes for phylogeny reconstruction in plants." Australian Systematic Botany 17, no. 2 (2004): 145. http://dx.doi.org/10.1071/sb03015.

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Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic

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32

Bian, Q. Q., G. H. Zhao, Y. Q. Jia, et al. "Characterization ofDicrocoelium dendriticumisolates from small ruminants in Shaanxi Province, north-western China, using internal transcribed spacers of nuclear ribosomal DNA." Journal of Helminthology 89, no. 1 (2013): 124–29. http://dx.doi.org/10.1017/s0022149x13000503.

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AbstractThe genetic variations in internal transcribed spacers (ITS) spanning ITS-1, 5.8S and ITS-2 rDNA ofDicrocoelium dendriticum, isolated from sheep and goats in four geographical regions in Shaanxi province, were examined. The lengths of ITS-1, 5.8S and ITS-2 rDNA sequences forD. dendriticumwere 749 bp, 161 bp and 234 bp, respectively. Intra-specific sequence variations ofD. dendriticumwere 0–0.5% for ITS-1 and 0–1.3% for ITS-2 rDNA, while the inter-specific variations among species in genusDicrocoeliumin ITS-2 rDNA were 3.4–12.3%. Phylogenetic analysis based on sequences of ITS-2 rDNA sh

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Ramsfield, Tod D., Elisa M. Becker, Sean M. Rathlef, et al. "Geographic variation of Chondrostereum purpureum detected by polymorphisms in the ribosomal DNA." Canadian Journal of Botany 74, no. 12 (1996): 1919–29. http://dx.doi.org/10.1139/b96-229.

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Variation in the ribosomal (rDNA) repeat was analyzed for 107 isolates of the pathogenic fungus Chondrostereum purpureum, collected from Europe, New Zealand, and North America. The rDNA repeat of a representative Canadian isolate of C. purpureum was cloned into the λ vector EMBL-3, and a detailed restriction map was constructed. Variation in the large non-transcribed spacer region of the rDNA was determined for the entire collection of isolates following amplification by the polymerase chain reaction (PCR) and analysis of restriction fragment length polymorphisms (RFLPs). Three distinct nuclea

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Kaliszewicz, Anita, Ninel Panteleeva, Magdalena Żmuda-Baranowska, et al. "Phylogenetic Relatedness within the Internally Brooding Sea Anemones from the Arctic-Boreal Region." Biology 10, no. 2 (2021): 81. http://dx.doi.org/10.3390/biology10020081.

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Phylogenetic analyses based on mitochondrial 16S rDNA, nuclear 28S rDNA, and morphological and ecological traits of Aulactinia, Urticina and Cribrinopsis sea anemones inhabiting the Arctic-boreal region indicate discordances between trees derived from molecular sequences and those based on morphological traits. Nuclear genes were more informative than mitochondrial and morphological datasets. Our findings indicate that 16S rDNA has limited applicability for phylogenetic analyses at lower taxonomic levels and can only be used for distinction of families. Although 28S rDNA allowed for the classi

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35

Ye, Junqiang, and Thomas H. Eickbush. "Chromatin Structure and Transcription of the R1- and R2-Inserted rRNA Genes of Drosophila melanogaster." Molecular and Cellular Biology 26, no. 23 (2006): 8781–90. http://dx.doi.org/10.1128/mcb.01409-06.

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ABSTRACT About half of the rRNA gene units (rDNA units) of Drosophila melanogaster are inserted by the retrotransposable elements R1 and R2. Because transcripts to R1 and R2 were difficult to detect on blots and electron microscopic observations of rRNA synthesis suggested that only uninserted rDNA units were transcribed, it has long been postulated that inserted rDNA units are in a repressed (inactive) chromatin structure. Studies described here suggest that inserted and uninserted units are equally accessible to DNase I and micrococcal nuclease and contain similar levels of histone H3 and H4

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36

Toussaint, Martin, Geneviève Levasseur, Maxime Tremblay, Michel Paquette, and Antonio Conconi. "Psoralen photocrosslinking, a tool to study the chromatin structure of RNA polymerase I - transcribed ribosomal genes." Biochemistry and Cell Biology 83, no. 4 (2005): 449–59. http://dx.doi.org/10.1139/o05-141.

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The chromatin structure of RNA polymerase I - transcribed ribosomal DNA (rDNA) is well characterized. In most organisms, i.e., lower eukaryotes, plants, and animals, only a fraction of ribosomal genes are transcriptionally active. At the chromatin level inactive rDNA is assembled into arrays of nucleosomes, whereas transcriptionally active rDNA does not contain canonical nucleosomes. To separate inactive (nucleosomal) and active (non-nucleosomal) rDNA, the technique of psoralen photocrosslinking has been used successfully both in vitro and in vivo. In Saccharomyces cerevisiae, the structure of

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Bolla, R. I., D. C. Braaten, Y. Shiomi, M. B. Hebert, and D. Schlessinger. "Localization of specific rDNA spacer sequences to the mouse L-cell nucleolar matrix." Molecular and Cellular Biology 5, no. 6 (1985): 1287–94. http://dx.doi.org/10.1128/mcb.5.6.1287.

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Mouse L-cell nucleoli were isolated from sonicated nuclei by centrifugation and extensively treated with pancreatic DNase or micrococcal nuclease to obtain "core nucleoli." Core nucleoli still contained the precursors to rRNA and about 1% of the total nuclear DNA, which remained tightly bound even after the removal of some chromatin proteins with 2 M NaCl. The core nucleolar DNA electrophoresed in a series of discrete bands, 20 to about 200 base pairs in length. Hybridization tests with specific DNA probes showed that the DNA was devoid of sequences complementary to mouse satellite, mouse Alu-

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Bolla, R. I., D. C. Braaten, Y. Shiomi, M. B. Hebert, and D. Schlessinger. "Localization of specific rDNA spacer sequences to the mouse L-cell nucleolar matrix." Molecular and Cellular Biology 5, no. 6 (1985): 1287–94. http://dx.doi.org/10.1128/mcb.5.6.1287-1294.1985.

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Abstract:

Mouse L-cell nucleoli were isolated from sonicated nuclei by centrifugation and extensively treated with pancreatic DNase or micrococcal nuclease to obtain "core nucleoli." Core nucleoli still contained the precursors to rRNA and about 1% of the total nuclear DNA, which remained tightly bound even after the removal of some chromatin proteins with 2 M NaCl. The core nucleolar DNA electrophoresed in a series of discrete bands, 20 to about 200 base pairs in length. Hybridization tests with specific DNA probes showed that the DNA was devoid of sequences complementary to mouse satellite, mouse Alu-

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Jin, Long Guo, Myung Sook Kim, Jae Suk Choi, Ji Young Cho, Hyung Joo Jin, and Yong Ki Hong. "Sequence Analysis of Nuclear 18S rDNA from the Seaweed Porphyra yezoensis (Rhodophyta) in Korea." Korean Journal of Fisheries and Aquatic Sciences 35, no. 6 (2002): 633–38. http://dx.doi.org/10.5657/kfas.2002.35.6.633.

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Fritz, Ann H. "Sequence Analysis of Nuclear rDNA of Anastrepha suspensa." Annals of the Entomological Society of America 99, no. 2 (2006): 369–73. http://dx.doi.org/10.1603/0013-8746(2006)099[0369:saonro]2.0.co;2.

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Wang, Zheng, Manfred Binder, Conrad L. Schoch, Peter R. Johnston, Joseph W. Spatafora, and David S. Hibbett. "Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny." Molecular Phylogenetics and Evolution 41, no. 2 (2006): 295–312. http://dx.doi.org/10.1016/j.ympev.2006.05.031.

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Li, Hong, Chi Kwan Tsang, Marcus Watkins, Paula G. Bertram, and X. F. Steven Zheng. "Nutrient regulates Tor1 nuclear localization and association with rDNA promoter." Nature 442, no. 7106 (2006): 1058–61. http://dx.doi.org/10.1038/nature05020.

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Al-Banna, Luma, Valerie Williamson, and Scott Lyell Gardner. "Phylogenetic Analysis of Nematodes of the GenusPratylenchusUsing Nuclear 26S rDNA." Molecular Phylogenetics and Evolution 7, no. 1 (1997): 94–102. http://dx.doi.org/10.1006/mpev.1996.0381.

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Schultheis, Lisa M., and Bruce G. Baldwin. "Molecular phylogenetics of Fouquieriaceae: evidence from nuclear rDNA ITS studies." American Journal of Botany 86, no. 4 (1999): 578–89. http://dx.doi.org/10.2307/2656819.

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GAST, REBECCA J., DOLENA R. LEDEE, PAUL A. FUERST, and THOMAS J. BYERS. "Subgenus Systematics of Acanthamoeba: Four Nuclear 18S rDNA Sequence Types." Journal of Eukaryotic Microbiology 43, no. 6 (1996): 498–504. http://dx.doi.org/10.1111/j.1550-7408.1996.tb04510.x.

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Tan, M. K., P. T. W. Wong, and M. P. Holley. "Characterization of nuclear ribosomal DNA (rDNA) in Gaeumannomyces graminis and correlation of rDNA variation with G. graminis varieties." Mycological Research 98, no. 5 (1994): 553–61. http://dx.doi.org/10.1016/s0953-7562(09)80479-6.

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Borisjuk, N., L. Borisjuk, G. Petjuch, and V. Hemleben. "Comparison of nuclear ribosomal RNA genes among Solanum species and other Solanaceae." Genome 37, no. 2 (1994): 271–79. http://dx.doi.org/10.1139/g94-038.

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The organization of the nuclear-encoded 18S, 5.8S, and 25S ribosomal RNA genes (ribosomal DNA; rDNA) of 21 New World species from different sections of the genus Solanum, of two Old World Solanum species, and of representatives of other Solanaceae (Nicotiana, Atropa, Datura, Physalis, and Capsicum) was analyzed by restriction enzyme mapping using different rDNA specific hybridization probes. All Solanum species investigated exhibited rDNA repeats between 8.7 and 9.3 kb in length; the only exception was S. neorossii with a repeat length of 10.3 kb. Sequence heterogeneity was observed mostly in

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Cartwright, Paulyn, Nathaniel M. Evans, Casey W. Dunn, et al. "Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria)." Journal of the Marine Biological Association of the United Kingdom 88, no. 8 (2008): 1663–72. http://dx.doi.org/10.1017/s0025315408002257.

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Hydroidolina is a group of hydrozoans that includes Anthoathecata, Leptothecata and Siphonophorae. Previous phylogenetic analyses show strong support for Hydroidolina monophyly, but the relationships between and within its subgroups remain uncertain. In an effort to further clarify hydroidolinan relationships, we performed phylogenetic analyses on 97 hydroidolinan taxa, using DNA sequences from partial mitochondrial 16S rDNA, nearly complete nuclear 18S rDNA and nearly complete nuclear 28S rDNA. Our findings are consistent with previous analyses that support monophyly of Siphonophorae and Lept

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SUAREZ, JUAN M., ALEXANDRA M. GOTTLIEB, and BERNARDO E. LECHNER. "A new and intriguing brown-spored Leucocoprinus species." Phytotaxa 479, no. 1 (2021): 44–54. http://dx.doi.org/10.11646/phytotaxa.479.1.3.

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Leucocoprinus brunneosporus sp. nov., collected at the Santa Catalina Reserve (Buenos Aires, Argentina), is proposed as a new species. We performed separate phylogenetic analyses of the nuclear rDNA large subunit (28S) and the complete nuclear rDNA internal transcribed spacer region (ITS) to establish the placement of the new species in the phylogeny of the Agaricaceae. This new species has a macromorphology similar to that of Lc. birnbaumii, but the spore print is light brown. Detailed descriptions and illustrations of the macro- and microscopic characters are provided.

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Zhan, Li, and Xu. "Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Ciliophora, Spirotrichea)." Microorganisms 7, no. 11 (2019): 493. http://dx.doi.org/10.3390/microorganisms7110493.

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Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conse

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