Academic literature on the topic 'ITS2 rDNA'
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Journal articles on the topic "ITS2 rDNA"
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Gong, Li, Wei Shi, Min Yang, and Xiaoyu Kong. "Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes: Cynoglossidae)." Animal Biology 68, no. 4 (2018): 353–65. http://dx.doi.org/10.1163/15707563-17000134.
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Abstract The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). In recent years, an increasing number of rDNA sequence polymorphisms have been identified in numerous species. In the present study, we provide 33 complete ITS (ITS1-5.8S-ITS2) sequences from two Symphurus plagiusa individuals. To the best of our knowledge, these sequences are the first detailed information on ITS sequences in Pleuronectiformes. Here, two divergent types (Type A and B) of the ITS1-5.8S-ITS2 rDNA sequence were found, which mainly differ in sequence length, GC content, nucleotide diversity (π), secondary structure and minimum free energy. The ITS1-5.8S-ITS2 rDNA sequence of Type B was speculated to be a putative pseudogene according to pseudogene identification criteria. Cluster analysis showed that sequences from the same type clustered into one group and two major groups were formed. The high degree of ITS1-5.8S-ITS2 sequence polymorphism at the intra-specific level indicated that the S. plagiusa genome has evolved in a non-concerted evolutionary manner. These results not only provide useful data for ribosomal pseudogene identification, but also further contribute to the study of rDNA evolution in teleostean genomes.
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Zagoskin, Maxim V., Valentina I. Lazareva, Andrey K. Grishanin, and Dmitry V. Mukha. "Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact." BioMed Research International 2014 (2014): 1–15. http://dx.doi.org/10.1155/2014/926342.
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The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that theMesocyclops,Thermocyclops,andMacrocyclopsgenera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.
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Qiu, J. H., Y. Lou, Y. Zhang, Q. C. Chang, Z. X. Liu, H. Duan, D. H. Guo, D. Z. Gao, D. M. Yue, and C. R. Wang. "Sequence variability in internal transcribed spacers of nuclear ribosomal DNA among isolates of the oxyurid nematodes Syphacia obvelata and Aspiculuris tetraptera from mice reared in laboratories in China." Journal of Helminthology 90, no. 1 (January 9, 2015): 81–85. http://dx.doi.org/10.1017/s0022149x1400087x.
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AbstractThis study examined sequence variability in internal transcribed spacers (ITS) of nuclear ribosomal DNA among Syphacia obvelata and Aspiculuris tetraptera isolates from laboratory mice from different geographical locations in China. ITS1, 5.8S and ITS2 rDNA were amplified separately from adult S. obvelata and A. tetraptera individuals by polymerase chain reaction (PCR), and the amplicons were subjected to sequencing from both directions. The lengths of the sequences of ITS1, 5.8S and ITS2 rDNA from both nematodes were 314 bp and 456 bp, 157 bp, and 273 bp and 419 bp, respectively. The intraspecific sequence variations in S. obvelata ITS1 were 0–0.3%. For A. tetraptera they were 0–0.7% in ITS1 and 0–1.0% in ITS2. However, the interspecific sequence differences among members of the infraorder Oxyuridomorpha were significantly higher, being 54.0–65.5% for ITS1 and 55.3–64.1% for ITS2. Phylogenetic analysis based on the combined partial sequences of ITS1 and ITS2 using three inference methods – Bayesian inference, maximum likelihood and maximum parsimony – revealed that all the S. obvelata and A. tetraptera samples formed independent monophyletic groups. Syphacia obvelata was closer to Syphacia muris than to A. tetraptera, consistent with morphological classification. These results demonstrate that ITS1 and ITS2 rDNA sequences are useful markers for population genetic studies of oxyurid nematodes.
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Su, X., Y. Zhang, X. Zheng, X. X. Wang, Y. Li, Q. Li, and C. R. Wang. "Characterization of the complete nuclear ribosomal DNA sequences of Eurytrema pancreaticum." Journal of Helminthology 92, no. 4 (June 27, 2017): 484–90. http://dx.doi.org/10.1017/s0022149x17000554.
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AbstractEurytrema pancreaticum is one of the most common trematodes of cattle and sheep, and also infects humans occasionally, causing great economic losses and medical costs. In this study, the sequences of the complete nuclear ribosomal DNA (rDNA) repeat units of five E. pancreaticum individuals were determined for the first time. They were 8306–8310 bp in length, including the small subunit (18S) rDNA, internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), large subunit (28S) rDNA and intergenic spacer (IGS). There were no length variations in any of the investigated 18S (1996 bp), ITS1 (1103 bp), 5.8S (160 bp), ITS2 (231 bp) or 28S (3669 bp) rDNA sequences, whereas the IGS rDNA sequences of E. pancreaticum had a 4-bp length variation, ranging from 1147 to 1151 bp. The intraspecific variations within E. pancreaticum were 0–0.2% for 18S rDNA, 0–0.5% for ITS1, 0% for 5.8S rDNA and ITS2, 0–0.2% for 28S rDNA and 2.9–20.2% for IGS. There were nine types of repeat sequences in ITS1, two types in 28S rDNA, but none in IGS. A phylogenetic analysis based on the 18S rDNA sequences classified E. pancreaticum in the family Dicrocoeliidae of Plagiorchiata, closely related to the suborder Opisthorchiata. These results provide useful information for the further study of Dicrocoeliidae trematodes.
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Hausner, Georg, and Xi Wang. "Unusual compact rDNA gene arrangements within some members of the Ascomycota: evidence for molecular co-evolution between ITS1 and ITS2." Genome 48, no. 4 (August 1, 2005): 648–60. http://dx.doi.org/10.1139/g05-037.
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The internal transcribed spacers of the ribosomal DNA tandem repeat were examined in members of the ascomycetous genus Sphaeronaemella. Species of Sphaeronaemella and its mitotic counterpart Gabarnaudia, have a compact rDNA gene arrangement due to unusually short internal transcribed spacer (ITS) regions. Examination of these regions from phylogenetically related taxa, Cornuvesica, Gondwanamyces, and Ceratocystis, showed that their ITS1 and ITS2 regions could be folded into central hairpin-like structures with the size reduction in species of Sphaeronaemella being due to length reduction of the main-hairpin and the loss of smaller hairpin-like structures that emanate from the main hairpin. A databank compilation, combined with newly obtained sequences, provided an ITS data set that includes sequences of 600 species belonging to the Ascomycota. Correlation analysis revealed that the sizes of ITS1 and ITS2 show a strong positive correlation, suggesting that the 2 rDNA regions have co-evolved. This supports biochemical evidence indicating that the ITS1 and ITS2 segments interact to facilitate the maturation of the rRNA precursor.Key words: rDNA, ITS1 and ITS2, Ascomycota, co-evolution.
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Fenille, Roseli C., Maísa B. Ciampi, Eiko E. Kuramae, and Nilton L. Souza. "Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences." Fitopatologia Brasileira 28, no. 4 (August 2003): 413–19. http://dx.doi.org/10.1590/s0100-41582003000400011.
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The aim of this study was to identify isolates of Rhizoctonia solani causing hypocotyl rot and foliar blight in soybean (Glycine max) in Brazil by the nucleotide sequences of ITS-5.8S regions of rDNA. The 5.8S rDNA gene sequence (155 bp) was highly conserved among all isolates but differences in length and nucleotide sequence of the ITS1 and ITS2 regions were observed between soybean isolates and AG testers. The similarity of the nucleotide sequence among AG-1 IA isolates, causing foliar blight, was 95.1-100% and 98.5-100% in the ITS1 and ITS2 regions, respectively. The nucleotide sequence similarity among subgroups IA, IB and IC ranged from 84.3 to 89% in ITS1 and from 93.3 to 95.6% in ITS2. Nucleotide sequence similarity of 99.1% and 99.3-100% for ITS1 and ITS2, respectively, was observed between AG-4 soybean isolates causing hypocotyl rots and the AG-4 HGI tester. The similarity of the nucleotide sequence of the ITS-5.8S rDNA region confirmed that the R. solani Brazilian isolates causing foliar blight are AG-1 IA and isolates causing hypocotyl rot symptoms are AG-4 HGI. The ITS-5.8S rDNA sequence was not determinant for the identification of the AG-2-2 IIIB R. solani soybean isolate.
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de la Fuente, Ana M., Noelia Caparrós, José M. Mora-Rodríguez, María Molina, Gaël Aleix-Mata, Roser Velarde, Luis E. Fidalgo, et al. "Characterization of New Molecular Markers of Three Botflies Parasitizing Cervid Hosts." Journal of Medical Entomology 58, no. 3 (February 4, 2021): 1463–69. http://dx.doi.org/10.1093/jme/tjab006.
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Abstract Specific identification of oestrid larvae is usually problematic not only when using morphobiometric features, but also when applying molecular criteria, since very few molecular markers have been described for this group of flies. New molecular markers for oestrid are needed for more reliable species identification, diagnostic purposes, and epidemiological surveys; moreover, they can help in phylogenetic reconstruction. Here, we report the characterization of COI, 28S rDNA, ITS1, and ITS2 in Cephenemyia stimulator from roe deer and in Cephenemyia auribarbis and Pharyngomyia picta from red deer. The COI and 28S rDNA are very uniform in length, while the ITSs sequences are highly variable at both intraspecific and interspecific levels. The described ITSs sequences were longer than those described for other dipteran species by the presence of simple repeats and tandem repeat sequences. In C. auribarbis both ITS1 and ITS2 appeared as two variants, one short and the other long. In general, the analyzed markers present low intraspecific genetic variation and high interspecific variation. ITSs showed the greatest amount of intraspecific and interspecific variation. Phylogenetic analysis demonstrated that the characterized sequences differentiate the species and genera of Oestridae.
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Zheng, Xu, Qiao-Cheng Chang, Yan Zhang, Si-Qin Tian, Yan Lou, Hong Duan, Dong-Hui Guo, Chun-Ren Wang, and Xing-Quan Zhu. "Characterization of the Complete Nuclear Ribosomal DNA Sequences ofParamphistomum cervi." Scientific World Journal 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/751907.
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Sequences of the complete nuclear ribosomal DNA (rDNA) gene from five individualParamphistomum cerviwere determined for the first time. The five complete rDNA sequences, which included the 18S rDNA, the internal transcribed spacer 1 (ITS1), the 5.8S rDNA, the internal transcribed spacer 2 (ITS2), the 28S rDNA, and the intergenic spacer (IGS) regions, had a length range of 8,493–10,221 bp. The lengths of the investigated 18S, ITS1, 5.8S, ITS2, and 28S rDNA sequences, which were 1,994 bp, 1,293 bp, 157 bp, 286 bp, and 4,186 bp, respectively, did not vary. However, the IGS rDNA sequences had a length range of 577–2,305 bp. The 5.8S and ITS-2 rDNA sequences had 100% identity among the five investigated samples, while the identities among the IGS had a range of 53.7–99.8%. A comparative analysis revealed that different types and numbers of repeats were found within each ITS1 and IGS region, which may be related to the length polymorphism of IGS. The phylogenetic position ofP. cerviin Paramphistomatidae was analyzed based on the 18S rDNA sequences. These results will aid in studying the intra- and interspecific variation of the Paramphistomatidae and the systematics and phylogenetics of Digenea.
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Schnabel, G., E. L. Schnabel, and A. L. Jones. "Characterization of Ribosomal DNA from Venturia inaequalis and Its Phylogenetic Relationship to rDNA from Other Tree-Fruit Venturia Species." Phytopathology® 89, no. 1 (January 1999): 100–108. http://dx.doi.org/10.1094/phyto.1999.89.1.100.
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A portion of the 18S ribosomal DNA (rDNA) gene, the internal transcribed spacers (ITS1 and ITS2), and the 5.8S rDNA gene were polymerase chain reaction-amplified from strains and field populations of Venturia inaequalis and assessed for genetic variation. A previously reported optional group I intron in the 18S rDNA gene of V. inaequalis was detected in 75.0% of 92 strains collected worldwide and in 61.1 and 71.2% of 54 and 59 strains from two Michigan orchards, respectively. Sequence and restriction analysis of rDNA revealed four intron alleles, three of which were present both in worldwide strains and in each field population. Two ITS1 alleles were detected and found to be linked to specific intron alleles. The ITS1-5.8S-ITS2 sequences from V. asperata V. carpophila, V. cerasi, V. inaequalis, V. nashicola, V. pyrina, and Cladosporium caryigenum were compared using phylogenetic analysis. Strains of the Venturia species were placed in three distinct monophyletic groups in a phylogenetic tree. The first group comprised V. inaequalis; the second, V. pyrina and V. nashicola; and the third, V. cerasi, V. carpophila, and V. asperata. The described intron and ITS1 alleles in V. inaequalis provide genetic markers for subdividing populations of V. inaequalis, and the ITS1-5.8S-ITS2 sequences are valuable in determining the relationship of the species from tree-fruit crops with other Venturia species.
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Zhan, Li, and Xu. "Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Ciliophora, Spirotrichea)." Microorganisms 7, no. 11 (October 26, 2019): 493. http://dx.doi.org/10.3390/microorganisms7110493.
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Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.
Dissertations / Theses on the topic "ITS2 rDNA"
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SILVA, Maria Aparecida. "Cyathus (Basidiomycota): relações filogenéticas de espécies do Nordeste brasileiro." Universidade Federal de Pernambuco, 2012. https://repositorio.ufpe.br/handle/123456789/15472.
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O gênero Cyathus Haller: Pers., junto com mais quatro gêneros, formou, por muito tempo, um grupo conhecido como “Bird’s nest fungi” devido a morfologia cônica com estrutura lenticulares em seu interior, lembrando ovos em seus ninhos. Os estudos morfológicos, durante muito tempo, forneceram a base para as diferentes construções de classificação infragenérica e, como muitas espécies se diferenciavam de forma tênue, isso gerava muita polêmica. Sequências de DNA vêm sendo usadas para esclarecer melhor a história evolutiva do grupo. No Brasil, o grupo é pouquíssimo estudado, de forma que mais trabalhos envolvendo a união da taxonomia molecular com a tradicional são necessários para uma melhor compreensão do gênero. Assim, o presente trabalho teve como objetivos inferir a filogenia de espécimes de Cyathus oriundas do nordeste brasileiro e, com a associação dos caracteres morfológicos, propor uma classificação melhor para o táxon. Para isso, foram examinadas 46 exsicatas, das quais seis eram do herbário JPB, cinco do Herbário HUEFS e 37 do herbário de Fungos UFRN, sendo que este último apresenta o maior número de exsicatas de Cyathus no Nordeste, somando um total de 19 espécies. Dos 46 espécimes, 33 foram utilizados para extração de DNA, resultando no sequenciamento da região ITS de seis espécies e da região LSU de oito espécies. As árvores filogenéticas mostram que essas espécies se encontram em clados separados das demais espécies oriundas de regiões não tropicais, no entanto, não altera a topologia geral dos principais clados sugeridos em trabalhos anteriores. De acordo com os estudos taxonômicos tradicionais, temos duas espécies que constituem segundo registro para o mundo: C. pedicelatus e C. setosus; uma primeira referencia para o Brasil de C. olivaceobrunneus, e a primeira referência para o Nordeste de C. bekerleyanus. A análise dos dados moleculares aponta para a delimitação de cinco novas espécies para a ciência. Todas as sequências de DNA geradas foram depositadas no GenBank e são novas para o banco de dados.
The genus Cyathus Haller: Pers., together with other four genera, formed a group known as bird's nest fungi due to their conic morphology with lenticular structures inside resembling bird’s eggs in their nests. Morphological studies, for a long time, provided the basis to the different constructions of infrageneric classification and, as many species differed weakly from one another, that generated much controversy. DNA sequences have been used to better clarify the evolutionary history of the group. In Brazil, the group is as yet poorly studied, hence, more work involving the union of the traditional and molecular taxonomy is needed for better understanding of the genus. Therefore, this work had the objectives of inferring the phylogeny of specimens of Cyathus from the Brazilian Northeast and, in association with morphological characters, to propose a better classification for the taxon. Forty six exsiccates were examined, being six from JPB herbarium, five from HUEFS herbarium and 37 of UFRN-Fungos herbarium. The latter has the largest number of exsiccates of this genus in the Northeast, totaling 19 species. Thirty-three specimens were chosen for DNA extraction, resulting in the sequencing of the ITS region of six species and the LSU region of eight species. The phylogenetic trees show that these species sampled in this work are positioned in clades separated from those reported from non-tropical regions, however, this does not change the general topology of the main clades suggested in the works published previously. According to the traditional taxonomy studies we have two species that constitute the second record to the world, C. pedicelatus and C. setosus; one first record to Brazil, C. olivaceobrunneus; and one first record to the Northeast region of C. bekerleyanus. Analysis of the molecular data suggests five new species to Science. All DNA sequences of the tropical species sampled were deposited in the GenBank and are new records for the database.
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Jasmina, Ludoški. "Evolucioni odnosi u rodu CheilosiaMeigen, 1822 (Diptera: Syrphidae)." Phd thesis, Univerzitet u Novom Sadu, Prirodno-matematički fakultet u Novom Sadu, 2008. http://dx.doi.org/10.2298/NS20080508LUDOSKI.
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U radu su analizirani nukleotidni diverzitet COI mtDNK i fenotipska varijabilnost veličinskih komponenti krila taksona roda Cheilosia. Dobijeni podaci su korišćeni u sagledavanju filogenetskih i evolucionih odnosa odabranih taksona. Amplificiran je i sekvenciran 3' kraj gena COI mtDNK 119 jedinki 14 vrsta roda Cheilosiasakupljenih na 8 lokaliteta Balkanskog poluostrva i u Laponiji, Finska (vrsta C. albitarsis). Analizom su bile obuhvaćene i sekvence COI mtDNK devet vrsta C. melanuragrupe i tri vrste C. canicularis grupe preuzete iz Banke Gena. Geometrijsko morfometrijskom metodom analizirane su veličinske komponente desnog krila (oblik i veličina) 4717 jedinki 29 vrsta roda Cheilosia poreklom sa 21 područja Balkanskog poluostrva.U radu su utvrđeni diferencijalni fenotipovi veličine i oblika krila i specijes-specifični haplotipovi COI mtDNK koji su omogućili identifikaciju i razdvajanje blisko srodnih vrsta roda Cheilosia. Analizom parametara krila kod većine analiziranih taksona utvrđene su značajne razlike između konspecifičkih populacija većine analiziranih taksona, kod je jasan polni dimorfizam u obliku krila uočen kod svih analiziranih vrsta.Usaglašeno filogenetsko stablo na osnovu sekvenci 3' COI mtDNK ukazuje na monofiletski rod Cheilosiau okviru kojeg se izdvajaju četiri jasno odvojene klade koje odgovaraju podrodovima Convocheila, Taeniochilosia, Eucartosyrphusi Cheilosias. str. definisanim na osnovu morfoloških karaktera tradicionalnom taksonomijom (((Cheilosia s. str. + Eucartosyrphus) + Taeniochilosia) + Convocheila). Unutar klade Cheilosias. str. sve analizirane vrste su formirale monofiletske klastere sa njima blisko srodnim vrstama. Fenogrami evolucionih odnosa konstruisani su UPGMA metodom na osnovu oblika krila su bili podudarni sa topologijom filogenetskih stabla analiziranih grupa vrsta.Nucleotide COI mtDNA diversity and phenotypic variation of wing parameters (size and shape) of taxa of the genus Cheilosiawere analysed. Obtained data were used to solve phylogenetic and evolutionary relationships of these taxa. A total of 119 specimens from 14 Cheilosiaspecies collected from eight localities on the Balkan Peninsula and one from Finnish Lapland (specimens of C. albitarsis) were used for DNA sequencing. Amplification was attempted for 3' end of COI mtDNA gene (and 5' COI mtDNA and ITS2 rDNA in C. laticornis species group). COI mtDNA sequences from nine species of the C. melanura group and three species of the C. canicularis group were obtained from GenBank. Geometric morphometric analysis of wing size and shape was conducted on 4717 specimens from 29 species collected from 21 localities on the Balkan Peninsula.Based on differential phenotypes of wing size and shape and species-specific COI mtDNA haplotypes it was possible to identify and delimitate closely related species of genus Cheilosia. It was estimated that size and shape variation occurred among conspecific populations. A consistent sexual wing shape dimorphism was revealed in all analyzed species.Strict consensus cladogram based on COI mtDNA data revealed monophyletic genus Cheilosia and subgeneric divisions that are congruent with subgenera described based on traditional morphological character (((Cheilosia s. str. + Eucartosyrphus) + Taeniochilosia) + Convocheila). Within the clade Cheilosias. str. closely related species group were supported as monophyletic. UPGMA phenograms of evolutionary relationships based od wing traits produced the same topology as the phylogenetictrees constructed using molecular data.
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Milana, Rakić. "Diverzitet makrogljiva i njihova uloga u monitoringu stanja šumskih ekosistema Srbije." Phd thesis, Univerzitet u Novom Sadu, Prirodno-matematički fakultet u Novom Sadu, 2019. https://www.cris.uns.ac.rs/record.jsf?recordId=110999&source=NDLTD&language=en.
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U okviru ove doktorske disertacije vršeno je istraživanje zajednica makrogljiva u okviru 5 šumskih staništa na Vidliču, Kopaoniku i Tari. Ispitivan je mikodiverzitet sa morfološkog, funkcionalnog i genetskog stanovišta. U istraživanju morološkog i funkcionalnog diverziteta, korišćene su različite klasične metode čiji rezultati suomogućili procenu stanja posmatranih mikocenoza, kao i samih šumskih staništa. Za analizu sastava vrsta u okviru mikocenoza, kao i procenu uticaja abiotičkih faktora na brojnost i sastav vrsta u okviru različitih funkcionalnih grupa, korišćeno je nekolikostatističkih metoda (PCA, PLS, CA i CCA). Osam vrsta, koje su pripadale najrasprostranjenijim i najzastupljenijim vrstama su odabrane za molekularne analize, koje su podrazumevale sekvenciranje ITS regiona rDNK, analizu njihovihpolimorfizama kao i filogenetske analize u okviru vrste/roda. U cilju procene zagađenja staništa, u plodnim telima makrogljiva i njihovom supstratu je određen sadržaj metala (atomskom apsorpcionom spektrofotometrijom) i radionuklida(gamaspektrometrijom). Dobijeni rezultati ukazuju na to da diverzitet makrogljiva oslikava stanje samog staništa i da dugoročnim monitoringom mogu ukazati na promene u njemu.Within the framework of this doctoral dissertation, monitoring of macrofungal communities, within 5 forest habitats on Vidlič, Kopaonik and Tara, was done. Mycodiversity was investigated from the morphological, functional and genetic point of view. Various classical methods used, enabled the assessment of the condition of macrofungal communities, as well as the observed forest habitats. Several statistical methods (PCA, PLS, CA and CCA) were used to analyze the composition of species within the mycocenosis, as well as the assessment of the effects of abiotic factors on the species richness and species composition within different functional groups.Some of the most represented species have been selected for molecular analyzes, which includedsequencing of the ITS region, the analysis of polymorphisms, as well as phylogenetic analyzes within the species/genus. In order to assess the pollution of habitats, the content of metals (atomic absorption spectrophotometry) and radionuclides (gamma spectrometry) was determined in the sporocarps of macrofungi and their substrate. The obtained results indicate that diversity of macrofungi reflects the state of the habitat itself and that long-term monitoring can indicate changes in it.
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Sibajev, Alexander. "Desenvolvimento de marcador molecular para o diagnóstico de variedades de leishmania circulantes na Região Norte do Brasil." Universidade Federal do Amazonas, 2005. http://tede.ufam.edu.br/handle/tede/3068.
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Previous issue date: 2005-12-14The determination of the prevailing species responsible for American Tegumentary Leishmaniasis (ATL) and the detection at species level of the varieties of the protozoan parasite agent of this endemic disease at the Amazon region are important for determination of the clinical evolution and to better indicate the therapeutic conduct due to the different responses to chemotherapeutic drugs by the Leishmania species. By now we are not aware of an available test to Leishmania (Viannia) guyanensis capable of detecting its intra-specific varieties obtained from human clinical presentations or from vertebrate and invertebrate hosts. We succeed to discriminate Leishmania (V.) guyanensis from Leishmania (V.) braziliensis and also from Leishmania (V.) panamensis through a polimerase chain reaction direct genomic DNA amplification aimed at the transcribed internal spacer (ITS) of the ribosomal RNA gene (rDNA). The positive reaction is visualized at the agarose gel electrophoresis by the presence of an aproximatedly 229 nucleotides size band for L. guyanensis that is absent for the two other species L. braziliensis and L. panamensis. The diagnosis can be done using culture material, skin biopsy or squashing the sand fly vector and having the DNA extracted. In a second step of the investigation, the ITS rDNA was sequenced in L. lainsoni; L. naiffi and four L. guyanensis strains, two of them presenting a muco-cutaneous form of Leishmaniasis. These sequences were compared to others available at the Genbank Database, confirming the previous data from multilocus enzyme electrophoresis and ITS restriction fragment lenght polymorphisms analysis, positioning L. lainsoni and L. naiffi as more divergent species as compared to L. braziliensis, L. panamensis and L. guyanensis species inside de Viannia sub-genus. A correlation was observed in grouping nearer the two L. guyanensis strains, respectively IM4243 and IM4235, responsible for the muco-cutaneous form. This protozoan belonging to sub-genus Viannia show clinical and epidemiological importance in South America north region, particularly the Amazon region and this study can be considered an advance in providing a tool to better understand the parasite species silvatic cycle and in providing tools to characterize the main species responsible for the clinical form presentation of tegumentary leishmaniasis in the human population at this region.
A determinação da espécie responsável pela Leishmaniose Tegumentar Americana e a detecção específica das variedades do protozoário agente dessa doença endêmica na Amazônia, é importante para determinação do comportamento clínico e indicação da conduta terapêutica, devido as diversas respostas aos quimioterápicos pelas espécies de Leishmania. No momento se desconhece um teste disponível para a Leishmania (Viannia) guyanensis, que seja capaz também de incluir suas variedades intra-específicas obtidas de casos humanos e de hospedeiros e vetores silvestres. Neste trabalho se conseguiu discriminar alguns isolados de Leishmania (Viannia) guyanensis, de Leishmania (Viannia) braziliensis e também de Leishmania (Viannia) panamensis através da reação em cadeia da polimerase direcionada para a amplificação do espaçador transcrito interno (ITS) do gene do RNA ribossomal. A reação positiva é dada pela visualização de um fragmento amplificado de cerca de 229 nucleotídeos, para L. (V.) guyanensis e ausente para as outras duas espécies. O diagnóstico pode ser feito com o DNA extraído de cultivo do parasita, diretamente das amastigotas da borda de lesão cutânea ulcerada ou do vetor infectado pela promastigota de Leishmania. Numa etapa seguinte a região ITS do rDNA foi sequenciada para L. lainsoni, L. naiffi e quatro cepas de L. guyanensis em que duas apresentavam forma muco-cutânea e duas outras a forma cutânea da leishmaniose. Essas sequências foram comparadas com as disponíveis em banco de dados como o Genbank, resultando na confirmação dos dados obtidos de variabilidade genética por outros autores, quando utilizada a técnica de isoenzimas e ITS-RFLP. O posicionamento de L. lainsoni e L. naiffi se mostrou mais divergente que L. guyanensis, L. braziliensis e L. panamensis, dentro do subgênero Viannia. Foi também encontrada uma relação de proximidade entre os isolados de L. guyanensis IM4243 e IM4235 apresentando lesão cutâneo-mucosa. As leishmânias do sub-gênero Viannia apresentam importância epidemiológica na América do Sul, sobretudo na região amazônica e esse estudo poder ser considerado importante ao desenvolver meios de diagnóstico específico do parasita, detectando sua presença em vetores e reservatórios silvestres em certas áreas e servindo como marcador para a principal espécie responsável pelas formas clínicas de leishmaniose nessa região.
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Ribeiro, Diorvania Cardoso. "Relação filogenética, por ITS-rDNA, de Colletotrichum spp., agente causal da mancha foliar da gala em macieira." Universidade do Estado de Santa Catarina, 2007. http://tede.udesc.br/handle/handle/1071.
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Previous issue date: 2007-02-26Conselho Nacional de Desenvolvimento Científico e Tecnológico
The apple is a temperate clime fruit with larger dispersion, consumption and the more marketed all over the world as fresh fruit. The apple production has been committed by the incidence of diseases, in which Apple Leaf Spot (ALS), whose causal agent is the Colletotrichum spp. Nowadays this disease is one of the largest concerns of the producers and researchers. The origin of this disease in apple tree plants is not still well known. Studies based on the phylogeny allow to relate evolutionarily the organisms and characterize possible divergence mechanisms origin. This will contribute in disease control and prevention of new races sprout. The objective of this work was to study the variation of the ITSs rDNA among apple tree pathogenic isolates of Colletotrichum spp. from apple, citrus and feijoa. All isolates were first cultivated on PDA, for one week at 24oC. In the PCR amplification of the rDNA was used initiators ITS1 and ITS4. The amplified fragment was digested with restriction enzymes (Rsa I, Alu I, Hinf I, Hpa II, Hha I, Xho I, Acc I, Eco RI and Taq I). The revelation was in 2% agarose gel. It was obtained a great variation with products of the cleaved PCR products, from 90 to 500 pb. The amplified fragment was purified (QIAquick Gel Extraction Kit 250 - Unisciense of Brazil) and the fragment (ITS of the rDNA) was sequenced for all isolates. The sequences were aligned with the ClustalW software and the phylogenetic tree was constructed in the Mega 3.1 software. The products obtained in the PCR amplification of the rDNA region (ITS1-5,8S-ITS2), with the initiators pair ITS1 and ITS4 revealed a fragment with approximately 600 pb, for all the isolated analyzed. Through the analysis for the ARDRA was possible to separate isolates groups in haplotypes, which was efficient for the correlation between haplotypes and hosts, containing in a same haplotypes of the same host. It was possible to group the isolates of Colletotrichum in species, using the phylogenetic tree, independent of his host. All of the obtained sequences presented more than 93% of similarity, fact that reinforces the hypothesis that the Colletotrichum spp., causal agent of ALS, is nearly related with citrus and feijoa Colletotrichum
A maçã é a fruta de clima temperado de maior dispersão, consumo e a mais comercializada como fruta fresca em todo o mundo. A produção de maçã no Brasil tem sido comprometida pela incidência de várias doenças, das quais a Mancha Foliar da Gala (MFG), cujo agente causal são espécies de Colletotrichum spp., tem sido, atualmente, uma das maiores preocupações dos produtores e pesquisadores. A origem desta doença em macieira ainda não está bem esclarecida e a utilização de estudos baseados na filogenia permitem relacionar os organismos evolutivamente, caracterizando possíveis mecanismos de divergência evolutiva e a origem do patógeno, contribuindo na adoção de medidas de controle e prevenção quanto ao surgimento de novas raças. O presente trabalho objetivou estudar a variação do DNA ribossomal, (rDNA) entre isolados de Colletotrichum spp. patogênicos em macieira, em citros e goiaba serrana. Todos os isolados foram cultivados em meio BDA, por uma semana a 24oC. A amplificação do rDNA foi realizada utilizando-se iniciadores ITS1 e ITS4, seguida pela digestão da região ITS (espaçador interno transcrito) com enzimas de restrição (Rsa I, Alu I, Hinf I, Hpa II, Hha I, Xho I, Acc I, Eco RI e Taq I). Os produtos obtidos na amplificação da região ITS1-5,8S-ITS2 do rDNA revelaram um fragmento de aproximadamente 600 pares de bases (pb), para todos os isolados analisados. Todos os fragmentos amplificados foram clivados, obtendo uma grande variação, a qual foi de 90 a 500 pb. Utilizando a técnica de ARDRA (Amplified Ribosomal DNA Restriction Analysis) foi possível separar e agrupar os isolados em haplótipos, a qual foi eficiente para a correlação entre haplótipo e hospedeiros, agrupando em um mesmo haplótipo isolados do mesmo hospedeiro. O fragmento amplificado foi purificado com kit QIAquick Gel Extraction Kit 250 (Qiagen, Hilden, Germany) e as amostras foram seqüenciadas na região ITS do rDNA de todos os isolados. As seqüências foram alinhadas no software ClustalW e a árvore filogenética foi construída no software Mega 3.1. Com o seqüenciamento de DNA foi possível inferir sobre a possível espécie de fungo que pertence o segmento de DNA analisado. A região ITS do rDNA mostrou-se muito eficaz para estudos de filogenia. A partir da árvore filogenética foi possível agrupar os isolados de Colletotrichum por espécies, independente do seu hospedeiro. Todas as seqüências obtidas apresentaram valores superiores a 93% de similaridade, fato esse, que reforça que o Colletotrichum spp., causador da MFG, possui relações de parentesco com o isolados de Colletotrichum spp. isolados de citros e de goiaba serrana
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Hansen, Mario Jens. "Genotyp-Identifizierung und Wechselwirkungen an zwei Populus-Chimären." Doctoral thesis, Humboldt-Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, 2005. http://dx.doi.org/10.18452/15385.
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Zwei Populus-Pfropfchimären (MA und AI), die aus P. x canadensis ‘Marilandica’ (M), P. maximowizcii x P. trichocarpa ‘Androscoggin’ (A) and P. nigra L. ’Italica’ (I) aufgebaut sind, wurden für Untersuchungen zur Laub- und Blütenblattentwicklung genutzt. In MA bildet M die äußere Lage (L1) und ihr Derivat, die Epidermis, während die inneren Lagen (L2, L3 etc.) von A gebildet werden. Bei AI stammt die L1 von A und L2, L3 etc. werden von I gebildet. Die genotypisch andersartige Epidermis bedingt bei Periklinal-Chimären morphologische Effekte wie zum Beispiel einen Fruchtknoten in einigen MA-Blüten. Morphologische Besonderheiten verschiedener Gewebe sowohl von M und A als auch von MA wurden verglichen, um festzustellen, wie sie durch die Gewebetransplantation verändert oder beeinflusst wurden und, um mögliche Genotyp- Interaktionen oder -Wechselwirkungen in einem Gewebe ausfindig zu machen. Für die Genotypidentifizierung in verschiedenen Organen wurde die RAPD-PCR getestet. Einer von 20 getesteten 10mer Zufallsprimern (GGAGTGGACA) ermöglichte bei der Verwendung von DNA aus Blattmaterial die Erzeugung verschiedener Bandenmuster für M und A. Bei der Verwendung von MA-Blattmaterial zeigte sich eine Kombination der Muster von M und A, sodass ein Chimärennachweis für das MA-Blattmaterial erbracht wurde. Für ein übertragbares System wurde die spezifische PCR getestet. Unter Verwendung spezifischer Primer für die 16s-rDNA zeigten die PCR-Produkte einheitliche Banden und nach anschließender Sequenzierung eine weitgehende Übereinstimmung der phylogenetischen Verwandtschaft von I, M und A. Weiterhin wurden die kernkodierten rDNA Bereiche ITS 1 und ITS 2 zwischen 18S und 25S getestet. Für I, M und A konnten jeweils zwei Banden von unterschiedlicher Größe und Sequenz ermittelt werden, die vermutlich auf funktionierende rDNA aber auch auf Pseudogene (beschnitten) in niedriger Kopienzahl hinweisen. Die ITS-Regionen von I, M und A wurden charakterisiert, um einen Einblick in die Struktur und Phylogenie der Salicacaee-Familie zu erhalten. Aus den Sequenzunterschieden konnten für I und A spezifische Primerpaare abgeleitet werden, die für die Identifizierung von I und A in AI und MA verwendet werden können. Mittels A-Marker konnte nachgewiesen werden, dass Fruchtknoten aus MA-Blüten neben M-Gewebe auch den A-Genotyp enthalten.Two Populus graft chimeras (MA and AI) produced of P. x canadensis ‘Marilandica’ (M), P. maximowizcii x P. trichocarpa ‘Androscoggin’ (A) and P. nigra L. ’Italica’ (I) were used for investigations of leaf and flower development. In MA the exogenous layer (L1) forms the epidermis and is derived from M while inner layers (L2, L3 etc.) descend from A whereas in AI L1 is formed by A while L2, L3 etc. descend from I. The exogenous epidermis of the periclinal chimeras imposes morphological effects such as an extra female sex in some of the MA flowers. The morphological characteristics of different plant tissues of parents and chimera were compared to determine how they were modified or altered by the tissue transplantation and possibly identify co-existing or interacting genotypes in one tissue. RAPD-PCR was tested for its usefulness to amplify polymorphic fingerprints including donor specific DNA fragments. One random 10mer primer (GGAGTGGACA) out of 20 tested revealed the amplification of patterns including donor specific DNA bands using extracts from leaf tissues of the M and A parents that were combined using extract from leaf tissue of the MA chimera. This indicates that the leaves of the MA chimera are formed by tissues of M and A. However, the inherent disadvantage of RAPD-PCR is the reproducibility of PCR product generation. Therefore the discriminative potential of the ITS region located between the rRNA genes was investigated. The application of specific 16S ribosomal DNA (rDNA) primers for amplification and sequencing of PCR products revealed a closely phylogenetic relationship between I, M and A. Consequently the ITS1 and ITS2 of nuclear rDNA between 18S and 25S were used. The amplified fragments were purified, cloned in E. coli and sequenced. Analyses of multiple clones demonstrated extensive paralogy within and between I, M and A ITS operons. For each parent were at least two rDNA operons as well as multiple paralogous sequences within operons identified. The use of PCR and sequence analyses showed that one of the operons encodes a putative expressed (functional) rDNA whereas the second encodes a pseudogen (truncated) in low copy number. We also characterized the ITS regions of I, M and A to gain insights into structure and phylogeny of the Salicacaee family. Based on sequence divergence primers were designed for A and I and used for the identification of A in MA carpels.
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Coimbra, Cíntia Schultz. "Inferências filogenéticas na ordem Fucales (Phaeophyceae), com ênfase no gênero Sargassum C. Agardh do Atlântico Sul." Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-22082007-101454/.
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O gênero Sargassum C. Agardh (Sargassaceae) constitui um dos mais representativos dentre os 41 gêneros da ordem Fucales (Phaeophyceae, Heterokontophyta), é amplamente distribuído nas regiões tropicais e subtropicais do globo e é considerado um importante componente da flora marinha. Devido ampla variabilidade fenotípica é considerado um dos gêneros de taxonomia mais complexa dentre as algas pardas, como são popularmente conhecidos os representantes da classe Phaeophyceae. A filogenia da ordem Fucales é bastante discutida para gêneros do hemisfério norte, mas ainda pouco elucidada. Os estudos de filogenia referentes ao gênero Sargassum são escassos, limitando-se a poucos marcadores moleculares, com baixa resolução no âmbito inter-específico e limitados à espécies de ocorrência nos oceanos Indo-Pacífico e Atlântico Norte. Nenhum estudo filogenético incluí espécies do Atlântico Sul para este gênero. Este estudo é pioneiro na análise de seqüências de diferentes marcadores moleculares para espécies do Atlântico Sul. Neste estudo, foram seqüenciados completamente os marcadores moleculares nucleares SSU rDNA e ITS2 para os táxons infra-genéricos Sargassum cymosum var. cymosum, S. cymosum var. nanum, S. furcatum, S. stenophyllum e S. vulgare. Todas as seqüências obtidas para ambos os marcadores apresentaram 100% de identidade entre os táxons analisados. Foram feitas seqüências também para o marcador molecular plastidial rbcL (parcial) e espaçador rbcLS para as espécies S. filipendula, S. stenophyllum e S. vulgare que resultaram também em 100% de identidade. Análises filogenéticas de cada um dos marcadores moleculares, incluindo nossas seqüências e aquelas disponíveis no Genbank e geradas pelos métodos de inferência \"Neigbour-joining\", máxima parcimônia e máxima verossimilhança se apresentaram robustas e corroboram outros resultados descritos na bibliografia referente a ordem Fucales e ao gênero Sargassum. Entretanto, tais resultados fornecem um forte indício da necessidade de busca de marcadores moleculares eficientes, devidamente respaldados por estudos de hibridação in vitro, dados ecológicos e de biogeografia para um melhor entendimento acerca das espécies ocorrentes na costa brasileira.The genus Sargassum C. Agardh (Sargassaceae) is one of the most conspicuous among the 41 genera of the order Fucales (Phaeophyceae, Heterokontophyta). The genus has a broad distribution in the tropical and subtropical regions of the world, and is considered an important component of the marine flora. Due to a high phenotipic variation, the taxonomy of the genus is considered of the most complex among the brown seaweeds, as are known the representatives of the class Phaeophyceae. The phylogeny of the order Fucales was studied for the North Hemisphere genera, but is still not well understood. The phylogenetic studies of the genus Sargassum are scarce and limited to a few molecular markers, presenting low resolution for inter-specific analysis and are available only for species from the Indo-Pacific and the North Atlantic. There are no phylogenetic studies including species from the South Atlantic for the genus. This study is the first to analyze sequences from different molecular markers for species from the South Atlantic. In this study, the nuclear SSU rDNA and ITS2 were completely sequenced for the infra-generic taxa Sargassum cymosum var. cymosum, S. cymosum var. nanum, S. furcatum, S. stenophyllum and S. vulgare. All the sequences for both markers presented 100% identity among analyzed taxa. Sequences were also obtained for the chloroplast marker rbcLS, including parcial rbcL and the spacer region rbcLS for the species S. filipendula, S. stenophyllum and S. vulgar. These sequences also presented 100% identity among analyzed taxa. Phylogenetic analysis of each of the molecular markers, including our sequences together with other sequences available in the Genbank and generated by the inference methods Neigbour-joining, maximum parsimony and maximum likelihood were robust and similar to other results described in the literature for the order Fucales and the genus Sargassum. Nonetheless, these results are an indicative of the need for more efficient molecular markers, associated with data from in vitro hibridization, ecology and biogeography for a better understanding about the taxa occurring on the brazilian coast.
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CAVALCANTI, Francinete Carla Nunes. "Variabilidade de isolados de Colletotrichum gloeosporioides, quanto a patogenicidade a frutos de mangueira (Mangifera indica L.), marcadores RAPD e região ITS do rDNA." Universidade Federal de Pernambuco, 2005. https://repositorio.ufpe.br/handle/123456789/765.
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Previous issue date: 2005A antracnose causada pelo fungo Colletotrichum gloeosporioides é uma das doenças mais graves da mangueira, sendo um fator limitante à produção de frutos sadios e comercializáveis. O presente trabalho objetivou analisar a variabilidade de isolados de C. gloeosporioides, quanto à patogenicidade a frutos de mangueira, marcadores RAPD e região ITS do rDNA. Foram utilizados cinco isolados obtidos de cebola e 10 de mangueiras de diferentes regiões do estado de Pernambuco. O teste de patogenicidade foi realizado em frutos das variedades Rosa e Espada. Para a análise de RAPD foram utilizados os iniciadores OPX-15, OPX-02, OPX-06, OPA-11 e OPA-02 e para a amplificação do locus ITS1-5.8S-ITS2 do rDNA, os iniciadores ITS1 e ITS4. Os isolados oriundos de mangueiras com sintomas de antracnose foram mais agressivos para as duas variedades estudadas do que os isolados de cebola. Do dendrograma gerado pela análise do RAPD, dois grupos foram delineados, separando todos os isolados de mangueiras dos isolados de cebola. Não houve polimorfismo entre os isolados de C. gloeosporioides pela análise dos produtos de amplificação da região ITS1-5.8S-ITS2 do rDNA, porém, a digestão do produto com a enzima Msp I evidenciou diferença para o isolado URM 4596 (Mangifera indica L./Ilha de Itamaracá-PE)
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Queiroz, Camila de Sousa. "Variação intragenômica de rDNA em Carapichea ipecacuanha (Rubiaceae): evolução em concerto incompleta e pseudogenes." Universidade Federal de Viçosa, 2010. http://locus.ufv.br/handle/123456789/4722.
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Previous issue date: 2010-02-24Conselho Nacional de Desenvolvimento Científico e Tecnológico
The investigation of intra-individual variation of the rDNA cistron ITS in Carapichea ipecacuanha was made from direct sequencing of 26 individuals and from sequencing of 240 clones, representing another 51 individuals. The secondary structures of 5.8S and ITS2 regions show the typical configurations present in angiosperms respectively for 20 and 48 haplotypes. The comparison with the conserved motifs in angiosperms and the secondary structures obtained for the 5.8S region, the most reliable markers of functional sequences in C. ipecacuanha, allowed the identification of 13 pseudogenes among 26 haplotypes of 5.8S. The analysis of the secondary structure of ITS2 added one haplotype to the set of pseudogenes. The loss of functionality in some haplotypes has occurred prior to the others copies due to the accumulation of a larger number of substitutions and the formation of groups of pseudogenes that belong to distinct populations.
A investigação da variação intra-individual do cistron de rDNA ITS em Carapichea ipecacuanha foi realizada a partir de seqüenciamento direto de fragmentos de PCR de 26 indivíduos e do seqüenciamento de 240 clones, representando outros 51 indivíduos. As estruturas secundárias das regiões 5.8S e ITS2 apresentam as configurações típicas presentes em angiospermas respectivamente em 20 e 48 haplótipos encontrados. A comparação com os motivos conservados em angiospermas e as estruturas secundárias obtidas para a região 5.8S, indicadores mais confiáveis da funcionalidade das seqüências em C. ipecacuanha, permitiram a identificação de 13 pseudogenes entre os 26 haplótipos de 5.8S encontrados. A análise da estrutura secundária do ITS2 adicionou um haplótipo ao conjunto de pseudogenes. A perda de funcionalidade em alguns haplótipos deve ser mais antiga do que em outros em razão do acúmulo de maior número de substituições e da formação de grupos de pseudogenes pertencentes a populações distintas.
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Bower, James Earl. "Concerted evolution of the rDNA ITS1 in the Anopheles punctulatus group." Access electronically, 2008. http://ro.uow.edu.au/theses/122.
Full textBooks on the topic "ITS2 rDNA"
Book chapters on the topic "ITS2 rDNA"
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Tandon, Veena, Devendra Kumar Biswal, Pramod Kumar Prasad, and Chenkual Malsawmtluangi. "Reconstructing the Phylogenetic Relationships of the Cyclophyllidean Cestodes: A Case Study Using ITS2 rDNA and Sequence-Structure Alignment." In Biomedical Engineering Systems and Technologies, 309–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-18472-7_24.
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Nesme, X., and P. Normand. "Section 3 update: Easy individual strain and community typing by rDNA ITS1 analysis." In Molecular Microbial Ecology Manual, 2573–89. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-2177-0_309.
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Hause, B., F. Baldauf, K. Stock, C. Wasternack, and M. Metzlaff. "Molecular Analysis of Mitochondrial DNA and Cloning of its rDNA Fragments from Tomato Cell Suspension Culture." In Metabolism and Enzymology of Nucleic Acids, 131–36. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4613-0749-5_19.
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Devictor, M., M. Hartung, and A. Stahl. "Distribution of rDNA and of its transcription sites in the nucleolus of the human Sertoli cell." In Chromosomes Today, 295–300. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-010-9166-4_28.
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Hyppönen, Konstantin, Miika Alonen, Sami Korhonen, and Virpi Hotti. "XHTML with RDFa as a Semantic Document Format for CCTS Modelled Documents and Its Application for Social Services." In Lecture Notes in Computer Science, 229–40. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-25953-1_19.
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Salauddin, Md. "A Brief Concept of Cell Culture: Challenges, Prospects and Applications." In Cell Culture [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.99387.
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Cell culture is an in vitro technique in which cells, tissues, or organs (animal origin) are artificially grown with the support of an artificial environment that encompasses culture medium, CO2 level, pH indicator, temperature keeping tissues alive and growing appropriately. Organ culture, Primary explant culture, and Cell culture among them cell culture widely used for the understanding of cell growth, normal functions, identification of growth factors, viral vaccine development, recombinant DNA (rDNA) technology, and immunobiological research. Due to high feasibility, cell culture practices highly demandable in the pharmaceutical industry. As well as animal cell culture used in laboratory research to study the cytotoxicity of new drug metabolic studies, aging, therapeutic proteins, the effects of drugs and toxic compounds on the cells and mutagenesis and carcinogenesis. There are a lot of issues in cell culture, Mycoplasma is one of the major. During cell culture, a single antibiotic often cannot kill the mycoplasma. Besides, culture media, pH indicator, incubation, cryopreservation, thawing, passaging of cells, and trypsinization have a great impact on cell culture. This chapter will help the reader to understand the whole process of cell culture and its applications, which will take them one step forward in their virology and cell culture research along with inspiration. This chapter also aids in the concept of cell count, cell suspension, CCF measurement, MOI (Multiplicity of Infection), and cell infection. Eventually, the reader will get a crystal clear concept of cell culture.
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"Phylogenetic Analysis within Genera Morchella (Ascomycota, Pezizales) and Macrolepiota (Basidiomycota, Agaricales) Inferred from rDNA ITS and EF-1a Sequences." In Systematics and Evolution of Fungi, 171–218. CRC Press, 2012. http://dx.doi.org/10.1201/b11606-10.
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"Phylogenetic Analyses of Phellinus s. l. and Inonotus s. l. (Hymenochaetales) Inferred from rDNA ITS Sequences and Morphological Data." In Systematics and Evolution of Fungi, 265–86. CRC Press, 2012. http://dx.doi.org/10.1201/b11606-12.
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Cooper, Frederick. "Claiming Citizenship." In Citizenship between Empire and Nation. Princeton University Press, 2014. http://dx.doi.org/10.23943/princeton/9780691161310.003.0005.
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This chapter explores different instances of African claim making. It first looks at the effort of the Rassemblement Démocratique Africain (RDA) in the Sudan and especially the Côte d'Ivoire to build up its political apparatus across the territory and the efforts of the government to combat what it saw as a countergovernment. The chapter then turns to ways in which African political leaders sought to change the very terms in which future politics was discussed—to rethink the meaning of nation and sovereignty. They were thinking about different levels of political belonging and political action. And as France entered into discussion of creating a European community, they were thinking of expanding the idea of a “Franco-African” political ensemble into something even wider, into “Eurafrica.”
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Herrmann-Fankhänel, Anja. "Utilization of Online Platforms by Social Entrepreneurs for Social Sustainable Development." In Strategic Marketing for Social Enterprises in Developing Nations, 75–102. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7859-8.ch004.
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Socially sustainable development can be driven by individuals, entrepreneurs, growing start-ups, and international companies. As social entrepreneurs, people opt for a form of organization that contributes to social improvement through entrepreneurial means. The question is: How do they do it? The resource dependence approach (RDA) assumes that all decisions and activities of a (social) enterprise are based on information about its environment. Therefore, the four key components of the social enterprise (individual, organization, social innovation, market orientation) must be appropriate. In this chapter, therefore, social enterprises are outlined as active participants and shapers of the economy and society. Since an active improvement with regard to socially sustainable development is focused by the social enterprises in Africa, a description of the social enterprise's environment is also given within the framework of topical focuses. The goal is to derive recommendations about action for social enterprises to achieve their goals.
Conference papers on the topic "ITS2 rDNA"
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Prokhorova, E. E., and R. R. Usmanova. "GENETIC POLYMORPHISM OF SNAILS SUCCINEA PUTRIS (GASTROPODA, PULMONATA)." In V International Scientific Conference CONCEPTUAL AND APPLIED ASPECTS OF INVERTEBRATE SCIENTIFIC RESEARCH AND BIOLOGICAL EDUCATION. Tomsk State University Press, 2020. http://dx.doi.org/10.17223/978-5-94621-931-0-2020-33.
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Genotypic diversity of snails Succinea putris L. (Linnaeus, 1758) collected in the north-west of Russia and in the Republic of Belarus was analysed. Homology between the nucleotide sequences of snails from different population made up 100% by the nucleotide sequence of ITS1-5.8S-ITS2 region of rDNA. Genetic variability based on mitochondrial markers was insignificant. Average genetic distances between samples made up 0,009 for СOI gene loci and 0.008 for CytB gene loci. Was found ten haplotypes of the mitochondrial gene CytB and nine haplotypes of the mitochondrial gene СOI. Perhaps the genetic homogeneity of snails S. putris found in the study explains a low variability of their parasites, trematodes from the genus Leucochloridium.
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"SYSTEMATIC POSITION AND PHYLOGENETIC RELATIONSHIPS OF THE CYCLOPHYLLIDEAN CESTODES - An In-silico Study using ITS2 rDNA and Sequence-structure Alignment." In International Conference on Bioinformatics. SciTePress - Science and and Technology Publications, 2010. http://dx.doi.org/10.5220/0002690500050012.
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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.
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Li, He, Guoying Zhou, and Junang Liu. "Sequence Analysis of rDNA ITS of Clinical Fusarium Species." In 2009 2nd International Conference on Biomedical Engineering and Informatics. IEEE, 2009. http://dx.doi.org/10.1109/bmei.2009.5305743.
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Liu, Jun-ang, Lin Li, Gouying Zhou, and Hui Wang. "Analysis rDNA ITS Sequence of Two High Quality Strains of Agaricus bisporus." In 2009 3rd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2009). IEEE, 2009. http://dx.doi.org/10.1109/icbbe.2009.5162367.
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Febriani, R., W. Sjamsuridzal, A. Oetari, I. Santoso, and I. G. Roosheroe. "ITS regions of rDNA sequence and morphological analyses clarify five Rhizopus strains from tempeh as Rhizopus oryzae." In PROCEEDINGS OF THE 3RD INTERNATIONAL SYMPOSIUM ON CURRENT PROGRESS IN MATHEMATICS AND SCIENCES 2017 (ISCPMS2017). Author(s), 2018. http://dx.doi.org/10.1063/1.5064156.
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Vebliza, Y., W. Sjamsuridzal, A. Oetari, I. Santoso, and I. G. Roosheroe. "Re-identification of five strains of Rhizopus arrhizus from tempeh based on ITS regions of rDNA sequence data." In PROCEEDINGS OF THE 3RD INTERNATIONAL SYMPOSIUM ON CURRENT PROGRESS IN MATHEMATICS AND SCIENCES 2017 (ISCPMS2017). Author(s), 2018. http://dx.doi.org/10.1063/1.5064164.
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Khasanah, M., W. Sjamsuridzal, A. Oetari, I. Santoso, and I. G. Roosheroe. "Phylogenetic analyses based on ITS regions of rDNA identified five Rhizopus strains from tempeh as R. delemar and R. oryzae." In PROCEEDINGS OF THE 3RD INTERNATIONAL SYMPOSIUM ON CURRENT PROGRESS IN MATHEMATICS AND SCIENCES 2017 (ISCPMS2017). Author(s), 2018. http://dx.doi.org/10.1063/1.5064138.
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Febriansyah, Evan, Iwan Saskiawan, Wibowo Mangunwardoyo, Tri Ratna Sulistiyani, and Eva Watamtin Widhiya. "Potency of growth promoting bacteria on mycelial growth of edible mushroom Pleurotus ostreatus and its identification based on 16S rDNA analysis." In INVENTING PROSPEROUS FUTURE THROUGH BIOLOGICAL RESEARCH AND TROPICAL BIODIVERSITY MANAGEMENT: Proceedings of the 5th International Conference on Biological Science. Author(s), 2018. http://dx.doi.org/10.1063/1.5050119.
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Lu, Xiaoyi, Dipti Shankar, Shashank Gugnani, and Dhabaleswar K. Panda. "High-performance design of apache spark with RDMA and its benefits on various workloads." In 2016 IEEE International Conference on Big Data (Big Data). IEEE, 2016. http://dx.doi.org/10.1109/bigdata.2016.7840611.
Full textReports on the topic "ITS2 rDNA"
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African Open Science Platform Part 1: Landscape Study. Academy of Science of South Africa (ASSAf), 2019. http://dx.doi.org/10.17159/assaf.2019/0047.
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This report maps the African landscape of Open Science – with a focus on Open Data as a sub-set of Open Science. Data to inform the landscape study were collected through a variety of methods, including surveys, desk research, engagement with a community of practice, networking with stakeholders, participation in conferences, case study presentations, and workshops hosted. Although the majority of African countries (35 of 54) demonstrates commitment to science through its investment in research and development (R&D), academies of science, ministries of science and technology, policies, recognition of research, and participation in the Science Granting Councils Initiative (SGCI), the following countries demonstrate the highest commitment and political willingness to invest in science: Botswana, Ethiopia, Kenya, Senegal, South Africa, Tanzania, and Uganda. In addition to existing policies in Science, Technology and Innovation (STI), the following countries have made progress towards Open Data policies: Botswana, Kenya, Madagascar, Mauritius, South Africa and Uganda. Only two African countries (Kenya and South Africa) at this stage contribute 0.8% of its GDP (Gross Domestic Product) to R&D (Research and Development), which is the closest to the AU’s (African Union’s) suggested 1%. Countries such as Lesotho and Madagascar ranked as 0%, while the R&D expenditure for 24 African countries is unknown. In addition to this, science globally has become fully dependent on stable ICT (Information and Communication Technologies) infrastructure, which includes connectivity/bandwidth, high performance computing facilities and data services. This is especially applicable since countries globally are finding themselves in the midst of the 4th Industrial Revolution (4IR), which is not only “about” data, but which “is” data. According to an article1 by Alan Marcus (2015) (Senior Director, Head of Information Technology and Telecommunications Industries, World Economic Forum), “At its core, data represents a post-industrial opportunity. Its uses have unprecedented complexity, velocity and global reach. As digital communications become ubiquitous, data will rule in a world where nearly everyone and everything is connected in real time. That will require a highly reliable, secure and available infrastructure at its core, and innovation at the edge.” Every industry is affected as part of this revolution – also science. An important component of the digital transformation is “trust” – people must be able to trust that governments and all other industries (including the science sector), adequately handle and protect their data. This requires accountability on a global level, and digital industries must embrace the change and go for a higher standard of protection. “This will reassure consumers and citizens, benefitting the whole digital economy”, says Marcus. A stable and secure information and communication technologies (ICT) infrastructure – currently provided by the National Research and Education Networks (NRENs) – is key to advance collaboration in science. The AfricaConnect2 project (AfricaConnect (2012–2014) and AfricaConnect2 (2016–2018)) through establishing connectivity between National Research and Education Networks (NRENs), is planning to roll out AfricaConnect3 by the end of 2019. The concern however is that selected African governments (with the exception of a few countries such as South Africa, Mozambique, Ethiopia and others) have low awareness of the impact the Internet has today on all societal levels, how much ICT (and the 4th Industrial Revolution) have affected research, and the added value an NREN can bring to higher education and research in addressing the respective needs, which is far more complex than simply providing connectivity. Apart from more commitment and investment in R&D, African governments – to become and remain part of the 4th Industrial Revolution – have no option other than to acknowledge and commit to the role NRENs play in advancing science towards addressing the SDG (Sustainable Development Goals). For successful collaboration and direction, it is fundamental that policies within one country are aligned with one another. Alignment on continental level is crucial for the future Pan-African African Open Science Platform to be successful. Both the HIPSSA ((Harmonization of ICT Policies in Sub-Saharan Africa)3 project and WATRA (the West Africa Telecommunications Regulators Assembly)4, have made progress towards the regulation of the telecom sector, and in particular of bottlenecks which curb the development of competition among ISPs. A study under HIPSSA identified potential bottlenecks in access at an affordable price to the international capacity of submarine cables and suggested means and tools used by regulators to remedy them. Work on the recommended measures and making them operational continues in collaboration with WATRA. In addition to sufficient bandwidth and connectivity, high-performance computing facilities and services in support of data sharing are also required. The South African National Integrated Cyberinfrastructure System5 (NICIS) has made great progress in planning and setting up a cyberinfrastructure ecosystem in support of collaborative science and data sharing. The regional Southern African Development Community6 (SADC) Cyber-infrastructure Framework provides a valuable roadmap towards high-speed Internet, developing human capacity and skills in ICT technologies, high- performance computing and more. The following countries have been identified as having high-performance computing facilities, some as a result of the Square Kilometre Array7 (SKA) partnership: Botswana, Ghana, Kenya, Madagascar, Mozambique, Mauritius, Namibia, South Africa, Tunisia, and Zambia. More and more NRENs – especially the Level 6 NRENs 8 (Algeria, Egypt, Kenya, South Africa, and recently Zambia) – are exploring offering additional services; also in support of data sharing and transfer. The following NRENs already allow for running data-intensive applications and sharing of high-end computing assets, bio-modelling and computation on high-performance/ supercomputers: KENET (Kenya), TENET (South Africa), RENU (Uganda), ZAMREN (Zambia), EUN (Egypt) and ARN (Algeria). Fifteen higher education training institutions from eight African countries (Botswana, Benin, Kenya, Nigeria, Rwanda, South Africa, Sudan, and Tanzania) have been identified as offering formal courses on data science. In addition to formal degrees, a number of international short courses have been developed and free international online courses are also available as an option to build capacity and integrate as part of curricula. The small number of higher education or research intensive institutions offering data science is however insufficient, and there is a desperate need for more training in data science. The CODATA-RDA Schools of Research Data Science aim at addressing the continental need for foundational data skills across all disciplines, along with training conducted by The Carpentries 9 programme (specifically Data Carpentry 10 ). Thus far, CODATA-RDA schools in collaboration with AOSP, integrating content from Data Carpentry, were presented in Rwanda (in 2018), and during17-29 June 2019, in Ethiopia. Awareness regarding Open Science (including Open Data) is evident through the 12 Open Science-related Open Access/Open Data/Open Science declarations and agreements endorsed or signed by African governments; 200 Open Access journals from Africa registered on the Directory of Open Access Journals (DOAJ); 174 Open Access institutional research repositories registered on openDOAR (Directory of Open Access Repositories); 33 Open Access/Open Science policies registered on ROARMAP (Registry of Open Access Repository Mandates and Policies); 24 data repositories registered with the Registry of Data Repositories (re3data.org) (although the pilot project identified 66 research data repositories); and one data repository assigned the CoreTrustSeal. Although this is a start, far more needs to be done to align African data curation and research practices with global standards. Funding to conduct research remains a challenge. African researchers mostly fund their own research, and there are little incentives for them to make their research and accompanying data sets openly accessible. Funding and peer recognition, along with an enabling research environment conducive for research, are regarded as major incentives. The landscape report concludes with a number of concerns towards sharing research data openly, as well as challenges in terms of Open Data policy, ICT infrastructure supportive of data sharing, capacity building, lack of skills, and the need for incentives. Although great progress has been made in terms of Open Science and Open Data practices, more awareness needs to be created and further advocacy efforts are required for buy-in from African governments. A federated African Open Science Platform (AOSP) will not only encourage more collaboration among researchers in addressing the SDGs, but it will also benefit the many stakeholders identified as part of the pilot phase. The time is now, for governments in Africa, to acknowledge the important role of science in general, but specifically Open Science and Open Data, through developing and aligning the relevant policies, investing in an ICT infrastructure conducive for data sharing through committing funding to making NRENs financially sustainable, incentivising open research practices by scientists, and creating opportunities for more scientists and stakeholders across all disciplines to be trained in data management.