Academic literature on the topic 'ITS (Intergenic Transcribed Spacer)'
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Journal articles on the topic "ITS (Intergenic Transcribed Spacer)"
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MAURICIO, I. L., J. R. STOTHARD, and M. A. MILES. "Leishmania donovanicomplex: genotyping with the ribosomal internal transcribed spacer and the mini-exon." Parasitology 128, no. 3 (March 2004): 263–67. http://dx.doi.org/10.1017/s0031182003004578.
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Intergenic region typing by restriction analysis of the ribosomal internal transcribed spacer (ITS) and mini-exon provide diagnostic markers for someLeishmania. Here, we evaluate restriction analysis of these targets for genotyping and phylogenetic analysis within theLeishmania donovanicomplex (agents of visceral leishmaniasis). Each method was useful for genotyping of bothL. donovanicomplex strains and Old WorldLeishmaniaspecies. The targets produced less robust groups than gp63 intergenic regions, but support the need for re-evaluation of the taxonomy of theL. donovanicomplex.
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Zhuo, Lang, S. L. Sajdak, and 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, no. 4 (August 1, 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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Dingman, Douglas W. "Paenibacillus larvae 16S–23S rDNA intergenic transcribed spacer (ITS) regions: DNA fingerprinting and characterization." Journal of Invertebrate Pathology 110, no. 3 (July 2012): 352–58. http://dx.doi.org/10.1016/j.jip.2012.03.026.
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McCullough, Michael J., Karl V. Clemons, John H. McCusker, and David A. Stevens. "Intergenic Transcribed Spacer PCR Ribotyping for Differentiation of Saccharomyces Species and Interspecific Hybrids." Journal of Clinical Microbiology 36, no. 4 (1998): 1035–38. http://dx.doi.org/10.1128/jcm.36.4.1035-1038.1998.
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The taxonomy of the genus Saccharomyces has undergone significant changes recently with the use of genotypic rather than phenotypic methods for the identification of strains to the species level. The sequence of rRNA genes has been utilized for the identification of a variety of fungi to the species level. This methodology, applied to species of Saccharomyces, allows unknown Saccharomyces isolates to be assigned to the type strains. It was the aim of the present study to assess whether typing of the intergenic spacer region by using restriction fragment length polymorphisms of PCR products (intergenic transcribed spacer PCR [ITS-PCR] ribotyping) could distinguish among type strains of the 10 accepted species of Saccharomyces and further to assess if this method could distinguish strains that were interspecific hybrids. Cellular DNA, isolated after the lysis of protoplasts, was amplified by PCR using ITS1 and ITS4 primers, purified by liquid chromatography, and digested with restriction endonucleases. Ribotyping patterns using the restriction enzymes MaeI and HaeIII could distinguish all species of Saccharomyces from each other, as well as from Candida glabrata, Candida albicans, and Blastomyces dermatitidis. The only exception to this was the inability to distinguish betweenSaccharomyces bayanus and S. pastorianus(S. carlsbergensis). Furthermore, interspecific hybrids resulting from the mating of sibling species ofSaccharomyces were shown to share the ITS-PCR ribotyping patterns of both parental species. It should now be possible, by this simple PCR-based technique, to accurately identify these strains to the species level, thereby allowing an increase in our understanding of the characteristics required by these interspecific hybrids for their particular ecological niches.
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Luchetti, Andrea, Franca Scanabissi, and Barbara Mantovani. "Molecular characterization of ribosomal intergenic spacer in the tadpole shrimp Triops cancriformis (Crustacea, Branchiopoda, Notostraca)." Genome 49, no. 8 (August 1, 2006): 888–93. http://dx.doi.org/10.1139/g06-047.
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Nuclear ribosomal DNA constitutes a multigene family, with tandemly arranged units linked by an intergenic spacer (IGS), which contains initiation/termination transcription signals and usually tandemly arranged subrepeats. The structure and variability of the IGS region are analyzed here in hermaphroditic and parthenogenetic populations of the "living fossil" Triops cancriformis (Branchiopoda, Notostraca). The results indicate the presence of concerted evolution at the population level for this G+C-rich IGS region as a whole, with the major amount of genetic variability found outside the subrepeat region. The subrepeats region is composed of 3 complete repeats (a, c, d) intermingled with 3 repeat fragments (b, e, f) and unrelated sequences. The most striking datum is the absolute identity of subrepeats (except type d) occupying the same position in different individuals/populations. A putative promoter sequence is present upstream of the 18S rRNA gene, but not in subrepeats, which is at variance with other arthropod IGSs. The absence of a promoter sequence in the subrepeats and subrepeat sequence conservation suggests that this region acts as an enhancer simply by its repetitive nature, as observed in some vertebrates. The putative external transcribed spacer (840 bp) shows hairpin structures, as in yeasts, protozoans, Drosophila, and vertebrates.Key words: concerted evolution, Crustacea, external transcribed spacer, intergenic spacer, ribosomal DNA, subrepeats, Triops cancriformis.
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HAYWARD, Glenys C., Dan J. BLANCHON, and H. Thorsten LUMBSCH. "Molecular data support Ramalina ovalis as a distinct lineage (Ramalinaceae, Ascomycota)." Lichenologist 46, no. 4 (July 2014): 553–61. http://dx.doi.org/10.1017/s0024282913000947.
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AbstractRamalina celastri is a highly variable, widely distributed pan-subtropical lichen species. In Australasia the species had been separated into two subspecies; R. celastri subsp. celastri and R. celastri subsp. ovalis. This study compares morphological variation, substratum preference and sequences of the internal transcribed spacer (ITS) and intergenic spacer (IGS) regions of ribosomal DNA from a range of specimens from New Zealand and one from Australia. Bayesian and ML trees generated using the sequence data form two well-supported clades corresponding to the two previously recognized subspecies. Molecular, morphological and geographical differences support the recognition of R. ovalis at the species rank.
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BAGHERI, ALI, FRANK R. BLATTNER, and REINHARD M. FRITSCH. "Allium gilanense, a new species of Allium sect. Codonoprasum (Amaryllidaceae) from Iran: evidence from morphological and molecular data." Phytotaxa 474, no. 3 (December 3, 2020): 283–92. http://dx.doi.org/10.11646/phytotaxa.474.3.7.
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As a result of recent botanical expeditions to the north of Iran, we describe here a new endemic Allium species from Gilan province named Allium gilanense. Molecular and morphological data indicate that it belongs to Allium sect. Codonoprasum. We provide a morphological description, comparing Allium gilanense with the closest relative taxa A. lenkoranicum and A. paniculatum, the preliminary karyotype of the new species, and molecular phylogenetic data derived from the nuclear ribosomal DNA internal transcribed spacers (ITS) and the chloroplast intergenic spacer trnH-psbA. The chromosome number of the new species is 2n = 16 with 0-3 B chromosomes.
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Friesen, Nikolai, and Ori Fragman-Sapir. "A new Allium species from section Molium from Israel: A. akirense (Amaryllidaceae)." Phytotaxa 173, no. 2 (June 25, 2014): 140. http://dx.doi.org/10.11646/phytotaxa.173.2.4.
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As part of the phylogenetic revision of the Eurasian representatives of the subgenus Amerallium we have discovered a new Allium species (section Molium) in Israel, related to A. qasyunense. It is described here as Allium akirense, based on living plants and recent herbarium specimens. Independence of the new species is confirmed by morphological and ecological features, and also by molecular ones. To learn more about the phylogenetic relationships within a group of closely related species of section Molium, we used maximum parsimony and Bayesian analyses of combined nuclear (ITS—internal transcribed and ETS—external transcribed spacers of rRNA genes) and chloroplast (rpl32–trnL intergenic spacer) dataset of 7 taxa. Discussion on geographic distribution, conservation status and habitat is provided, as well as an identification key including the closest related species.
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Sutar, Rajeshwari, Joseph K. David, K. Ganesan, Anup K. Ghosh, Sunit Singhi, Arunaloke Chakrabarti, and Anand K. Bachhawat. "Comparison of ITS and IGS1 regions for strain typing of clinical and non-clinical isolates of Pichia anomala." Journal of Medical Microbiology 53, no. 2 (February 1, 2004): 119–23. http://dx.doi.org/10.1099/jmm.0.05436-0.
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Pichia anomala is an emerging nosocomial pathogen and there is a need for methods that distinguish between different P. anomala strains. In the typing of several clinical as well as non-clinical P. anomala strains, the sequence variation of the internal transcribed spacer (ITS) was found to be inadequate for typing purposes. The intergenic spacer 1 (IGS1) region of the rDNA of several P. anomala strains was therefore investigated in detail. The IGS1 region (which varied from 1213 to 1231 bp in length) was interspersed with repeats and had more variation than the ITS regions. Comparative analysis in cases where analysis by the ITS was ambiguous clearly revealed the IGS1 region to be a more discriminatory tool in the typing of P. anomala strains.
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Guo, Zhansheng, Zhen Wang, and Xuguang Hou. "Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria." Fishes 6, no. 3 (September 17, 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.
Dissertations / Theses on the topic "ITS (Intergenic Transcribed Spacer)"
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Cadel-Six, Sabrina. "A propos de quelques métabolites remarquables de cynobactéries : cyanopeptoline, aéruginosine et anatoxine-a." Paris 6, 2007. http://www.theses.fr/2007PA066305.
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Les cyanobactéries sont des organismes procaryotes photosynthétiques capables de produire de nombreux métabolites secondaires. Cette thèse s’intéresse à la caractérisation moléculaire de cyanobactéries productrices de neurotoxines (anatoxine-a et homoanatoxine-a) ainsi qu’à la mise en évidence d’un gène codant pour une activité halogénase dans les clusters de gènes de biosynthèse des métabolites : cyanopeptoline et aéruginosine. De nombreux cas d'intoxications neurotoxiques d'animaux sauvages et domestiques sont régulièrement reportés en France. Nous avons mis en évidence sur deux sites pour lesquels des épisodes mortels ont été rapportés la présence de neurotoxines de cyanobactéries. Les cyanobactéries productrices d’anatoxine-a ont été isolées et déposées dans la collection de cyanobactéries de l’Institut Pasteur PCC. La caractérisation phénotypique et génétique des souches axéniques obtenues montre qu’il s’agit de souches du genre Oscillatoria. Sur la base des séquences codant pour les ARNr16S et ITS (Internal Transcribed Spacer) les relations phylogénétiques des nouvelles souches neurotoxiques au sein du genre Oscillatoria ont été étudiées. Une étude du contenu métabolique en cyanopeptoline et aéruginosine et de la présence des leur clusters de gènes de biosynthèse a été entreprise chez une trentaine de souches de Microcystis. Elle a permis de mettre en évidence la présence d’halométabolites et d’identifier les gènes portant l’activité halogénase au sein des clusters aer et mcn. L’histoire évolutive des clusters aer et mcn au sein du genre Microcystis a été reconstituée par analyse des séquences ITS. Le gène halogénase semble avoir été acquis par la cyanobactérie probablement d'une protéobactérie ancestrale par transfert horinzontalThis work of PhD is cantered around three secondary metabolites produced by cyanobacteria (cyanopeptolin, aeruginosin and anatoxin-a). The first part of this work reports the results about isolating and purifing neurotoxic cyanobacteria from natural samples. Repeated dog deaths occurred in the last years in southern France. Signs of intoxication indicated acute poisoning due to a neurotoxin. Samples were collected at the border of tarn river in summers 2005 and 2006 from six different sites along 30 km. The cyanobacterial neurotoxines anatoxin-a and homoanatoxin-a were detected in extracts of most samples examined by gas chromatography-mass spectrometry. Fifteen filamentous cyanobacteria of the order Oscillatoriales were isolated and displayed four distinct phenotypes. Three of the phenotypes are assignable to the genera Oscillatoria/Phormidium, the fourth to the genus Geitlerinema. The genetic relatedness of the new isolates was evaluated by comparison of the ITS sequences with those of six oscillatorian strains from the PCC collection. Our findings prove that neurotoxic oscillatorian cyanobacteria exist in the Tarn river and thus were most likely implicated in the reported dog poisonings. Furthermore, they re-emphasise the importance of monitoring benthic cyanobacteria in aquatic environments. The second part of this work presents the evolution of the halogenase genes of the strains Microcystis sp. Producing chloreted cyanopeptolin and aeruginosin. Twenty-eight axenic strains of Microcystis aeruginosa from the PCC and NIES culture collections were screened by MALDI-TOF mass spectrometry and their genome analysed by degenerated oligonucleotides. Two putative halogenase genes present in cyanopeptoline and aeruginosin synthetase clusters were identified. Their nucleotide and deduced amino acid sequences were analysed in detail. A phylogenetic study was conducted on thirty halogenase and putative halogenase genes from different microorganisms
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Bodo, Slotta Tracey A. "Phylogenetic Analysis of Iliamna (Malvaceae) Using the Internal Transcribed Spacer Region." Thesis, Virginia Tech, 2000. http://hdl.handle.net/10919/33211.
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The genus Iliamna Greene has a taxonomically complex history. Since its desciption in 1906, the genus was not recognized for some time, several species were initially placed into other genera, and the species status of a few was questioned. Today, eight species of Iliamna are recognized. Six species are located in western North America and two are found isolated to the east. Species in Iliamna are very similar morphologically with only a few characters distinguishing several as separate entities. The need for systematic study became apparent since all but one species are considered rare or endangered. Also, the differentiation between two endangered species, I. corei and I. remota, was unclear in a previous study using random amplified polymorphic DNA fragments. Of the western species, four overlap in distribution (I. crandallii, I grandi ora, I. longisepala, and I. rivularis) and their recognition as separate species has been questioned. The focus of this study was to develop a phylogeny for Iliamna using sequences from the internal transcribed spacer region (ITS) of the nuclear ribosomal
RNA genes in order to determine its biogeographical and evolutionary history. Cladistic analysis was performed and the resulting phylogeny is presented. The ITS data provide new insights in the origination of the genus and its distribution. In Iliamna, the ITS region is 677 base pairs long with 120 sites providing information in the formation of phylogenetic trees. Iliamna forms a well-supported clade distinct from related genera and is monophyletic. Three well-supported groups are formed. One contains representatives from the Pacific Northwest. Another contains all of the remaining species with the third clade nested therein. This last clade contains the two eastern species, I. corei and I. remota, but there is not enough variability to support the divergence of these taxa as distinct species. There is also not sufficient variability in the ITS region to identify the western species I. crandallii, I. grandi ora, I. longisepala and I. rivularis as distinct entities.Master of Science
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Meireles, Jose Eduardo de Carvalho. "Revisão taxonomica e filogenia de Poecilanthe s.l. (Leguminosae, Papilionoideae, Brongniartieae)." [s.n.], 2007. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314808.
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Orientador: Ana Maria Goulart de Azevedo TozziDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-09T03:16:51Z (GMT). No. of bitstreams: 1 Meireles_JoseEduardodeCarvalho_M.pdf: 5457639 bytes, checksum: 2254e34efd86c3760ca5a245abf9eaf6 (MD5) Previous issue date: 2007
Resumo: Poecilanthe (Leguminosae, Papilionoideae, Brongniartieae) é em gênero sul-americano que inclui atualmente dez espécies. A heterogeneidade morfológica e química encontrada em Poecilanthe dificulta sua circunscrição e coloca em dúvida sua monofilia. Além disso, limites interespecíficos imprecisos e falta de chave de identificação dificultam o reconhecimento das espécies. Este trabalho tem como objetivos testar a monofilia de Poecilanthe e estabelecer as relações entre suas espécies, bem como revisar a taxonomia do gênero. Para tanto, uma análise filogenética de máxima parcimônia baseada em caracteres morfológicos e seqüências de ITS/5.8S (nrDNA) foi realizada. Como subsídio para a análise cladística, foi feito um estudo sobre a morfologia das sementes e embriões de Poecilanthe, que resultou no reconhecimento de quatro padrões distintos de morfologia. Os resultados da filogenia mostram que Poecilanthe não é um gênero monofilético, sendo composto por três clados parafiléticos em relação à tribo. Estes três clados foram caracterizados morfologicamente e considerados como gêneros distintos. Poecilanthe é recircunscrito para incluir apenas as espécies extra-amazônicas (Poecilanthe s.s.), compreendendo então seis espécies. O gênero Amphiodon é restabelecido, e P. ovalifolia combinada neste. Um gênero novo é descrito para incluir P. amazonica e P. hostmannii. Cada um destes gêneros foi tratado taxonomicamente, constando em cada tratamento descrições, ilustrações e chave para a identificação das espécies
Abstract: The genus Poecilanthe (Leguminosae, Papilionoideae, Brongniartieae) currently comprises ten South-American species. The morphological and chemical diversity that is found within this genus renders its circumscription imprecise and brings Poecilanthe¿s monophyly into question. This work aims to test the monophyly of Poecilanthe and to revise the taxonomy of the genus. A parsimony analysis based on both morphological and ITS/5.8S data was carried out. In order to provide characters to the cladistic analysis, the morphology of the seeds and embryos of Poecilanthe was analyzed, and resulted in the identification of four different morphological patterns. The phylogeny does not support Poecilanthe as monophyletic, but resolves three different well-supported lineages that are paraphyletic with respect to the tribe. These clades are morphologically characterized and ranked at the generic level. Poecilanthe is recircumscribed to include the six extra-Amazonian species only. The genus Amphiodon is reinstated and P. ovalifolia is combined. Poecilante amazonica and P. hostmannii are segregated into a new genus. Each genus was revised and descriptions, illustrations and identification key for the species are presented.
Mestrado
Biologia Vegetal
Mestre em Biologia Vegetal
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Magalon, Hélène. "Dispersion du corail Pocillopora meandrina et de ses algues symbiotiques en Polynésie Française." Paris 6, 2005. http://www.theses.fr/2005PA066100.
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Woods, Kristi Yvonne. "Nymphaea odorata (Water-lily, Nymphaeaceae): Analyses of molecular and morphological studies." Thesis, Virginia Tech, 2003. http://hdl.handle.net/10919/41234.
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Molecular and morphologic studies were used to determine the evolution, classification and differentiation of Nymphaea odorata. Molecular analyses of the nuclear internal transcribed spacer (ITS) region, the chloroplast trnL-F region, and inter-simple sequence repeat (ISSR) markers determined the variation present between and within two species of Nymphaea. The ITS region resulted in a phylogeny depicting strong separation between species (N. mexicana and N. odorata) and some separation between N. odorataâ s subspecies. The ITS region contained polymorphisms, which upon SAHN clustering and principle coordinate (PCOA) and minimum spanning tree (MST) analyses produced groups similar to the clades in the ITS phylogeny. Sixteen accessions were chosen for trnL-F analysis, where a subspecies-specific molecular marker was found. In most accessions the marker confirmed the original subspecies classification. Molecular analyses using ISSRs characterized among population variation in N. odorata and N. mexicana using five primers. ISSR markers among populations were highly variable within a species and were used in UPGMA, PCOA and MST analysis, which resulted in separation between the subspecies.
Both univariate and multivariate analyses were performed on quantitative and qualitative morphological characters. An analysis of variance resulted in six morphological characteristics that were statistically significant (P< 0.05), the majority being leaf blade characteristics. Multivariate statistics of principle component analysis and discriminate analysis resulted in groups for each subspecies, both emphasized the importance of quantitative leaf blade characteristics. Overall, both morphology and molecular characteristics supported the classification of subspecies for ssp. odorata and ssp. tuberosa, due a lack of strong segregation of characteristics.Master of Science
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Tozkar, Ozge Cansu. "Comparative Sequence Analysis Of The Internal Transcribed Spacer 2 Region Of Turkish Red Pine (pinus Brutia Ten.) And Natural Aleppo Pine (pinus Halepensis Mill.) Populations From Turkey." Master's thesis, METU, 2007. http://etd.lib.metu.edu.tr/upload/2/12608313/index.pdf.
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ABSTRACT
COMPARATIVE SEQUENCE ANALYSIS OF THE INTERNAL TRANSCRIBED SPACER 2 REGION OF TURKISH RED PINE (Pinus brutia TEN.) AND NATURAL ALEPPO PINE (Pinus halepensis MILL.) POPULATIONS FROM TURKEY
Tozkar, Özge M.S., Department of Biology Supervisor: Prof. Dr. Zeki Kaya April, 2007, 107 pages Turkish red pine (Pinus brutia) is wide-spread and an important forest tree species in Turkey, occurring mainly in southern, western and north-western Turkey and as small isolated populations in the Black Sea region. Aleppo pine (Pinus halepensis) has naturally found only in Adana and Mugla provinces as small population in mixture with Turkish red pine. Although Turkish red pine and Aleppo pine are morphologically different, Turkish red pine has been regarded as subspecies of Aleppo pine by some taxonomists due to occurrence of natural hybridization between these two species. However, the phylogenic relationship between these species needs to be explored further. In the present study, by sampling overlapped populations of both species from Mugla and Adana provinces (4 populations of Turkish red pine and 3 populations of Aleppo pine), internal transcribed spacer (ITS) region of ribosomal DNA were comparatively studied with sequence analysis. Although ITS1, 5.8s and ITS2 regions of ribosomal DNA were studied with ITS primers, only ITS2 region was successfully amplified with polymerase chain reaction (PCR). The complete data set for this region was analysed using MEGA3.1 and Arlequin softwares. Analysis of molecular variance (AMOVA) demonstrated the highest genetic differentiation between Turkish red pine and Aleppo pine in Mugla with 100 percentage of variation. AMOVA analysis also indicated the possibility of low-level migration of genes between Turkish red pine and Aleppo pine populations in Adana with 50.65 percent of molecular variance. Haplotype comparison revealed that two major haplotypes were represented Based on the results of ITS2 region sequence analysis, Turkish populations of Aleppo pine and Turkish red pine populations could not be fully differentiated. In Mugla province Turkish red pine and Aleppo pine revealed more differentiation due to reproductive isolation. But in Adana province, two species shared more common genetic background due to possible hybridization. Since ITS2 region of nuclear ribosomal DNA revealed a few variable and parsimony informative sites for both species, thus, only ITS2 region of ribosomal DNA does not appear to be sufficient for fully resolving genetic relationships between Turkish red pine and Aleppo pine populations. Further studies including ITS1 and 5.8s regions of ribosomal DNA and populations included from major Aleppo pine distribution areas will be useful to understand the evolutionary relationship between Aleppo pine and Turkish red pine populations in Turkey.
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Müller, Juceli. "Qualidade fisiológica e associação de Fusarium spp. a sementes de sorgo sacarino." Universidade Federal de Santa Maria, 2017. http://repositorio.ufsm.br/handle/1/11796.
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The present work aims to determine the physiological and sanitary quality of Sweet sorghum (Sorghum bicolor (L.) Moench) seeds, as well as to identify pathogens associated with seed, their transmission to seedlings and the subsequent pathogenicity of isolates obtained, In addition, molecularly identify the fungal species pathogenic to this crop. The experiments were carried out in the Teaching and Seed Research Laboratory (TSRL), of the Plant Engineering Department; In the Elocy Minussi Phytopathology Laboratory, Department of Plant Protection, and at the Biological Institute of São Paulo. Sweet sorghum seeds were used, all without chemical treatment. Sanitary quality was evaluated by sanity test, and physiological characteristics by germination and vigor tests (seedling length, dry mass, emergence, rate of emergence and accelerated aging). It was performed the test of transmission of the pathogens associated to the seeds and the subsequent pathogenicity of the obtained isolates, culminating with the molecular characterization of the identified pathogens, in which were sequenced the Internal Transcribed Spacer (ITS) genomic regions and the Elongation Factor 1 - alpha (TEF1-α) gene. The design used was the completely randomized design, with four cultivars of Sweet sorghum (BRS 506, F19, BRS 511 and BRS 509); For the evaluation of pathogenicity, the factorial scheme is represented by four cultivars and three isolates of Fusarium spp., besides the witness. The seeds of the BRS 509 cultivar were considered to have lower physiological quality than the other cultivars. The DNA sequencing allowed identifying the Fusarium thapsinum species as a pathogenic agent in the sweet sorghum crop, and proven its transmission via seeds.O presente trabalho teve como objetivo determinar a qualidade fisiológica e sanitária de sementes de cultivares de sorgo sacarino (Sorghum bicolor (L.) Moench), bem como identificar os patógenos associados à semente, sua transmissão às plântulas e a posterior patogenicidade de isolados obtidos, além disso, identificar molecularmente as espécies fúngicas patogênicas a esta cultura. Os experimentos foram realizados no Laboratório Didático e de Pesquisas em Sementes (LDPS), do Departamento de Fitotecnia; no Laboratório de Fitopatologia Elocy Minussi, do Departamento de Defesa Fitossanitária e, no Instituto Biológico de São Paulo. Foram utilizadas sementes de sorgo sacarino, todas sem tratamento químico. A qualidade sanitária foi avaliada pelo teste de sanidade, e as características fisiológicas por meio dos testes de germinação e de vigor (comprimento de plântulas, massa seca, emergência, índice de velocidade de emergência e envelhecimento acelerado). Foi realizado o teste de transmissão dos patógenos associados à semente e a posterior patogenicidade dos isolados fúngicos obtidos, culminando com a caracterização molecular dos patógenos identificados, na qual foram sequenciadas as regiões genômicas Internal Transcribed Spacer (ITS) e o gene do fator de elongação 1-α (TEF1α). O delineamento utilizado foi o inteiramente casualizado com quatro cultivares de sorgo sacarino (BRS 506, Fepagro 19, BRS 511 e BRS 509); já para a avaliação da patogenicidade, o esquema fatorial foi representado pelas quatro cultivares e três isolados de Fusarium sp., além da testemunha. As sementes da cultivar BRS 509 foram consideradas de qualidade fisiológica inferior as demais cultivares. O sequenciamento de DNA permitiu identificar a espécie Fusarium thapsinum como agente patogênico na cultura do sorgo sacarino, sendo comprovada sua transmissão via sementes.
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Glass, Pamela Michele. "Evidence of Ecological Speciation in Phacelia." Digital Commons @ East Tennessee State University, 2007. https://dc.etsu.edu/etd/2143.
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Phacelia purshii Buckley and P. fimbriata Micheaux are two species that are nearly morphologically indistinguishable. Seed germination experiments showed that the high elevation endemic, P. fimbriata requires lower temperatures to trigger germination. Following interspecific crosses, pollen tubes enter ovules and maternal tissue of the gynoecium matures but hybrid diploid and triploid organs fail to develop. DNA sequences from the ribosomal DNA internal transcribed region showed that P. fimbriata and P. purshii comprise a monophyletic clade but that P. fimbriata is more differentiated from related species. In contrast, P. purshii supported significantly higher levels of intraspecific polymorphism. Phacelia fimbriata and P. purshii are sister species with similar morphology but they are unable to hybridize, they are differentiated in physiological characteristics related to environment, and they inhabit different elevations. This pattern of relationship and differentiation suggests P. fimbriata may be the product of ecological speciation.
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Marques, Cálita Pollyanna. "Padronização da análise dos produtos da PCR/RFLP que amplifica os genes Ribossomal Internal transcribed spacer (ITS) e Glucose-6- phosphate dehydrogenase (G6PD) para identificação de Leishmania spp. em gel de poliacrilamida." Universidade Federal de Goiás, 2017. http://repositorio.bc.ufg.br/tede/handle/tede/7789.
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Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG
American Cutaneous Leishmaniasis (LTA) is caused by protozoa of the genus Leishmania and it attacks the skin and/or mucous membranes. It is an endemic zoonosis in Brazil being notified in all the Regions. There is a relation between the species of parasite and the clinical manifestations, contributing to the diagnostic complexity, which up to the present, did not exist species-specific diagnosis. In the present work, the proposal was to standardize the analysis of the PCR/RFLP products to the ITS and G6PD genes in polyacrylamide gel. In order to standardize PCR/RFLP analysis on the ITS and G6PD genes, DNA from the reference Leishmania spp. Sample was used and 5%, 6%, 7% 8% and 10% polyacrylamide were tested. The protocol design considered the size of the amplicons generated by the PCR / RFLP, correlating the concentration of the polyacrylamide. To standardize the electrophoresis time the migration of the dyes used in the DNA sample buffer was monitored. To validate the technique, we selected 521 samples from Tocantins patients fixed on slides and 43 samples of parasite isolates stored in Leishbank. The samples from the patients from Tocantins were analyzed by PCR/RFLP to the kDNA and were selected to those positive for the validation. The concentration of the matrix for analysis of the PCR and RFLP products to the ITS gene was standardized in 6% and 8%, respectively, and distinguished the species L. (L.) amazonensis, but the species L. (V.) braziliensis, L. (V.) guyanensis and L. (V.) lainsoni were not distinguished among themselves, occurring the same between L. (V.) naiffi and L. (V.) shawi. The concentration of the matrix for analysis of the PCR products to the G6PD gene was standardized in 6% and distinguished L. (V.) braziliensis from the others. The validation of the polyacrylamide gel analysis of the PCR products to the ITS target from samples of patients fixed in slides was not performed, since of the 256 samples analyzed only 4 amplified. The validation of the analysis of the products of the PCR to the G6PD target in polyacrylamide gel from 48 samples fixed in slides characterized 81% as L. (V.) braziliensis and, characterized 63% of the isolates of parasites as L. (V.) braziliensis. The PCR/RFLP analyzes performed to discriminate Leishmania spp. are complementary and thus contribute to the species-specific diagnosis of LTA.
A Leishmaniose Tegumentar Americana (LTA) é causada por protozoários do gênero Leishmania e acomete pele e/ou mucosas. É uma zoonose endêmica no Brasil sendo notificada em todas as Regiões. Há uma relação entre a espécie de parasito e as manifestações clínicas, contribuindo à complexidade diagnóstica, que até o presente, não existi o diagnóstico espécie-específico. No presente trabalho, a proposta foi padronizar a análise dos produtos da PCR/RFLP aos genes ITS e G6PD em gel de poliacrilamida. Para padronizar as análises dos produtos da PCR/RFLP aos genes ITS e G6PD, foram utilizadas DNA da amostra de Leishmania spp., de referência, sendo testada a poliacrilamida na concentração de 5%, 6%, 7% 8% e 10%. O delineamento do protocolo considerou o tamanho dos amplicons gerados pela PCR/RFLP, correlacionando-o a concentração da poliacrilamida. Para padronizar o tempo da eletroforese foi monitorada a migração dos corantes usados no tampão da amostra de DNA. Para validar a técnica, foram selecionadas 521 amostras de pacientes tocantinenses fixadas em lâminas e 43 amostras de isolados de parasitos armazenados no Leishbank. As amostras dos pacientes tocantinenses foram analisadas pela PCR/RFLP ao kDNA e foram selecionadas àquelas positivas para a validação. A concentração da matriz para analise dos produtos da PCR e RFLP ao gene ITS ficou padronizada respectivamente em 6% e 8% e distinguiu a espécie L.(L.) amazonensis, porém as espécies L. (V.) braziliensis, L. (V.) guyanensis e L. (V.) lainsoni não foram distinguidas entre si, ocorrendo o mesmo entre L. (V.) naiffi e L. (V.) shawi. A concentração da matriz para analise dos produtos da PCR ao gene G6PD ficou padronizada em 6% e distinguiu L. (V.) braziliensis das demais. A validação da análise em gel de poliacrilamida dos produtos da PCR ao alvo ITS a partir de amostras de pacientes fixadas em lâminas não ser realizada, pois das 256 amostras analisadas somente 4 amplificaram. A validação da análise dos produtos da PCR ao alvo G6PD em gel de poliacrilamida a partir de 48 amostras fixadas em lâminas caracterizou 81% como L. (V.) braziliensis e, caracterizou 63% dos isolados de parasitos como L. (V.) braziliensis. As análises pela PCR/RFLP realizadas para discriminar Leishmania spp. se complementam e, assim, contribuem para o diagnóstico espécie-específico da LTA.
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González, Gaarslev Natalia. "Growth and biodegradation by Sporidiobolales yeasts in vanillin-supplemented medium." Thesis, Högskolan i Gävle, Avdelningen för arbets- och folkhälsovetenskap, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:hig:diva-24678.
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Studies of biodegradation in lignins by basidiomycetes yeasts show the conversion of lignin in various degradation products among which vanillin, a valuable substance, suggested to be a strong inhibitor of both fermentation and growth of yeasts, stands. Sporidiobolales yeasts used in these experiments were aimed to be identified by their highly conserved ITS region as well as studied in vanillinsupplemented medium through, vanillin-supplemented plates, TLC and Neubauer’s chamber to find out which, among the several isolates tested, were the most resistant ones, understand how they take up vanillin and how their growth is affected by the presence of the phenolic compound. Two strains were identified as Rhodotorula babjevae. One of them, L4, together with LS22, Rhodosporidium kratochvilovae, could withstand and biodegrade high concentrations of vanillin, producing biodegradation products with Rf values similar to the ones know for vanillic acid and vanillyl alcohol. Better growth in medium supplemented with small doses of vanillin was found, as well as disparity among the same species and their metabolic features, therefore, herbicides resistance was suggested as a reason for strains divergence. Further morphological-species comparison could also describe if there exist a relation between them.Estudios sobre la biodegradación de ligninas por levaduras basidiomicetes muestran la conversión de lignina en distintos productos de degradación, entre los cuales se encuentra la vainillina, un fuerte inhibidor de la fermentación y el crecimiento de levaduras. Las levaduras Sporidiobolales utilizadas en estos experimentos han intentado ser identificadas a través de la región ETI, muy conservada, además de estudiadas en medios suplementados con vainillina mediante placas suplementadas con vainillina, CCF y cámara de Neubauer para averiguar cuáles son las cepas más resistentes, entender cómo metabolizan la vainillina y cómo su crecimiento se ve afectado por la presencia de dicho compuesto. Dos cepas fueron identificadas como Rhodotorula babjevae. Una de ellas, L4, junto con con la cepa LS22, Rhodosporidium kratochvilovae, pudieron soportar y biodegradar elevadas concentraciones de vainillina, originando productos de biodegradación con valores de Rf similares a los del ácido vanílico y alcohol vanílico previamente conocidos. Se encontró un crecimiento mejor en medios suplementados con pequeñas dosis de vainillina además de una disparidad entre mismas especies y sus características metabólicas, así, herbicidas han sido sugeridos como una posible causa en dicha divergencia. Una futura comparación morfología-especie podrá describir si existe relación entre ambos.
Book chapters on the topic "ITS (Intergenic Transcribed Spacer)"
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Fujita, Shin-ichi. "Internal Transcribed Spacer (ITS)-PCR Identification of MRSA." In Methods in Molecular Biology, 97–102. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-664-1_5.
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Fujita, Shin-ichi. "Internal Transcribed Spacer (ITS)-PCR Identification of MRSA." In Methods in Molecular Biology, 51–57. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-468-1_4.
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Gürtler, Volker, Gangavarapu Subrahmanyam, Malathi Shekar, Biswajit Maiti, and Indrani Karunasagar. "Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequences." In Methods in Microbiology, 253–74. Elsevier, 2014. http://dx.doi.org/10.1016/bs.mim.2014.07.004.
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"Plant DNA Barcoding." In Advances in Environmental Engineering and Green Technologies, 133–64. IGI Global, 2021. http://dx.doi.org/10.4018/978-1-7998-4312-2.ch006.
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DNA barcoding has evolved as an effective species identification tool in diverse areas such as phylogeny, ecology, population genetics, and biodiversity. In this approach, a short DNA sequence from a standardized locus is employed for species identification. The technique is simple, time and cost effective, and accurate. Selection of correct DNA marker is the main criterion for success in DNA barcoding. Compared to animals, DNA barcoding is more difficult in plants, as there are multiple consensuses about selection of barcoding markers for plants DNA barcoding. Some common plant barcoding markers are chloroplast genes such as matK, rbcL, ropC1, ropB, and trnL; chloroplast intergenic specers trnH-psbA, atpF-atpH, and pdbK-psbI; and the nuclear ribosomal internal transcribed spacer (ITS). These markers can be used alone or in combinations with other markers or spacers. In this chapter, the basic requirements, selection of markers, databases, advantages, and limitations of DNA barcoding have been discussed.
Conference papers on the topic "ITS (Intergenic Transcribed Spacer)"
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da Silva, M. L. R. B., V. A. L. B. Cavalcanti, A. C. E. S. Mergulhão, and M. C. C. P. de Lyra. "Sequencing of the region of ribosomal internal transcribed spacer (ITS) of Metarhizium anisopliae in Pernambuco state." In Proceedings of the III International Conference on Environmental, Industrial and Applied Microbiology (BioMicroWorld2009). WORLD SCIENTIFIC, 2010. http://dx.doi.org/10.1142/9789814322119_0028.
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Chen, Ren-Fang, Li Xu, Mao-De Yu, Xiu-Qun Liu, and Long-Qing Chen. "Determination of the Origin and Evolution of Morus (Moraceae) by Analyzing the Internal Transcribed Spacer (ITS) Sequences." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5518058.
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Peck, Kayla, Robert Stedtfeld, Jordan RoseFigura, Brett Reed, Drew McUsic, Jon Irish, Brett Etchebarne, Timothy Johnson, Laurie Kurihara, and Vladimir Makarov. "Abstract 1484: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-1484.
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Peck, Kayla, Robert Stedtfeld, Jordan RoseFigura, Brett Reed, Drew McUsic, Jon Irish, Brett Etchebarne, Timothy Johnson, Laurie Kurihara, and Vladimir Makarov. "Abstract 1484: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1484.
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Rosa, Marcos P., Jose V. C. Vargas, Vanessa M. Kava, Fernando G. Dias, Daiani Savi, Beatriz Santos, Wellington Balmant, Andre B. Mariano, Andre Servienski, and Juan C. Ordóñez. "Hydrogen and Compounds With Biological Activity From Microalgae." In ASME 2019 13th International Conference on Energy Sustainability collocated with the ASME 2019 Heat Transfer Summer Conference. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/es2019-3965.
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Abstract Microalgae have a high biotechnological potential as a source of biofuels (biodiesel, biohydrogen) and other high-added value products (e.g., pharmaceuticals, proteins, pigments). However, for microalgae cultivation to be economically competitive with other fuel sources, it is necessary to apply the concept of biorefinery. This seems to be the most ambitious strategy to achieve viability. Therefore, the objectives of this study were to isolate and identify the main microalgae line used to produce biofuels at Federal University of Parana, Brazil, using the rDNA sequence and micromorphological analysis, and to evaluate the potential of this lineage in the production of hydrogen and co-products with biological activity. For the purification of the lineage (LGMM0001), an aliquot was seeded into solid CHU culture medium and an isolated colony was selected. The genomic DNA was purified using a commercial kit (Macherey-Nagel, Düren, Germany) for molecular identification, the ITS region (ITS1, 5.8S and ITS2) (Internal Transcribed Spacer) was amplified and sequenced using primers LS266 and V9G. Morphological characterization was performed as described by Hemschemeier et al. [1]. Finally, for biological activity research, secondary metabolites were extracted by fractionation and evaluated against bacteria of clinical interest. Through microscopic analysis, general characteristics shared by the genus Tetradesmus were observed. The plasticity of the morphological characteristics of this genus reinforces the need for further studies to classify correctly the species in this group, using DNA sequencing. ITS sequence analysis of LGMM0001 showed 100% homology with sequences from the Tetradesmus obliquus species, so, the lineage was classified as belonging to this species. The evaluated microalgae strain was able to produce hydrogen, showing positive results for gas formation. Biological activity was observed with the extract obtained from the residual culture carried out with alternative medium used in the photobioreactors (PBR), against the Staphylococcus aureus pathogenic lineage. In conclusion, the microalgae strain used in this work was identified as Tetradesmus obliquus (= Acutodesmus obliquus), and was able to produce a compound with economic potential in association with the existing biofuel production process.