Articles de revues : « 5.8S –ITS rDNA »

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Wu, Zuo-Wei, et Feng-Yan Bai. « Kazachstania aquatica sp. nov. and Kazachstania solicola sp. nov., novel ascomycetous yeast species ». International Journal of Systematic and Evolutionary Microbiology 55, n^o 5 (1 septembre 2005) : 2219–24. http://dx.doi.org/10.1099/ijs.0.63675-0.

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The unidentified strains AS 2.0706T, preserved in the China General Microbiological Culture Collection Center (CGMCC), Academia Sinica, Beijing, China, and CBS 6904T, preserved in the Centraalbureau voor Schimmelcultures (CBS), Utrecht, The Netherlands, were shown to represent two novel ascomycetous yeast species of the genus Kazachstania by 18S rDNA, internal transcribed spacer (ITS) region (including 5·8S rDNA) and 26S rDNA D1/D2 domain sequence analysis and electrophoretic karyotype comparison. The names Kazachstania aquatica sp. nov. and Kazachstania solicola sp. nov. are proposed for strains AS 2.0706T and CBS 6904T, respectively. Phylogenetically, the two novel species are closely related to Kazachstania aerobia, Kazachstania servazzii and Kazachstania unispora.

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HOEVERS, J. D., et K. F. SNOWDEN. « Analysis of the ITS region and partial ssu and lsu rRNA genes ofBlastocystisandProteromonas lacertae ». Parasitology 131, n^o 2 (25 avril 2005) : 187–96. http://dx.doi.org/10.1017/s0031182005007596.

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Blastocystisis a common single-celled enteric parasite found in a large variety of hosts. Recent molecular analysis supports the concept that this eukaryotic organism is a stramenopile most closely related toProteromonas lacertae, a parasite of reptiles. In this study, the internal transcribed spacer region, partial small subunit rRNA and large subunit rRNA genes from 7Blastocystisisolates (5 human, 1 pig and 1 sheep), and aProteromonas lacertaeisolate were amplified by PCR, cloned and sequenced.Blastocystiswas found to be a typical eukaryote with both ITS1 and ITS2 regions present. Phylogenetic analysis based on the entire PCR amplicon revealed that theBlastocystisisolates did not segregate according to host or geographic origin. The highest sequence identities with the conservedBlastocystis5·8S rDNA sequence were with the stramenopilesFibrocapsa japonica,Chattonella marina,Cylindrotheca closteriumandHyphochytrium catenoides. The most parsimonious tree based on the 5·8S rDNA sequence fromP. lacertae, 11 other stramenopiles, 2 fungi, 3 algae and 3 alveolates showedBlastocystispositioned within the stramenopiles, withP. lacertaeas its closest relative. This work therefore supports the hypothesis thatBlastocystisis most closely related toP. lacertae, and that it should be regarded as an unusual stramenopile.

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Coêlho, Marcela, Maria Celeste Gonçalves Vidigal, Pedro Soares Vidigal Filho, Rodrigo Chimenez Franzon et Vanusa Silva Ramos Martins. « Genetic diversity of Colletotrichum lindemuthianum races based on ITS-rDNA regions ». Agronomy Science and Biotechnology 6 (27 novembre 2020) : 1–18. http://dx.doi.org/10.33158/asb.r112.v6.2020.

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Colletotrichum lindemuthianum is the causal agent of anthracnose in common bean. Favorable conditions for this disease might result in up to 100% yield losses. One of the main challenges for common bean producers and breeders still remains the management disease, since this pathogen exhibits a wide genetic variability probably due to its recombination sexual reproduction. The 5·8S gene and the flanking internal transcribed spacer regions (ITS1 and ITS2) of 40 different isolates of C. lindemuthianum collected in Brazil were amplified by PCR, and sequenced in order to determine genetic variability. The results revealed that 46.88% of SNPs were detected in the ITS1 region, while 53.12% of them were located in the ITS2 region. The genetic distance ranged from 0.000 to 0.169 between races. The greatest distance was observed between the races 10 and 73 with a value of 0.169, indicating a wide genetic variability between them. The phylogenetic tree was composed of three groups. Group I had five subgroups. Similar results were also observed through population structure analysis, which revealed the presence of three clusters. These results suggest that sequence analysis of ITS rDNA regions of C. lindemuthianum may be a valuable tool to identify this pathogen through design of specific primers.

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ZHU, X. Q., D. E. JACOBS, N. B. CHILTON, R. A. SANI, N. A. B. Y. CHENG et R. B. GASSER. « Molecular characterization of a Toxocara variant from cats in Kuala Lumpur, Malaysia ». Parasitology 117, n^o 2 (août 1998) : 155–64. http://dx.doi.org/10.1017/s0031182098002856.

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The ascaridoid nematode of cats from Kuala Lumpur, Malaysia, previously identified morphologically as Toxocara canis, was characterized using a molecular approach. The nuclear ribosomal DNA (rDNA) region spanning the first internal transcribed spacer (ITS-1), the 5·8S gene and the second internal transcribed spacer (ITS-2) was amplified and sequenced. The sequences for the parasite from Malaysian cats were compared with those for T. canis and T. cati. The sequence data showed that this taxon was genetically more similar to T. cati than to T. canis in the ITS-1, 5·8S and ITS-2. Differences in the ITS-1 and ITS-2 sequences between the taxa (9·4–26·1%) were markedly higher than variation between samples within T. canis and T. cati (0–2·9%). The sequence data demonstrate that the parasite from Malaysian cats is neither T. canis nor T. cati and indicate that it is a distinct species. Based on these data, PCR-linked restriction fragment length polymorphism (RFLP) and single-strand conformation polymorphism (SSCP) methods were employed for the unequivocal differentiation of the Toxocara variant from T. canis and T. cati. These methods should provide valuable tools for studying the life-cycle, transmission pattern(s) and zoonotic potential of this parasite.

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SAINI, AJAY, SREENIVASULU K. REDDY et NARENDRA JAWALI. « Intra-individual and intra-species heterogeneity in nuclear rDNA ITS region of Vigna species from subgenus Ceratotropis ». Genetics Research 90, n^o 4 (août 2008) : 299–316. http://dx.doi.org/10.1017/s001667230800983x.

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SummaryThe extent of intra-individual and intra-species heterogeneity in the nuclear rDNA internal transcribed spacer (ITS) was investigated among the ‘Asiatic Vigna’ species (subgenus Ceratotropis). High intra- and inter-individual ITS polymorphism was observed among Vigna radiata accessions, where multiple ITS length variants ranging from ~700 to ~770 bp were detected on PCR amplification. Subsequent analysis revealed that the variants are ‘heteroduplex ITS fragments’ generated during the PCR process. Analysis of ITS from wild and cultivated forms of ten Vigna species from subgenus Ceratotropis revealed substantial intra-species divergence in four species: Vigna umbellata, Vigna trilobata, V. radiata and Vigna minima. However, no other species analysed showed intra-individual ITS heterogeneity as observed in V. radiata. The results demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. radiata. Evidence indicates that intra-species hybridization and a slow ‘molecular drive’ are responsible for this phenomenon. Sequence analysis of 5·8S, ITS1 and ITS2 and secondary-structure analysis of ITS regions indicate that the ITS variants do not belong to pseudogenic rDNA repeat units. Further, reverse transcriptase-PCR (RT-PCR) analysis showed that rDNA repeat units harbouring certain intra-individual ITS variants were transcriptionally inactive, indicating the regulation of these loci by epigenetic gene silencing. The V. radiata ITS variants, when analysed together, did not cause any phylogenetic errors at the species level.

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Nisiotou, A. A., et G. R. Gibson. « Isolation of culturable yeasts from market wines and evaluation of the 5·8S-ITS rDNA sequence analysis for identification purposes ». Letters in Applied Microbiology 41, n^o 6 (15 novembre 2005) : 454–63. http://dx.doi.org/10.1111/j.1472-765x.2005.01795.x.

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Morgan, J. A. T., et D. Blair. « Nuclear rDNA ITS sequence variation in the trematode genus Echinostoma : an aid to establishing relationships within the 37-collar-spine group ». Parasitology 111, n^o 5 (décembre 1995) : 609–15. http://dx.doi.org/10.1017/s003118200007709x.

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SUMMARYThe taxonomic history of members of the 37-collar-spine group within the genus Echinostoma has been very confused. We obtained DNA sequence data from the nuclear rDNA ITS1, 5·8S and ITS2 of 7 nominal species belonging to this group, Echinostoma trivolvis (Cort, 1914), E. revolution (Frölich, 1802), E. caproni Richard, 1964, E. liei Jeyarasasingam et al. 1972, E. paraensei Lie & Basch, 1967, two African isolates, E. sp.I and E. sp.II, and of one 28-collar-spined echinostome, E. hortense (Asada, 1926). Five of the eight species were clearly distinguishable using ITS data. Sequences from the remaining three taxa, E. caproni, E. sp.II and E. liei were identical to one another and the group containing these taxa was distant from other 37-collar-spine species on a phylogenetic tree. E. trivolvis and E. paraensei form a second, but less distinct group within the 37-collar-spine group. The resolution obtained using DNA sequencing will assist in the current reclassification of the group. It also provides a model for future work on sibling species.

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Mattsson, Jan-Eric, et Mats Wedin. « Phylogeny of the Parmeliaceae–DNA Data Versus Morphological Data ». Lichenologist 30, n^o 4-5 (juillet 1998) : 463–72. http://dx.doi.org/10.1006/lich.1998.0143.

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AbstractIn order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.

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Lott, Timothy J., Randall J. Kuykendall et Errol Reiss. « Nucleotide sequence analysis of the 5·8S rDNA and adjacent ITS2 region ofCandida albicans and related species ». Yeast 9, n^o 11 (novembre 1993) : 1199–206. http://dx.doi.org/10.1002/yea.320091106.

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MORGAN, U. M., P. DEPLAZES, D. A. FORBES, F. SPANO, H. HERTZBERG, K. D. SARGENT, A. ELLIOT et R. C. A. THOMPSON. « Sequence and PCR–RFLP analysis of the internal transcribed spacers of the rDNA repeat unit in isolates of Cryptosporidium from different hosts ». Parasitology 118, n^o 1 (janvier 1999) : 49–58. http://dx.doi.org/10.1017/s0031182098003412.

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The Cryptosporidium ITS1, 5·8S and ITS2 rDNA regions from a number of Cryptosporidium isolates from different hosts and geographical areas were cloned and sequenced in order to investigate the extent of sequence heterogeneity between human and cattle-derived isolates from different geographical locations and also between isolates of Cryptosporidium from different hosts such as cats, pigs, mice and a koala. Calf-derived isolates from different continents were virtually identical as were human-derived isolates from the UK and Australia. Genetic differences between Cryptosporidium isolates were extensive and were in fact greater than the level of nucleotide divergence between Toxoplasma gondii and Neospora caninum rDNA sequences. Based on the sequence information derived from this study, PCR–RFLP of the ITS1 region was undertaken in order to directly amplify and genotype Cryptosporidium isolates from different hosts. This PCR–RFLP approach can now be used for molecular epidemiology studies, circumventing the need for costly sequencing and allowing a wider range of genetically different isolates to be examined.

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SMEJKALOVÁ, PAVLA, KLÁRA J. PETRŽELKOVÁ, KATEŘINA POMAJBÍKOVÁ, DAVID MODRÝ et IVAN ČEPIČKA. « Extensive diversity of intestinal trichomonads of non-human primates ». Parasitology 139, n^o 1 (26 septembre 2011) : 92–102. http://dx.doi.org/10.1017/s0031182011001624.

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SUMMARYDespite the fact that the non-human primates are our closest relatives and represent a species-rich mammalian group, little is known about their intestinal protistan parasites/commensals. Particularly, the intestinal trichomonads represent a neglected part of the fauna of the primate digestive system. We have established 30 trichomonad strains isolated from feces of 11 primate species kept in 3 Czech zoos and performed an analysis of their SSU rDNA and ITS1-5·8S rDNA-ITS2. Our results showed that intestinal trichomonads are rather common among non-human primates. Molecular phylogenetic analysis showed that the strains are unexpectedly diversified, belonging to 8 or 9 distinct species. Interestingly, the vast majority of the strains from non-human primates belonged to the genus Tetratrichomonas while no member of this genus has been found in the human intestine so far. In addition, hominoid and non-hominoid primates differed in their intestinal trichomonads. Our results suggest that captive primates possibly may be infected by intestinal trichomonads of other vertebrates such as pigs, cattle, birds, tortoises and lizards.

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MENDONÇA, M. B. A., N. S. NEHME, S. S. SANTOS, E. CUPOLILLO, N. VARGAS, A. JUNQUEIRA, R. D. NAIFF et al. « Two main clusters within Trypanosoma cruzi zymodeme 3 are defined by distinct regions of the ribosomal RNA cistron ». Parasitology 124, n^o 2 (février 2002) : 177–84. http://dx.doi.org/10.1017/s0031182001001172.

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Trypanosoma cruzi is currently classified into 2 major phylogenetic lineages, T. cruzi I and II, that correlate with the formerly described zymodeme 1 and 2, respectively. Another isoenzymic group (zymodeme 3–Z3) was also described. In this study, we analysed the genetic diversity among Z3 isolates of the Brazilian Amazon by restriction fragment length polymorphism of the intergenic transcribed spacers (ITSs) of the ribosomal RNA cistron and the size of the divergent domain D7 of the 24Sα rRNA gene. DNAs from 12 T. cruzi Z3 isolates obtained from humans (2), Panstrongylus geniculatus (1), and Rhodnius brethesi (9) were submitted to PCR amplification of the ITSs plus the 5·8S rDNA. The PCR products were digested with 4 distinct endonucleases and the profiles analysed by a numerical methodology. The phenetic dendrogram revealed a clear dichotomy in the Z3 group, defining 2 groups that were named Z3-A and Z3-B. Dimorphism was also found in the band sizes of the amplified D7 divergent domain of the 24Sα rDNA, which showed a perfect correlation with the ITSs clustering. The organization of the ribosomal cistron was investigated by Southern blotting and shown to be conserved in the genome of the 2 Z3 groups. This study shows that the rDNA cistron allows the definition of 2 distinct subclusters in Z3 isolates.

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Bowden, BF, JC Coll et IM Vasilescu. « Studies of Australian Soft Corals. XLVI. New Diterpenes From a Briareum Species (Anthozoa, Octocorallia, Gorgonacea) ». Australian Journal of Chemistry 42, n^o 10 (1989) : 1705. http://dx.doi.org/10.1071/ch9891705.

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The structures and relative stereochemistry of nine new briaran -based diterpenes from a Briareum species have been deduced from 2-D n.m.r. experiments at high field, and nuclear Overhauser effect experiments. The new compounds are (1R*2R*,3R*,5Z,7S*,8S*,9S*,10S*,11R*,-12S*,14S*,17R*)-2,3,14-triacetoxy-8,17:11,12-bisepoxy-9-hydroxybriar-5-en-18-one (5), (1R* ,2R* ,3R* ,5Z*,7S*,8S* ,9S*,10S*,11R*,12S*, 14S*, 17R*)-3,14-diacetoxy-2-butyryloxy-8,17:11,12-bisepoxy-9-hydroxybriar-5-en-18-one (6),(1R*,2R*,3R*,5Z,7S*,8S*,9S*,10S*,11R*,12S*,14S)-2,3,14-triacetoxy-11,12-epoxybriara-5,8(17)-dien-18-one(17),(1S*,2S*,4R*,5Z,7S*,8S*,9S*,10S*,2,4,9.12-tetraacetoxy-8,17-epoxy-11-hydroxybriara-5,13-dien-18-one (8),(1S*, 2S*,4R*, 5Z,7S*,8S*,9S*,10S*, 11S*, 12R*,13Z,17R*)-2,4,9-triacetoxy-8,17-epoxy-11,12-dihydroxybriara-5,13-dien-18-one (9), (1S *,2S*,4R*,5Z,7S*,8S*,9S*,10S*, 11S *,12R*,13Z,17R*)-2,4,9,12-tetraacetoxy-8,17-epoxy-11-hydroxybriara-5,13-dien-18-one(10),(1Si,2S*,5Z,7S',8S*,-9S*,10S*,11R*,12R*,13Z,17R*)-2,12-diacetoxy-8,17-epoxy-9-hydroxybriara-5,13-dien-18-one(ll), (1R*,2R*,3Si,5Z,7S* ,8S* ,9S* ,10S* ,11Z,14S*,17R*)-2,14-diacetoxy-3-butyryloxy-8,17-epoxy-9-hydroxybriara-5,11-dien-18-one (12) and (1R *,2R*,3S*,5Z,7S*,8S*,9S*,10S*,11Z,-14S',17R*)-2,3,14-triacetoxy-8,17-epoxy-9-hydroxybriara-5,11-dien-18-one (13). In addition to the nine new briaran derivatives, the same coral afforded two cladiellane derivatives (1R*,4R*,5S*,6R*,8R*,12R*,13R*,14R*)-cladiellane-4,8,12-triol (14) and its 4-acetoxy derivative (15). Aknowncembranoid diterpene (1R *,4R*,ZE,7E,l1E)-cembra-2,7,11-trien-4-ol(21) wasalso isolated together with an unprecedented perhydrophenanthrene-based diterpene (20): (1R *, 1aR*,4S*,4aR*,5aR*,8aR*)-4-isopropyl-l,8a-dimethyl-5-methylenetetradecahydrophenanthren-1-ol. The extraordinary biosynthetic ability of soft corals from the genus Briareum is once more revealed.

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Holmdahl, O. J. M., et J. G. Mattsson. « Rapid and sensitive identification ofNeospora caninumbyin vitroamplification of the internal transcribed spacer 1 ». Parasitology 112, n^o 2 (février 1996) : 177–82. http://dx.doi.org/10.1017/s0031182000084742.

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SummaryNeospora caninumandN. caninum-like organisms are cyst-forming coccidian parasites known to cause neuromuscular disorders in dogs and abortion in cattle. In this article we report on the use of the polymerase chain reaction (PCR) for the detection of DNA fromN. caninum. After determining the sequence of the internal transcribed spacer 1 (ITSl) ofN. caninumandToxoplasma gondii, and part of the sequences for & species ofSarcocystis, we designed a primer set for the amplification of a 279-base-pair fragment of ITSl fromN. caninum. The PCR system made possible the specific detection of 5N. caninumorganisms and no amplification was observed from any of the other cyst-forming coccidia tested, including the closely relatedT. gondii. Furthermore, we were also able to demonstrate the presence ofN. caninumin brain and lung tissue samples from experimentally infected mice. Our data also link the 5-8S rRNA gene forT. gondiiandN. caninumto the 16S-like rRNA gene, within the rDNA unit.

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Yao, M. C., S. G. Zhu et C. H. Yao. « Gene amplification in Tetrahymena thermophila : formation of extrachromosomal palindromic genes coding for rRNA ». Molecular and Cellular Biology 5, n^o 6 (juin 1985) : 1260–67. http://dx.doi.org/10.1128/mcb.5.6.1260-1267.1985.

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Tetrahymena thermophila contains in the macronucleus multiple copies of extrachromosomal palindromic genes coding for rRNA (rDNA) which are generated from a single chromosomal copy during development. In this study we isolated the chromosomal copy of rDNA and determined the structure and developmental fate of the sequence surrounding its 5' junction. The result indicates that specific chromosomal breakage occurs at or near the 5' junction of rDNA during development. The breakage event is associated with DNA elimination and telomeric sequence addition. Similar results were also found previously for the 3' junction of this gene. These results could explain how the extrachromosomal rDNA is first generated. Near both junctions of the chromosomal rDNA, a pair of 20-nucleotide repeats was found. These sequences might serve as signals for site-specific breakage. In addition, we found a pair of perfect inverted repeats at the 5' junction of this gene. The repeats are 42 nucleotides long and are separated by 28 nucleotides. The existence of this structure provides a simple explanation for the formation of the palindromic rDNA.

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Yao, M. C., S. G. Zhu et C. H. Yao. « Gene amplification in Tetrahymena thermophila : formation of extrachromosomal palindromic genes coding for rRNA. » Molecular and Cellular Biology 5, n^o 6 (juin 1985) : 1260–67. http://dx.doi.org/10.1128/mcb.5.6.1260.

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Tetrahymena thermophila contains in the macronucleus multiple copies of extrachromosomal palindromic genes coding for rRNA (rDNA) which are generated from a single chromosomal copy during development. In this study we isolated the chromosomal copy of rDNA and determined the structure and developmental fate of the sequence surrounding its 5' junction. The result indicates that specific chromosomal breakage occurs at or near the 5' junction of rDNA during development. The breakage event is associated with DNA elimination and telomeric sequence addition. Similar results were also found previously for the 3' junction of this gene. These results could explain how the extrachromosomal rDNA is first generated. Near both junctions of the chromosomal rDNA, a pair of 20-nucleotide repeats was found. These sequences might serve as signals for site-specific breakage. In addition, we found a pair of perfect inverted repeats at the 5' junction of this gene. The repeats are 42 nucleotides long and are separated by 28 nucleotides. The existence of this structure provides a simple explanation for the formation of the palindromic rDNA.

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VORONOVA, A. N., G. N. CHELOMINA, V. V. BESPROZVANNYKH et V. V. TKACH. « Genetic divergence of human pathogens Nanophyetus spp. (Trematoda : Troglotrematidae) on the opposite sides of the Pacific Rim ». Parasitology 144, n^o 5 (1 décembre 2016) : 601–12. http://dx.doi.org/10.1017/s0031182016002171.

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SUMMARYHuman and animal nanophyetiasis is caused by intestinal flukes belonging to the genus Nanophyetus distributed on both North American and Eurasian coasts of Northern Pacific. In spite of the wide geographical distribution and medical and veterinary importance of these flukes, the intra-generic taxonomy of Nanophyetus spp. remains unresolved. The two most widely distributed nominal species, Nanophyetus salmincola and Nanophyetus schikhobalowi, both parasitizing humans and carnivorous mammals, were described from North America and eastern Eurasia, respectively. However, due to their high morphological similarity their interrelationships remained unclear and taxonomic status unstable. In this study, we explored genetic diversity of Nanophyetus spp. from the Southern Russian Far East in comparison with that of samples from North America based on the sequence variation of the nuclear ribosomal gene family (18S, internal transcribed spacers, ITS1-5·8S-ITS2 and 28S). High levels of genetic divergence in each rDNA region (nucleotide substitutions, indels, alterations in the secondary structures of the ITS1 and ITS2 transcripts) as well as results of phylogenetic analysis provided strong support for the status of N. salmincola and N. schikhobalowi as independent species.

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Nogaroto, Viviane, Larissa Glugoski, Orlando Moreira Filho et Marcelo Ricardo Vicari. « rDNA 5S e rearranjos cromossômicos em Rineloricaria (Siluriformes : Loricariidae) ». Semina : Ciências Biológicas e da Saúde 38, n^o 1supl (16 février 2018) : 230. http://dx.doi.org/10.5433/1679-0367.2017v38n1suplp230.

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Dados citogenéticos de Loricariidae (Siluriformes) revelam uma extensiva variação de número diploide e plasticidade cromossômica no grupo. Nestes peixes, a localização in situ de sítios de rDNA 5S em regiões co-localizadas a sítios teloméricos intersticiais (ITS) evidenciaram o envolvimento de múltiplos clusters de rDNA 5S em rearranjos cromossômicos nas subfamílias Loricariinae e Ancistrinae. Vestígios de sequências (TTAGGG)n em sítios internos podem corresponder à locais de rearranjos cromossômicos e também são considerados como pontos quentes para quebras cromossômicas, os “sítios frágeis”. Este trabalho teve como objetivo a caracterização molecular de segmentos duplicados (SD) de rDNA 5S, discutir seu envolvimento como sítio frágil, além da sua localização in situ em duas populações de Rineloricaria latirostris. Rineloricaria latirostris (rio das Pedras) apresentou 2n = 46 cromossomos e 5 pares marcados com rDNA 5S, além de um par portador de ITS/rDNA 5S co-localizado, enquanto R. latirostris (rio Piumhi) apresentou 2n = 48 cromossomos, 2 pares com sítios para rDNA 5S e ausência de ITS. Fragmentos isolados de rDNA 5S de 222 pb mostraram identidade com rDNAs 5S de outras espécies, além disso um amplificado de 702 pb apresentou inserção de um segmento do TE hAT em sua sequência, clone rDNA 5S degenerado. Ensaios de dupla-FISH evidenciaram a co-localização de rDNA 5S/rDNA 5S degenerado, rDNA 5S/hAT e ITS/rDNA 5S em R. latirostris do rio das Pedras, enquanto na outra população estudada apenas marcações de rDNA 5S foram detectadas. Segundo nossos dados, a invasão do TE hAT no rDNA 5S gerou a região de SD rDNA 5S degenerado, a qual atuou como sítio frágil para quebras cromossômicas e fusão Robertsoniana (Rb) em Rineloricaria. Assim, a evidência do SD rDNA 5S em pontos de fusão Rb em outras espécies sugerem que esta região é um sítio frágil para genomas de Loricariidae e, poderia explicar parte dos eventos Robertsonianos neste grupo de peixes.APOIO: Fundação Araucária, CNPq.

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Shiragaki, Kumpei, Shuji Yokoi et Takahiro Tezuka. « Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region ». Horticulturae 6, n^o 4 (20 novembre 2020) : 87. http://dx.doi.org/10.3390/horticulturae6040087.

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The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.

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Müller, Wolfgang, Uwe Heinemann et Karin Berlin. « Cholecystokinin Activates CCKB-Receptor–Mediated Ca-Signaling in Hippocampal Astrocytes ». Journal of Neurophysiology 78, n^o 4 (1 octobre 1997) : 1997–2001. http://dx.doi.org/10.1152/jn.1997.78.4.1997.

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Müller, Wolfgang, Uwe Heinemann, and Karin Berlin. Cholecystokinin activates CCKB-receptor–mediated Ca-signaling in hippocampal astrocytes. J. Neurophysiol. 78: 1997–2001, 1997. Cholecystokinin-8S (CCK-8S) is the most abundant neuropeptide in the mammalian cortex and the limbic system; however, its physiological functions remained largely obscure. We studied effects of CCK on astrocytic Ca signaling, which has met considerable interest as a second messenger in astrocytic-neuronal signaling, by digital ratio-imaging of Fura-2/AM loaded rat and mouse hippocampal astrocytes in dissociated culture. Superfusion of CCK-8S (5–50 nM for 2 min) evoked repetitive Ca increases of several hundred nanomolar in a subpopulation of astrocytes. Mouse astrocytes appeared to be more responsive to CCK than rat cells with respect to the fraction of cells responding as well as to the amplitudes of Ca increases. The Ca responses persisted in the absence of extracellular Ca, indicating that release of Ca from intracellular stores is the primary source of these Ca increases. The CCK-8S–induced Ca increases were blocked by the CCKB receptor antagonist PD135158 (100 nM) but not by the CCKA antagonist lorglumide (100 nM). We surmise that astrocytes might be a major primary target for CCK in the CNS.

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Chang, Chin-Feng, Cheng-Hsu Yao, Shuh-Sen Young, Savitree Limtong, Rungluk Kaewwichian, Nantana Srisuk et Ching-Fu Lee. « Candida gosingica sp. nov., an anamorphic ascomycetous yeast closely related to Scheffersomyces spartinae ». International Journal of Systematic and Evolutionary Microbiology 61, n^o 3 (1 mars 2011) : 690–94. http://dx.doi.org/10.1099/ijs.0.020511-0.

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During surveys on yeast diversity in forest soils from Taiwan and Thailand, ten yeast strains isolated from different samples were found to have similar molecular and physiological characteristics. Sequence analysis of small subunit (SSU) rDNA, the D1/D2 domain of large subunit (LSU) rDNA and internal transcribed spacer (ITS)-5.8S rDNA demonstrated that these strains were closely related to Scheffersomyces spartinae. The novel strains could be differentiated from S. spartinae by a 0.9 % sequence divergence (5 substitutions, 0 gaps) in the D1/D2 domain of LSU rDNA, a 1.5 % divergence (8 substitutions, 0 gaps) in the ITS-5.8S rDNA and a 0.7 % divergence (12 substitutions, 2 gaps) in the SSU rDNA. The novel strains also showed specific patterns of electrophoretic karyotypes that differed from that of S. spartinae. Therefore, a novel yeast species, Candida gosingica sp. nov., is proposed to accommodate these strains. The type strain SJ7S11T (=BCRC 23194T=CBS 11433T) was assigned and deposited in the Bioresource Collection and Research Center (BCRC), Food Industry Development and Research Institute, Hsinchu, Taiwan, and Centraalbureau voor Schimmelcultures (CBS), Utrecht, The Netherlands.

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Purnomo, Purnomo, Budi Setiadi Daryono et Hironobu Shiwachi. « Phylogenetic Relationship of Indonesian Water Yam (Dioscorea alata L.) Cultivars Based on DNA Marker Using ITS-rDNA Analysis ». Journal of Agricultural Science 9, n^o 2 (11 janvier 2017) : 154. http://dx.doi.org/10.5539/jas.v9n2p154.

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Research on genetic diversity and intra-species classification of Indonesian Dioscorea alata L. based on morphological characters has been done, and the result shows that there are 4 sub-groups of green cultivars group, and 5 sub-groups of purplish-red cultivars group. The objectives of this study are to determine the phylogenetic relationship cultivars of D. alata Indonesia compared to D. bulbifera as nearest species as well as 3 cultivars from GenBank. The young leaves of 18 water yam cultivar accessions were collected from Java, Madura, South Sumatera, South Kalimantan, Centre Celebes (Sulawesi), Ternate, West Papua, and Nusa Tenggara islands of Indonesia. DNA Isolation was conducted using Phytopure reagent. DNA amplification was conducted using thermocycler, predenaturation at 95 oC 5 minutes, denaturation at 95 oC 1 minutes, annealing at 60 oC 3 minutes, and elongation at 72 oC 2 minutes along with 30 cycles. The PCR products were electrophoresed in 1.5% agarose and visualized under UV transiluminator. Fifty-five µl of PCR products with positive targeted band between 700-800 bp were sent to 1st Base Singapore for purification and sequencing of 18S, ITS-1, 5.8S, ITS-2, and 28S rDNA. The DNA sequences were compared and aligned by BioEdit program (version 7.0.5.2) and MEGA programs. Comparison of entire sequences of the tested samples were aligned by software ClustalW (version 1.83). Phylogenetic trees were based on hierarchical clustering of the alignments of 18S, ITS-1, 5.8S, ITS-2, and 28S rDNA and produced by Neigbor-Joining using MEGA 5 software of the bootstrap values (1000 replicates). The study result shows that D. alata cultivars have high genetic variability on ITS-1, 5.8S, and ITS-2 rDNA region. Groups of green and purplish red cultivars formed based on morphological characters are not formed based on ITS-rDNA markers. Sub-groups were formed based on ITS-rDNA molecular markers derived from both the green and purplish-red cultivar groups. This result revealed that two cultivar groups are not similar with RAPD and morphological characters.

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Sha, Li-na, Rui-wu Yang, Xing Fan, Xiao-li Wang et Yong-hong Zhou. « Phylogenetic Analysis of Leymus (Poaceae : Triticeae) Inferred from Nuclear rDNA ITS Sequences ». Biochemical Genetics 46, n^o 9-10 (15 août 2008) : 605–19. http://dx.doi.org/10.1007/s10528-008-9175-5.

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Maccarone, L. D., M. J. Barbetti, K. Sivasithamparam et R. A. C. Jones. « Molecular Genetic Characterization of Olpidium virulentus Isolates Associated with Big-Vein Diseased Lettuce Plants ». Plant Disease 94, n^o 5 (mai 2010) : 563–69. http://dx.doi.org/10.1094/pdis-94-5-0563.

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Lettuce plants showing symptoms of lettuce big-vein disease were collected from fields in the Perth Metropolitan region of southwest Australia. When root extracts from each plant were tested by polymerase chain reaction (PCR) using primers specific to the rDNA internal transcribed spacer (ITS) region of Olpidium brassicae and O. virulentus, only O. virulentus was detected in each of them. The nucleotide sequences of the complete rDNA ITS regions of isolates from five of the root samples and 10 isolates of O. virulentus from Europe and Japan showed 97.9 to 100% identities. However, with the six O. brassicae isolates, their identities were only 76.9 to 79.4%. On phylogenetic analysis of the complete rDNA-ITS region sequences of the five Australian isolates and 10 others, the Australian isolates fitted within two clades of O. virulentus (I and II), and within clade I into two of its four subclades (Ia and Id). Japanese isolates had greatest sequence diversity fitting into both clades and into all of clade I subclades except Ib, while European isolates were restricted to subclades Ib and Id. When the partial rDNA-ITS region sequences of two additional southwest Australian isolates, four from Europe, and four from the Americas were included in the analyses, the Australian isolates were within O. virulentus subclades Ia and Id, the European isolates within subclade Ic, and the American isolates within subclades Ia and Ib. These findings suggest that there may have been at least three separate introductions of O. virulentus into the isolated Australian continent since plant cultivation was introduced following its colonization by Europeans. They also have implications regarding numbers of different introductions to other isolated regions. Lettuce big-vein associated virus and Mirafiori lettuce big-vein virus were both detected when symptomatic lettuce leaf tissue samples corresponding to the root samples from southwest Australia were tested using virus-specific primers in reverse transcription–PCR, so presence of both viruses was associated with O. virulentus occurrence.

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Yuan, Hai-Sheng, et Xian-Zhen Wan. « Morphological and ITS rDNA-based phylogenetic identification of two new species in Tinctoporellus ». Mycological Progress 11, n^o 4 (6 mars 2012) : 947–52. http://dx.doi.org/10.1007/s11557-012-0810-5.

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CALLEJÓN, ROCÍO, MANUEL DE ROJAS, CARLOS FELIÚ, FRANCISCO BALAO, ÁNGELA MARRUGAL, HEIKKI HENTTONEN, DIEGO GUEVARA et CRISTINA CUTILLAS. « Phylogeography of Trichuris populations isolated from different Cricetidae rodents ». Parasitology 139, n^o 13 (20 août 2012) : 1795–812. http://dx.doi.org/10.1017/s0031182012001114.

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SUMMARYThe phylogeography of Trichuris populations (Nematoda) collected from Cricetidae rodents (Muroidea) from different geographical regions was studied. Ribosomal DNA (Internal Transcribed Spacers 1 and 2, and mitochondrial DNA (cytochrome c- oxidase subunit 1 partial gene) have been used as molecular markers. The nuclear internal transcribed spacers (ITSs) 1 and 2 showed 2 clear-cut geographical and genetic lineages: one of the Nearctic region (Oregon), although the second was widespread throughout the Palaearctic region and appeared as a star-like structure in the minimum spanning network. The mitochondrial results revealed that T. arvicolae populations from the Palaearctic region were separated into 3 clear-cut geographical and genetic lineages: populations from Northern Europe, populations from Southern (Spain) and Eastern Europe (Croatia, Belarus, Kazahstan), and populations from Italy and France (Eastern Pyrénean Mountains). Phylogenetic analysis obtained on the basis of ITS1-5·8S-ITS2 rDNA sequences did not show a differential geographical structure; however, these markers suggest a new Trichuris species parasitizing Chionomys roberti and Cricetulus barabensis. The mitochondrial results revealed that Trichuris populations from arvicolinae rodents show signals of a post-glacial northward population expansion starting from the Pyrenees and Italy. Apparently, the Pyrenees and the Alps were not barriers to the dispersal of Trichuris populations.

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FELLEISEN, R. S. J. « Comparative sequence analysis of 5·8S rRNA genes and internal transcribed spacer (ITS) regions of trichomonadid protozoa ». Parasitology 115, n^o 2 (août 1997) : 111–19. http://dx.doi.org/10.1017/s0031182097001212.

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The taxonomic situation in the genus Tritrichomonas is the subject of controversial discussion: potentially T. foetus and T. suis, the tritrichomonads from cattle and swine, respectively, could belong to the same species. In order to shed some light on this question, a molecular biological analysis was performed. The 5·8S rRNA gene and the flanking internal transcribed spacer regions (ITS1 and ITS2) of 12 different isolates of 3 Tritrichomonas species T. foetus, T. suis and T. mobilensis were enzymatically amplified by PCR and subcloned. Also, the corresponding regions of the trichomonads Trichomonas vaginalis, T. tenax, T. gallinae and Pentatrichomonas hominis were included in this study. Sequence analysis of cloned fragments was used to compare the parasite isolates. The genus Tritrichomonas exhibited an extremely high degree of homogeneity. All T. foetus and T. suis isolates had identical sequences, and only 1 substitution was found in the ITS2 region of T. mobilensis. In contrast, the genus Trichomonas shared more diversity. The results obtained in this study support a possible future revision of the taxonomic classification of tritrichomonads.

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Sánchez-Gorostiaga, Alicia, Carlos López-Estraño, Dora B. Krimer, Jorge B. Schvartzman et Pablo Hernández. « Transcription Termination Factor reb1p Causes Two Replication Fork Barriers at Its Cognate Sites in Fission Yeast Ribosomal DNA In Vivo ». Molecular and Cellular Biology 24, n^o 1 (1 janvier 2004) : 398–406. http://dx.doi.org/10.1128/mcb.24.1.398-406.2004.

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ABSTRACT Polar replication fork barriers (RFBs) near the 3′ end of the rRNA transcriptional unit are a conserved feature of ribosomal DNA (rDNA) replication in eukaryotes. In the mouse, in vivo studies indicate that the cis-acting Sal boxes required for rRNA transcription termination are also involved in replication fork blockage. On the contrary, in the budding yeast Saccharomyces cerevisiae, the rRNA transcription termination factors are not required for RFBs. Here we characterized the rDNA RFBs in the fission yeast Schizosaccharomyces pombe. S. pombe rDNA contains three closely spaced polar replication barriers named RFB1, RFB2, and RFB3 in the 3′ to 5′ order. The transcription termination protein reb1 and its two binding sites, present at the 3′ end of the coding region, were required for fork arrest at RFB2 and RFB3 in vivo. On the other hand, fork arrest at the strongest RFB1 barrier was independent of the above transcription termination factors. Therefore, RFB2 and RFB3 resemble the barriers present in the mouse rDNA, whereas RFB1 is similar to the budding yeast RFBs. These results suggest that during evolution, cis- and trans-acting factors required for rRNA transcription termination became involved in replication fork blockage also. S. pombe is suggested to be a transitional species in which both mechanisms coexist.

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Pfister et LoBuglio. « Lost and found : the Bermudan Donadinia seaveri found in North America, with comments on its juniper associates ». Mycologia 110, n^o 1 (2 janvier 2018) : 215–21. http://dx.doi.org/10.1080/00275514.2017.1409052.

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Collections of a species referred to Sarcosomataceae (Pezizomycetes) from eastern North America were studied both morphologically and using nuc rDNA internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2 = ITS) and approximately 800 bp from the 5′ region of the nuc 28S rDNA (28S) to construct a phylogeny. The analyses indicate that these collections are Donadinia seaveri, a species previously known only from Bermuda. Because the associated tree, Juniperus bermudiana, has declined as a result of insect attack, it was thought that D. seaveri might be extinct. This work indicates that it is not extinct but is present in eastern North America. The species is described, new distributional records are given, and its association with the genus Juniperus is discussed.

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Appels, R., L. B. Moran et J. P. Gustafson. « The structure of DNA from the rye (Secale cereale) NOR R1 locus and its behaviour in wheat backgrounds ». Canadian Journal of Genetics and Cytology 28, n^o 5 (1 octobre 1986) : 673–85. http://dx.doi.org/10.1139/g86-097.

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The nucleotide sequence of a 4.5-kilobase (kb) segment of rye DNA (in the clone pScR4) containing the major spacer region of ribosomal DNA, 0.25 kb of the 5′ end of the 18S gene and approximately 1.2 kb of the 3′ end of the 26S gene is presented. The 5′ end of the 18S gene, and most of the 3′ end of the 26S gene, could be readily defined by comparisons with previously published sequences. The major spacer region was dominated by the presence of 10 repeating units, with a basic length of 134 base pairs (bp), which showed sequence variability in that deletions of sections of the sequence as well as base-pair changes were common. A portion of the sequence which was common to almost all the spacer repeats and is also found in the corresponding wheat spacer repeats (in pTa250), with only two mismatches (using a consensus sequence of the rye spacer repeats as a comparison), is GCGACATGGAAAACCGGGCAAAACCACGTAC. The occurrence of this conserved sequence between more divergent sequences in both wheat and rye suggests that it may be important in forming the pretranscription complex involving RNA polymerase I and other protein cofactors. Probes were isolated from the spacer region to preferentially assay the rye rDNA in wheat backgrounds. In situ hybridization studies revealed that when 1R was the only NOR-containing chromosome present the rDNA was in a dispersed state. This dispersed state correlates with nucleolus formation and presumably with rDNA transcription. In the presence of chromosomes 1B and (or) 6B of wheat (these chromosomes carry NOR loci) the dispersed state of rye rDNA was generally suppressed, but not completely, suggesting that 1R retains some potential for activity.Key words: rye, NOR R1 locus, nucleotide sequence, transcription.

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Casanova, A. « tRNA genes were found in Piscirickettsia salmonis 16S–23S rDNA spacer region (ITS) ». FEMS Microbiology Letters 197, n^o 1 (1 avril 2001) : 19–22. http://dx.doi.org/10.1016/s0378-1097(01)00029-5.

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He, Haohua, Liang Xu, Xiaosong Peng, Guangsheng Yang, Changlan Zhu, Zunwen Liu et Guoyou Ye. « Molecular tagging of the male fertility restorer gene for the 501-8S cytoplasmic male sterility in rapeseed (Brassica napus L.) ». Australian Journal of Agricultural Research 58, n^o 8 (2007) : 753. http://dx.doi.org/10.1071/ar06369.

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The cytoplasmic male sterile (CMS) system has been successfully used to explore heterosis in rapeseed (Brassica napus L.). A newly developed male sterile line (501-8S) was characterised for its male fertility response to temperature and photoperiod, and the inheritance of fertility restoration. Segregation analysis using F1 and F2, BC1, and F3 populations of the crosses between the 501-8S and fertile lines of B. napus revealed that fertility restoration was conferred by a dominant nuclear gene (Rf). The F2 population of the cross 501-8S × Yuyou1 was used as a mapping population to map the Rf gene. A combination of bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) methodology was used to identify putative markers linked to the Rf gene. Twenty-nine of the 1280 primer combinations tested revealed polymorphism between the 2 extreme bulks. Further testing of these primer combinations in individual plants identified 5 AFLP markers tightly linked to the Rf gene with a map distance of less than 5.0 cM. All 5 markers were on one side of the restoration gene in the coupling phase. The closest marker, EA02MG03-260, is only 0.4 cM from the Rf gene. The EA02MG03-260 marker was converted to a dominant sequence characterised amplified region (SCAR) marker (SCARE2M3-214). Amplification using this locus-specific primer generated specific bands with male fertile plants when tested using the mapping population. Specific amplification of SCARE2M3-214 was also detected in all 3 male sterile plants and their F1 hybrids, with 5 restorer lines used for verification. Thus, SCARE2M3-214 will be very useful for the development of new restorer lines by the transfer of the Rf gene into other breeding lines. It can also be used for isolating the Rf gene by means of map-based cloning.

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ZHAO, YA-NAN, SHI-LIANG LIU, KAREN K. NAKASONE et SHUANG-HUI HE. « Coniophoropsis bambusicola sp. nov. (Coniophoraceae, Basidiomycota) from southern Vietnam ». Phytotaxa 360, n^o 2 (13 juillet 2018) : 153. http://dx.doi.org/10.11646/phytotaxa.360.2.7.

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Coniophoropsis bambusicola sp. nov. is described and illustrated from southern Vietnam based on morphological and molecular evidence. It is the second species in the genus, and differs from the type, C. obscura, by having much smaller basidiospores measuring 5.5–7 × 4–5 µm and growing on the culms of dead bamboo. The phylogenetic analyses based on a combined dataset of nuc rDNA ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S) sequences of Boletales show that Coniophoropsis bambusicola is closely related to Coniophora.

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Zhang, Daming, et Tao Sang. « Chromosomal structural rearrangement of Paeonia brownii and P. californica revealed by fluorescence in situ hybridization ». Genome 41, n^o 6 (1 décembre 1998) : 848–53. http://dx.doi.org/10.1139/g98-079.

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Chromosomal structural rearrangement in Paeonia brownii and P. californica (2n = 10) was studied by in situ hybridization using 18S rDNA probes. Six major rDNA sites were detected in mitotic cells of P. californica; six major and two minor rDNA sites were found in P. brownii. Two cytotypes (A and B), with different chromosomal morphology and (or) rDNA locations, were observed in the population of P. californica. Cytotype A, with rDNA sites only on the short arms of chromosomes, was considered to be the normal cytotype. Both translocation and pericentric inversion may have occurred to give rise to cytotype B, in which one homolog of chromosome 4 has rDNA sites on both arms while its homolog has no rDNA sites; one homolog of chromosome 3 has a rDNA site on the long arm. Two rearranged cytotypes, C and D, were observed in the population of P. brownii. Given that the normal cytotype of P. brownii is most likely to have six major rDNA sites on the short arms of chromosomes 3, 4, and 5, and two minor sites on the short arms of chromosome 2, cytotype C may have resulted from a translocation between the short arm of one homolog of chromosome 2 and the long arm of one homolog of chromosome 4, and cytotype D may have resulted from a translocation between the short arm of one homolog of chromosome 3 and the long arm of one homolog of chromosome 4. These results supported previous observations, based on meiotic configurations, that chromosomal structural rearrangement occurred frequently in P. brownii and P. californica.Key words: chromosomal structural rearrangement, in situ hybridization, rDNA, translocation, pericentric inversion, Paeonia.

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Cao, Shunan, Fang Zhang, Hongyuan Zheng, Fang Peng, Chuanpeng Liu et Qiming Zhou. « Coccomyxa greatwallensis sp. nov. (Trebouxiophyceae, Chlorophyta), a lichen epiphytic alga from Fildes Peninsula, Antarctica ». PhytoKeys 110 (2 novembre 2018) : 39–50. http://dx.doi.org/10.3897/phytokeys.110.26961.

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A single-celled green alga Coccomyxagreatwallensis Shunan Cao & Qiming Zhou, sp. nov., isolated from a specimen of Antarctic lichen Psoromahypnorum (Vahl) Gray, is described and illustrated based on a comprehensive investigation of morphology, ultrastructure, ecology and phylogeny. The cells of C.greatwallensis are ovoid to long ellipsoidal and measured 3–5 µm × 6–12 µm. The new species has distinct ITS rDNA and SSU rDNA sequences and differs from the phylogenetic closely related species C.antarctica, C.arvernensis and C.viridis in cell size, distribution and habitat.

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Chakrabarti, Rajarshi, Sulagna Sanyal, Amit Ghosh, Kaushik Bhar, Chandrima Das et Anirban Siddhanta. « Phosphatidylinositol-4-phosphate 5-Kinase 1α Modulates Ribosomal RNA Gene Silencing through Its Interaction with Histone H3 Lysine 9 Trimethylation and Heterochromatin Protein HP1-α ». Journal of Biological Chemistry 290, n^o 34 (7 juillet 2015) : 20893–903. http://dx.doi.org/10.1074/jbc.m114.633727.

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Phosphoinositide signaling has been implicated in the regulation of numerous cellular processes including cytoskeletal dynamics, cellular motility, vesicle trafficking, and gene transcription. Studies have also shown that nuclear phosphoinositide(s) regulates processes such as mRNA export, cell cycle progression, gene transcription, and DNA repair. We have shown previously that the nuclear form of phosphatidylinositol-4-phosphate 5-kinase 1α (PIP5K), the enzyme responsible for phosphatidylinositol 4,5-bisphosphate synthesis, is modified by small ubiquitin-like modifier (SUMO)-1. In this study, we have shown that due to the site-specific Lys to Ala mutations of PIP5K at Lys-244 and Lys-490, it is unable to localize in the nucleus and nucleolus, respectively. Furthermore, by using chromatin immunoprecipitation assays, we have observed that PIP5K associates with the chromatin silencing complex constituted of H3K9me3 and heterochromatin protein 1α at multiple ribosomal DNA (rDNA) loci. These interactions followed a definite cyclical pattern of occupancy (mostly G1) and release from the rDNA loci (G1/S) throughout the cell cycle. Moreover, the immunoprecipitation results clearly demonstrate that PIP5K SUMOylated at Lys-490 interacts with components of the chromatin silencing machinery, H3K9me3 and heterochromatin protein 1α. However, PIP5K does not interact with the gene activation signature protein H3K4me3. This study, for the first time, demonstrates that PIP5K, an enzyme actively associated with lipid modification pathway, has additional roles in rDNA silencing.

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Reimer, J. D., K. Takishita, S. Ono et T. Maruyama. « Diversity and evolution in the zoanthid genus Palythoa (Cnidaria : Hexacorallia) based on nuclear ITS-rDNA ». Coral Reefs 26, n^o 2 (12 avril 2007) : 399–410. http://dx.doi.org/10.1007/s00338-007-0210-5.

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Zhuo, Lang, S. L. Sajdak et R. B. Phillips. « Minimal intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA of lake trout (Salvelinus namaycush) ». Genome 37, n^o 4 (1 août 1994) : 664–71. http://dx.doi.org/10.1139/g94-094.

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Intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA (rDNA) in lake trout was examined by restriction mapping and sequencing of these regions amplified by the polymerase chain reaction. The length of the first internal transcribed spacer region (ITS-1) was 566 bases and the second internal transcribed spacer region (ITS-2) was 368 bases in lake trout. When the 1.4-kb region including the ITS-1, the 5.8S coding region, and the ITS-2 was amplified from 12 individuals from four populations and digested with eight different enzymes only one intraindividual polymorphism was found that occurred in each population. When the amplified ITS-1 region was sequenced from an additional 10 individuals from five populations, no interindividual variation was found in the sequence. A 6-kb portion of the rDNA repeat unit including 1.6 kb of the 18S coding region, the 5′ external spacer region (5′ ETS), and part of the adjacent intergenic spacer was cloned and a restriction map was prepared for these regions in lake trout. No intraspecific variation was found in the region adjacent to the 18S rDNA, which includes the 5′ ETS, although intraspecific and intraindividual length variation was found in the intergenic spacer region 3–6 kb from the 18S. Sequencing of a 609-b segment of the 5′ ETS adjacent to the 18S coding region revealed the presence of two 41-b repeats. The 198-b sequence between the repeats had some similarity to the 18S coding region of other fishes. Primers were designed for amplification of 559 b of the 5′ ETS using the polymerase chain reaction. No intraspecific variation in this region in lake trout was found when the DNA amplified from this region in 12 individuals from four populations was digested with eight restriction enzymes.Key words: ribosomal DNA, internal transcribed spacer regions, 5′ external spacer region, transcribed spacer, lake trout.

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Guo, Zhansheng, Zhen Wang et Xuguang Hou. « Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria ». Fishes 6, n^o 3 (17 septembre 2021) : 42. http://dx.doi.org/10.3390/fishes6030042.

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Ruditapes philippinarum and Mercenaria mercenaria are economically important bivalve species. The complete ribosomal DNA (rDNA) unit sequences of R. philippinarum and M. mercenaria, with as-sembled rDNA unit lengths of 12,910 and 12,100 bp, respectively, were obtained in this study for the first time. The rDNA unit structural organisation was similar to that in other eukaryotes, in-cluding the following elements in order: 18S rRNA-internal transcribed spacer 1 (ITS1); 5.8S rRNA-ITS2-28S rRNA-intergenic spacer (IGS) (3′ external transcribed spacer (ETS); non-transcribed spacer (NTS)-5′ ETS). The genetic differences between R. philippinarum and M. mercenaria were mainly attributable to non-coding regions (ITS1, ITS2 and IGS), especially the IGS region. The boundaries of putative 3′ ETS, NTS and 5′ ETS were confirmed. Seven and three sub-repeat fragments were found in R. philippinarum and M. mercenaria, respectively. These frag-ments ranged from 4 to 154 bp in length, and were located at the NTS and 5′ ETS regions. Five and six cytosine–guanine (CpG) islands were detected in R. philippinarum and M. mercenaria, respec-tively, and these covered 85.58% and 79.29% of the entire IGS sequence, respectively. The phylo-genetic tree was constructed based on Veneridae ITS and 18S rRNA sequences using the maxi-mum likelihood (ML) method. The ML tree based on ITS revealed that species within the same genus clearly clustered together with relatively high supporting values, and all the genera were recovered as monophyletic. The phylogenetic analyses using 18S rRNA provided a weaker phy-logenetic signal than ITS.

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Mahelka, Václav, Karol Krak, David Kopecký, Judith Fehrer, Jan Šafář, Jan Bartoš, Roman Hobza, Nicolas Blavet et Frank R. Blattner. « Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages ». Proceedings of the National Academy of Sciences 114, n^o 7 (30 janvier 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 current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.

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BURGER, MIEKE A. A., et ROBERT D. ADLARD. « Phenotypic variation in a significant spore character in Kudoa (Myxosporea : Multivalvulida) species infecting brain tissue ». Parasitology 137, n^o 12 (14 juin 2010) : 1759–72. http://dx.doi.org/10.1017/s0031182010000673.

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SUMMARYSome Kudoa species display variations in the number of polar capsules in spores within an individual pseudocyst. Nonetheless, there is usually a dominant morphotype which forms a significant element of diagnosis. In 2007, a Kudoa isolate from whiting (spores with 5 (dominant) or 6 (minor) polar capsules) was characterized by Burger et al. (2007) as being 100% identical in SSU rDNA to Kudoa yasunagai (spores with 7 polar capsules) from a halibut, despite its obvious morphological differences. The authors hypothesized that either SSU rDNA had reached its level of resolution or that the genetic identity revealed conspecificity. To further investigate these hypotheses, SSU and LSU rDNA sequence data were coupled with principal components, correlation, and regression analyses of morphometric data from different kudoid isolates that infect brain tissue to determine the relationships between spore morphotypes and different kudoid isolates. The trends in morphometrics between the spores of particular isolates were so similar that it was concluded that the molecular results did indicate conspecificity rather than SSU reaching its level of resolution. This phenotypic influence on a significant diagnostic character within the Kudoidae has a major impact on the diagnosis of this, and potentially other, pathogenic species.

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Duttweiler, K. B., G. Y. Sun, J. C. Batzer, T. C. Harrington et M. L. Gleason. « An RFLP-Based Technique for Identifying Fungi in the Sooty Blotch and Flyspeck Complex on Apple ». Plant Disease 92, n^o 5 (mai 2008) : 794–99. http://dx.doi.org/10.1094/pdis-92-5-0794.

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A restriction fragment length polymorphism (RFLP)-based technique was developed to identify members of the sooty blotch and flyspeck (SBFS) disease complex on apple because these fungi are difficult to identify using agar-plate isolation and morphological description. The method includes polymerase chain reaction (PCR) amplification of the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) using a fungal-specific forward primer (ITS1-F) and an SBFS-specific reverse primer (Myc1-R), followed by digestion of the PCR product by the HaeIII restriction enzyme. When applied to previously identified isolates of 24 SBFS-causing species in nine genera, the PCR-RFLP assay produced 14 unique banding patterns. Different genera never shared the same RFLP pattern. To evaluate performance in vivo, the technique was applied to DNA extracted directly from SBFS colonies on apple fruit from three Iowa orchards. The primers amplified the rDNA of only SBFS fungi, with the exception of a Cladosporium sp.; however, its RFLP banding pattern was distinct from those of SBFS fungi. The majority (60%) of SBFS colonies in the in vivo trial were identified to genus by RFLP analysis. The PCR-RFLP assay greatly streamlined the identification process by minimizing the need for culturing, indicating its value as a tool for field studies of the SBFS complex.

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Gautam, Ragini, S. K. Singh et Vinay Sharma. « RAPD and Nuclear rDNA ITS Polymorphism Within Macrophomina phaseolina Isolated from Arid Legumes of Western Rajasthan ». Proceedings of the National Academy of Sciences, India Section B : Biological Sciences 84, n^o 1 (9 juillet 2013) : 171–81. http://dx.doi.org/10.1007/s40011-013-0207-5.

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Coll, JC, BW Skelton, AH White et AD Wright. « Tropical Marine Algae. V. The Structure Determination of Two Novel Sesquiterpenes From the Red Alga Laurencia tenera (Rhodophyceae, Ceramiales, Rhodomelaceae) ». Australian Journal of Chemistry 42, n^o 10 (1989) : 1695. http://dx.doi.org/10.1071/ch9891695.

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Laurencia tenera has been shown to contain two novel sesquiterpenes. The structure of the less abundant metabolite (3) was determined by single-crystal X-ray diffraction as (1S,2R,4S,5R,6R,8S,9R)-4,8-dibromo-2,5,6,9-tetramethyltricyclo[7.2.0.01.6] undecane-3-one.‡ The more abundant, but less stable metabolite (4) was investigated by extensive high-field N.M.R. spectroscopy. Its structure is proposed as (1S*,2R*,4R*,5R*,6R*,8R*)-4-bromo-2,5,6-trimethyl-11-methylenetricyclo[6.2.1.01.6]undecan-3-one.§ The sesquiterpene (3) is isomeric with the known metabolite perforatone (5).

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VELAVAN, T. P., H. SCHULENBURG et N. K. MICHIELS. « Detection of multiple infections by Monocystis strains in a single earthworm host using ribosomal internal transcribed spacer sequence variation ». Parasitology 137, n^o 1 (20 août 2009) : 45–51. http://dx.doi.org/10.1017/s0031182009990722.

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SUMMARYMonocystis sp. are sporocyst-forming apicomplexan parasites common in seminal vesicles of the earthworm Lumbricus terrestris where they may account for temporary castration. This study describes the internal transcribed spacer (ITS) region of the ribosomal cistron of Monocystis sp. This region, including ITS-1, the 5·8S ribosomal RNA gene, and ITS-2, was PCR amplified, cloned, and sequenced for Monocystis sp. isolated from the seminal vesicles of several wild-caught L. terrestris. Our analysis revealed substantial polymorphisms, also within single host organisms, indicating intra-host diversity of parasites. These genetic markers are the first that allow distinction of Monocystis sp. genotypes, opening new avenues for the study of parasite diversity within and between hosts.

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BURGER, M. A. A., T. H. CRIBB et R. D. ADLARD. « Patterns of relatedness in the Kudoidae with descriptions of Kudoa chaetodoni n. sp. and K. lethrini n. sp. (Myxosporea : Multivalvulida) ». Parasitology 134, n^o 5 (mai 2006) : 669–81. http://dx.doi.org/10.1017/s0031182006001995.

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SUMMARYTwo morphologically novel Kudoa species are characterized from brain tissue of fish, Kudoa chaetodoni n. sp. from Chaetodon unimaculatus (Chaetodontidae) and Kudoa lethrini n. sp. from Gymnocranius audleyi and Lethrinus harak (Lethrinidae). Additionally we characterized a 5-spore valve (SV) Kudoa species from the brain of Sillago ciliata (Sillaginidae). Intriguingly, its 18S rDNA sequence was identical to that of the 7 SV Kudoa yasunagai extracted from the brain of a paralichthyid halibut in Japan. These 2 species may either prove to be con-specific, even though morphology and distribution differ, or demonstrate the limit of specific resolution in the small subunit rDNA gene region. Small subunit rDNA sequences from these new species were used in molecular phylogenetic analyses of kudoids to examine congruence of phylogeny with tissue tropism, geographical distribution, and host specificity. There was significant correlation between tissue tropism in the form of well-supported brain and heart-infecting clades. Host specificity and geographical distribution showed some correlations with genotype.

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Yakoubou, Sabarimatou, Dong Xu et Jean-Charles Côté. « Phylogeny of the Order Bacillales inferred from 3’ 16S rDNA and 5’ 16S-23S ITS nucleotide sequences ». Natural Science 02, n^o 09 (2010) : 990–97. http://dx.doi.org/10.4236/ns.2010.29121.

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Giaretta, Diorvania Ribeiro, Amauri Bogo, Cileide Maria Medeiros Coelho, Altamir Frederico Guidolin, Adriana Cibele de Mesquita Dantas et Eliane Aparecida Gomes. « ITS-rDNA phylogeny of Colletotrichum spp. causal agent of apple Glomerella leaf spot ». Ciência Rural 40, n^o 4 (9 avril 2010) : 806–12. http://dx.doi.org/10.1590/s0103-84782010005000051.

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Several diseases have affected apple production, among them there is Glomerella leaf spot (GLS) caused by Colletotrichum spp. The first report of this disease in apple was in plants nearby citrus orchards in São Paulo State, Brazil. The origin of this disease is still not clear, and studies based on the molecular phylogeny could relate the organisms evolutionarily and characterize possible mechanisms of divergent evolution. The amplification of 5.8S-ITS (Internal Transcribed Spacer) of rDNA of 51 pathogenic Colletotrichum spp. isolates from apples, pineapple guava and citrus produced one fragment of approximately 600 bases pairs (bp) for all the isolates analyzed. The amplified fragments were cleaved with restriction enzymes, and fragments from 90 to 500bp were obtained. The sequencing of this region allowed the generation of a phylogenetic tree, regardless of their hosts, and 5 isolated groups were obtained. From the "in silico" comparison, it was possible to verify a variation from 93 to 100% of similarity between the sequences studied and the Genbank data base. The causal agent of GLS is nearly related (clustered) to isolates of pineapple guava and to the citrus isolates used as control.

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Ridderbusch, Daniela C., Roland W. S. Weber, Timm Anke et Olov Sterner. « Tulasnein and Podospirone from the Coprophilous Xylariaceous Fungus Podosordaria tulasnei ». Zeitschrift für Naturforschung C 59, n^o 5-6 (1 juin 2004) : 379–83. http://dx.doi.org/10.1515/znc-2004-5-616.

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Tulasnein (1), a new metabolite with strong antimicrobial and weaker cytotoxic and phytotoxic activity, was isolated from culture filtrates of three strains of the xylariaceous coprophilous fungus Podosordaria tulasnei. The producing strains were identified by their rhizomorphs and by ITS rDNA sequence analysis. A second new metabolite, podospirone (2), was also produced by all three strains whereas the weakly cytotoxic (+)-3,4-anhydroshikimic acid methyl ester (3) was detected in only one strain.

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Chen, Wei Qing, et Yan Yan Liu. « Isolation and Identification of Halomonas sp. ZSCW-10 : A Moderately Halophilic Bacteria Strain with Cellulase Activity ». Advanced Materials Research 749 (août 2013) : 236–41. http://dx.doi.org/10.4028/www.scientific.net/amr.749.236.

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A moderately halophilic bacteria strain with cellulase (CMCase) activity, ZSCW-10, which can survive under wide range of NaCl concentration (1 %~15 %, w/v) and pH (4.5~9.0), was isolated from the sediment of intertidal zone located in the Xiangshan Island, Zhejiang Province. The strain was identified based on 16S rDNA sequence determination and phylogenetic analysis together with its morphological and physiological characterization. The results indicated that the 16S rDNA homologies were 97% between strain ZSCW-10 and some strains of Halomonas sp.. The phylogenetic tree was constructed with Molecular Evolutionary Genetics Analysis version 5 (MEGA5), showed the closest relationship between strain ZSCW-10 and Halomonas venusta. Based on its physiological and biochemical properties, homology and phylogenetic analysis, strain ZSCW-10 was identified as a subspecies of Halomonas sp.. The optimum culture conditions were: NaCl 6.0%, 32°C, pH 7.5.

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