Relevant bibliographies by topics / TrnL intron

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Academic literature on the topic 'TrnL intron'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "TrnL intron"

1

Nguyen, Sy Dinh, and Hunseung Kang. "Comprehensive analysis of chloroplast intron-containing genes and conserved splice sites in dicot and monocot plants." Science and Technology Development Journal - Natural Sciences 1, T1 (March 31, 2017): 60–68. http://dx.doi.org/10.32508/stdjns.v1it1.435.

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Despite the increasing knowledge on the importance of the intron splicing of chloroplast genes during plant growth and stress responses, identification of intron-containing chloroplast genes and determination of splice sites in chloroplast introns are still lacking. Here, we carried out a comprehensive analysis of the chloroplast genome sequences in important plants and crops, including four dicots (Arabidopsis thaliana, Coffea arabica, Nicotiana tabacum, and Panax schinseng) and four monocots (Musa acuminata, Oryza sativa, Triticum aestivum, and Zea mays). The results showed that both dicot and monocot chloroplast genomes harbor 6 intron-containing tRNAs (trnA, trnG, trnI, trnK, trnL, and trnV) and 10-12 intron-containing mRNAs (atpF, rpl2, rpl16, rps16, ndhA, ndhB, petB, petD, rpoC1, rps12, ycf3, and clpP). Notably, rpoC1 and clpP lacked introns in monocot plants, except M. acuminata. Analysis of the nucleotide sequences of chloroplast introns revealed that the 5’-splice sites, 3’-splice sites, and branch-point sites of the chloroplast introns were highly conserved among dicots and monocots. Notably, the 5’-splice sites and 3’-splice sites of the chloroplast introns were similar to those of the nuclear U12 introns, whereas the branch-point sites of the chloroplast introns were homologous to those of the nuclear U2 introns. Taken together, these results indicated that the chloroplast genomes contained strictly limited intron-containing genes with conserved splice sites, suggesting that splicing of chloroplast introns was important for chloroplast biogenesis and function in both dicot and monocot plants.
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Widyatmoko, AYPBC, and Susumu Shiraishi. "Inter- and intraspecific variation of chloroplast mini- and microsatellites DNA in the four closed related Acacia species." Indonesian Journal of Biotechnology 19, no. 1 (December 31, 2015): 1. http://dx.doi.org/10.22146/ijbiotech.8639.

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Mini- and microsatellites of four Acacia species, A. aulacocarpa, A. auriculiformis, A. crassicarpa and A.mangium were investigated on four non-coding regions of cpDNA, the intron of trnL, and the intergenicspacers of trnL - trnP, trnD - trnY, and trnP – trnW. Nine single base substitutions and six informative miniandmicrosatellites were detected in the the four cpDNA non-coding regions. Based on the substitutionsand mini- and microsatellites, ten cpDNA haplotypes (A - J) could be distinguished. Acacia auriculiformispossessed fi ve haplotypes, A. aulacocarpa, four haplotypes, and A. crassicarpa, three haplotypes. All samplesof A. mangium possessed the same haplotype. Mini- and microsatellites recognized in this study can beused for species identifi cation of the four Acacia species. The ten haplotypes could divided the four speciesinto 2 groups, A. aulacocarpa-A.crassicarpa group and A. auriculiformis-A. mangium group. By developing thePCR-based markers based on the sequence information, many experiments can be carried out for the Acaciaimprovement programs.
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Jarret, Robert L. "DNA Barcoding in a Crop Genebank: The Capsicum annuum Species Complex." Open Biology Journal 1, no. 1 (October 28, 2008): 35–42. http://dx.doi.org/10.2174/1874196700801010035.

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Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnCrpoB, rps16 and matK, and the nuclear waxy introns was examined in seven species of Capsicum (C. annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense and C. rhomboideum) in order to evaluate the feasibility of utilizing these loci for DNA barcoding within the C. annuum complex. Numerous insertions/deletions (indels) and substitutions were detected in all cpDNA introns. However, none was sufficient to differentiate the individual members of the C. annuum complex (C. annuum, C. chinense and C. frutescens). Variation within trnL-trnT, trnF-trnL and trnH-psbA enabled the differentiation of the complex from the other taxa examined. In contrast, single base indels and substitutions within the waxy introns permitted the differentiation of all taxa within the plant materials examined. The use of trnH-psbA or trnL-trnT, and the waxy introns is proposed for barcoding members of the C. annuum complex.
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Sun, Jianying, Xiaofeng Dong, Qinghe Cao, Tao Xu, Mingku Zhu, Jian Sun, Tingting Dong, Daifu Ma, Yonghua Han, and Zongyun Li. "A systematic comparison of eight new plastome sequences from Ipomoea L." PeerJ 7 (March 11, 2019): e6563. http://dx.doi.org/10.7717/peerj.6563.

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Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.
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Sedláková, V., P. Sedlák, D. Zeka, J. Domkářová, P. Doležal, and P. Vejl. "Evaluation of variations in plastid DNA non-coding regions in selected species of the genus Solanum." Czech Journal of Genetics and Plant Breeding 53, No. 3 (September 13, 2017): 127–31. http://dx.doi.org/10.17221/76/2015-cjgpb.

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The diversity of three non-coding plastid DNA loci (trnL/trnF spacer, trnV/16SrRNA spacer, trnL/trnL intron) was assessed in 16 Solanum L. species (135 individuals). Polymorphisms were detected by denaturing gradient gel electrophoresis (DGGE) and verified by direct sequencing. No intraspecific diversity and only poor interspecific diversity was detected. Unique S. mochiquense Ochoa specific length polymorphism at the trnL/trnL locus represented by duplication of an 18 bp segment was discovered. The detected DGGE interspecific trnL/trnF locus polymorphism did not specifically associate with single point mutations in the sequence confirmed by sequencing. The DGGE method was found to be a simple and cheap pre-exploring tool for mutation detection in compared DNA regions. Some identified polymorphisms can be used in the management of genetic resources.
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Haider, Nadia, and Imad Nabulsi. "Identification of Bread and Durum Wheats from their Diploid Ancestral Species Based on Chloroplast DNA." Agriculture (Pol'nohospodárstvo) 66, no. 2 (July 1, 2020): 56–66. http://dx.doi.org/10.2478/agri-2020-0006.

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AbstractSpecies that have been identified as the genome donors to cultivated polyploid durum and bread wheats (Triticum durum L. and T. aestivum L., respectively) are potential gene sources for the breeding of these two crops. Therefore, their accurate identification facilitates their use in the improvement of these crops. Based on chloroplast DNA analysis (rpL2 and rps16 introns, psbC-trnS, trnT-L, and trnL-F) using polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP), an attempt was made in 2018 (Department of Molecular Biology and Biotechnology/AECS) to identify durum and bread wheats from each of their proposed diploid ancestral species (i.e., T. monococcum, T. urartu, Aegilops speltoides, and Ae. tauschii). The use of two PCR markers (psbC-trnS and trnL-F) and three PCR-RFLP locus-enzyme combinations (rps16 intron-Tru 1I, rpL2 intron-Taq I, and trnT-L-Taq I) allowed the identification of all species involved. Reliable and accurate identification of diploid ancestors of durum and bread wheats using these candidate species-specific cpDNA markers will be useful for wheat breeding programs, in situ and ex situ conservation efforts, verification of seed purity in commercial seed stocks, and ensuring identity and integrity of accessions held within a collection does not change through unwanted gene flow or by genetic drift after regeneration by seed.
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Oksanen, Ilona, Katileena Lohtander, Kaarina Sivonen, and Jouko Rikkinen. "Repeat-type distribution in trnL intron does not correspond with species phylogeny: comparison of the genetic markers 16S rRNA and trnL intron in heterocystous cyanobacteria." International Journal of Systematic and Evolutionary Microbiology 54, no. 3 (May 1, 2004): 765–72. http://dx.doi.org/10.1099/ijs.0.02928-0.

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tRNALeu UAA (trnL) intron sequences are used as genetic markers for differentiating cyanobacteria and for constructing phylogenies, since the introns are thought to be more variable among close relatives than is the 16S rRNA gene, the conventional phylogenetic marker. The evolution of trnL intron sequences and their utility as a phylogenetic marker were analysed among heterocystous cyanobacteria with maximum-parsimony, maximum-likelihood and Bayesian inference by comparing their evolutionary information to that of the 16S rRNA gene. Trees inferred from the 16S rRNA gene and the distribution of two repeat classes in the P6b stem–loop of the trnL intron were in clear conflict. The results show that, while similar heptanucleotide repeat classes I and II in the P6b stem–loop of the trnL intron could be found among distant relatives, some close relatives harboured different repeat classes with a high sequence difference. Moreover, heptanucleotide repeat class II and other sequences from the P6b stem–loop of the trnL intron interrupted several other intergenic regions in the genomes of heterocystous cyanobacteria. Cluster analyses based on conserved intron sequences without loops P6b, P9 and parts of P5 corresponded in most clades to the 16S rRNA gene phylogeny, although the relationships were not resolved well, according to low bootstrap support. Thus, the hypervariable loop sequences of the trnL intron, especially the P6b stem–loop, cannot be used for phylogenetic analysis and conclusions cannot be drawn about species relationships on the basis of these elements. Evolutionary scenarios are discussed considering the origin of the repeats.
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ZHANG, WEI, JIAO QIN, RUI YANG, YI YANG, and SHI-BAO ZHANG. "Two new natural hybrids in the genus Pleione (Orchidaceae) from China." Phytotaxa 350, no. 3 (May 23, 2018): 247. http://dx.doi.org/10.11646/phytotaxa.350.3.4.

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Several species in the genus Pleione (Orchidaceae) have same or overlapping geographical distribution in China. In this study, two new natural hybrids, Pleione × baoshanensis and Pleione × maoershanensis, were described and illustrated. The parentage for these two hybrids was confirmed using molecular data from ITS of the nuclear ribosomal, trnT-trnL spacer and trnL-trnF region (trnL intron and trnL-trnF spacer) of the plastid DNA. Pleione × baoshanensis is intermediate between P. albiflora and P. yunnanensis, and characterized by its erose lamellae on the lip. Meanwhile, Pleione × maoershanensis is intermediate between P. hookeriana (P. chunii) and P. pleionoides, and characterized by its deep lacerate lamellae on the lip. For the individuals tested, molecular data suggest that P. albiflora is the maternal parent of Pleione × baoshanensis, and P. hookeriana (P. chunii) is the maternal parent of Pleione × maoershanensis. The history and taxonomic status of P. chunii is also discussed.
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Murphy, Daniel J., Frank Udovicic, and Pauline Y. Ladiges. "Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) by using sequence variations of an intron and two intergenic spacers of chloroplast DNA." Australian Systematic Botany 13, no. 5 (2000): 745. http://dx.doi.org/10.1071/sb99027.

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Three regions of chloroplast DNA are assessed for their utility for phylogenetic analysis of Acacia subgenus Phyllodineae: psbA–trnH intergenic spacer, the trnL intron and the trnL–trnF intergenic spacer. There are large differences in the lengths of the psbA–trnH spacer (155–440 bp) and trnL–trnF intergenic spacer (101–422 bp) regions, and large multi-residue indels were coded as multistate characters. Overall information content in these regions is relatively low, but the total evidence tree has 12 nodes resolved, five with jackknife support. By using Parkia timoriana as the outgroup, Acacia subgenus Acacia (A. farnesiana) is basal and Acacia subgenus Aculeiferum (A. senegal) is the sister taxon to subgenus Phyllodineae. Although based on a small sample size, within subgenus Phyllodineae, the results of this study have shown that section Alatae is not monophyletic, section Lycopodiifoliae is monophyletic and Botrycephalae is related to members of section Phyllodineae with racemose inflorescences.
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MAMONTOV, YURIY S., NADEZHDA A. KONSTANTINOVA, and ANNA A. VILNET. "One more species in the genus Jungermannia (Marchantiophyta: Jungermanniaceae)." Bryophyte Diversity and Evolution 40, no. 2 (December 27, 2018): 79. http://dx.doi.org/10.11646/bde.40.2.6.

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Jungermannia afoninae is described from the mountains of South Siberia based on a complex taxonomical approach exploring critical reinvestigation of morphological features and analyses of newly obtained trnL–trnF and trnG-intron cpDNA sequences from six Jungermannia specimens incorporated into a previously published dataset. Description and illustrations of the new species are provided with notes on its differentiation from allied species, ecology and distribution.
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Dissertations / Theses on the topic "TrnL intron"

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Dizkirici, Ayten. "Evolutionary Relationships Among Astragalus Species Native To Turkey." Phd thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614427/index.pdf.

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Evolutionary relationships within and among three Astragalus sections (Incani DC., Hypoglottidei DC., and Dissitiflori DC.) that were native to Turkey were inferred from variations of nucleotide sequences of both chloroplast and nuclear genome regions. In the current study, Fifty-six species included in the three Astragalus sections were utilized to figure out phylogenetic relationships and estimate evolutionary divergence time based on DNA sequence of trnL intron (trnL5&rsquo
-L3&rsquo
) , trnL3&rsquo
-F(GAA) (trnL-F intergenic spacer), trnV intron, matK (maturase kinase) cpDNA (chloroplast) and ITS (internal transcribed spacer) nDNA (nuclear) regions. Fifty-six Astragalus species with their replicas and one Cicer species as outgroup were analyzed by polymerase chain reaction amplification and DNA sequencing methods. Eleven unknown samples were also used in the current study to understand their section and species name. The results of the study indicated that unknown A35 and A52 samples could be named as A. dasycarpus, while unknown A65 and A66 samples as A. ovatus and lastly unknown A2 sample as A. nitens or A. aucheri. Section of unknown A3, A16, A20, A108, A109 and A110 samples were determined as Incani, but the exact species identification of these samples were not possible because of their close phylogenetic associations with more than one species. Highest genetic diversity was observed when the DNA sequences of ITS nrDNA (nuclear ribosomal) region comprising three subregions as ITS1, 5.8S and ITS2 was used, while the lowest one was calculated when DNA sequence of trnL-F cpDNA region was analyzed. The genetic divergence between Incani and Dissitiflori sections was highest whereas between Hypoglottidei and Dissitiflori was lowest based on all used regions. To figure out phylogenetic relationships among Astragalus species distributed in Turkey and in other regions of the World, DNA sequences of studied regions of foreign samples were collected from the NCBI database and were evaluated with DNA sequence of Turkish species used in the curent study. The Iranian samples either scattered in the phylogenetic tree or attached to our samples externally. South and North American samples (New World Astragalus or Neo Astragalus group) were nested within a different subcluster, which was located in the main cluster produced by samples of Old World Astragalus group (Turkish samples). With these results, we can say that New World Astragalus group is monophyletic and diverged from Old World Astragalus group. Evolutionary divergence time for Astragalus genus was estimated as about 12.5 - 14.5 million years (Ma), and that of New World Astragalus group as 5.0 - 4.0 Ma when rates of nucleotide substitutions of trnL intron and matK cpDNA regions were analyzed. In addition to evolutionary divergence time estimation for Astragalus and New World Astragalus group, divergence times among used three sections of the genus were also calculated by using DNA sequences of trnL, trnV intron and matK cpDNA regions and results indicated that Hypoglottidei and Dissitiflori sections diverged about 5.0-7.0 million years later than Incani section.
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Fougère-Danezan, Marie. "Phylogénie moléculaire et morphologique des Detarieae résinifères (Leguminosae : Caesalpinioideae) : contribution à l'étude de l'histoire biogéographique des légumineuses." Thèse, Toulouse 3, 2005. http://hdl.handle.net/1866/6594.

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Nicolas, Antoine. "UNDERSTANDING EVOLUTIONARY RELATIONSHIPS IN THE ANGIOSPERM ORDER APIALES BASED ON ANALYSES OF ORGANELLAR DNA SEQUENCES AND NUCLEAR GENE DUPLICATIONS." VCU Scholars Compass, 2009. http://scholarscompass.vcu.edu/etd/1701.

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I studied evolutionary history in the angiosperm order Apiales, with a special emphasis on interactions between form, time, and space. Four broad categories of problems were addressed: interfamilial relationships in Apiales, the assignment of genera traditionally assigned to the Apiaceae subfamily Hydrocotyloideae, the estimation of divergence times of the major clades, and the reconstruction of the biogeographic history of Apiales. We used molecular markers with different evolutionary properties and rates derived from the plastid (trnD-trnT and rpl16), nuclear (RPB2), and mitochondrial (nad1 intron 2) genomes, from more than 250 species representing all major clades in the order. The nuclear RPB2 region exhibited evidence of at least six duplication events in Apiales and provided a rich source of information for understanding the origins of polyploid lineages, especially in Araliaceae. Sequence comparisons among the copies show that exon regions are highly conserved. All copies appear to be functional but may have undergone subfunctionalization. Phylogenetic analyses of the three genomes suggest that Hydrocotyloideae should be divided into as many as six evolutionary lineages, but that most taxa should be included in subfamilies Azorelloideae and Mackinlayoideae. Relationships among and within the major clades of Azorelloideae need further analyses since many genera appeared non-monophyletic (e.g., Azorella, Schizeilema, and Eremocharis). Mackinlayoideae appeared as the earliest diverging lineage of Apiaceae, but the plastid and nuclear trees were incongruent in the placement of the Platysace clade relative to Mackinlayoideae and the rest of Apiaceae. Among the remaining clades of suborder Apiineae, Myodocapaceae appeared sister to Apiaceae in both plastid and nuclear trees, preceded by the divergence of Araliaceae and then Pittosporaceae. At the base of the gene trees in Apiales, Griseliniaceae and Torricelliaceae formed successive sisters to Apiineae. The placement of Pennantiaceae as sister to the rest of Apiales was confirmed by plastid data, but was not found in the nuclear trees. The order appears to have originated in the Cretaceous, with Apiineae having an age of c. 100 Mya. Australasia appears to be the most likely center of origin for Apiineae and most of its major clades, except Azorelloideae (South America) and Apioideae-Saniculoideae (sub-Saharan Africa).
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Nist, Richard Neil. "Maturation of tRNA in Haloferax volcanii." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1308066223.

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Crawley, Sunny Sheliese. "Rethinking phylogenetics using Caryophyllales (angiosperms), matK gene and trnK intron as experimental platform." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/77276.

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The recent call to reconstruct a detailed picture of the tree of life for all organisms has forever changed the field of molecular phylogenetics. Sequencing technology has improved to the point that scientics can now routinely sequence complete plastid/mitochondrial genomes and thus, vast amounts of data can be used to reconstruct phylogenies. These data are accumulating in DNA sequence repositories, such as GenBank, where everyone can benefit from the vast growth of information. The trend of generating genomic-region rich datasets has far outpaced the expasion of datasets by sampling a broader array of taxa. We show here that expanding a dataset both by increasing genomic regions and species sampled using GenBank data, despite the inherent missing DNA that comes with GenBank data, can provide a robust phylogeny for the plant order Caryophyllales (angiosperms). We also investigate the utility of trnK intron in phylogeny reconstruction at relativley deep evolutionary history (the caryophyllid order) by comparing it with rapidly evolving matK. We show that trnK intron is comparable to matK in terms of the proportion of variable sites, parsimony informative sites, the distribution of those sites among rate classes, and phylogenetic informativness across the history of the order. This is especailly useful since trnK intron is often sequenced concurrently with matK which saves on time and resources by increasing the phylogenetic utility of a single genomic region (rapidly evolving matK/trnK). Finally, we show that the inclusion of RNA edited sites in datasets for phylogeny reconstruction did not appear to impact resolution or support in the Gnetales indicating that edited sites in such low proportions do not need to be a consideration when building datasets. We also propose an alternate start codon for matK in Ephedra based on the presense of a 38 base pair indel in several species that otherwise result in pre-mature stop codons, and present 20 RNA edited sites in two Zamiaceae and three Pinaceae species.
Ph. D.
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Saini, Harleen. "Intron and Small RNA Localization in Mammalian Neurons." eScholarship@UMMS, 2019. https://escholarship.umassmed.edu/gsbs_diss/1044.

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RNA molecules are diverse in form and function. They include messenger RNAs (mRNAs) that are templates for proteins, splice products such as introns that can generate functional noncoding RNAs, and a slew of smaller RNAs such as transfer RNAs (tRNAs) that help decode mRNAs into proteins. RNAs can show distinct patterns of subcellular localization that play an important role in protein localization. However, RNA distribution in cells is incompletely understood, with prior studies focusing primarily on RNAs that are long (>200 nucleotides), fully processed, and polyadenylated. We examined the distribution of RNAs in neurons. Neuronal compartments can be separated by long distances and play distinct roles, raising the possibility that RNA localization is especially overt and functionally meaningful in these cells. In our exploration, we physically dissected projections from cell bodies of neurons from the rat brain and sequenced total RNA. We describe two main findings. First, we identified excised introns that are enriched in neuronal projections and confirmed their localization by single- molecule fluorescence in situ hybridization. These are a previously unknown set of circular RNAs in neuronal projections: tailless lariats that possess a non- canonical C branchpoint. Second, we observed a highly abundant population of small (20-150 nucleotide) RNAs in neuronal projections, most of which are tRNAs. For both circular introns and tRNAs, we did not observe known RNA localization signals. Thus, many types of RNA, if sufficiently stable, appear free to diffuse to distant locations, their localization perhaps aided by the movement of large organelles in the confines of neuronal projections. Our survey of RNA molecules across subcellular compartments provides a foundation for investigating the function of these molecules and the mechanisms that localize them.
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Chen, Xin. "Interaction of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase with group I introns." Access restricted to users with UT Austin EID Full text (PDF) from UMI/Dissertation Abstracts International, 2002. http://wwwlib.umi.com/cr/utexas/fullcit?p3077620.

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Thompson, Leo Douglas. "Substrate recognition properties of the tRNA[superscript Trp] intron endonuclease from the archaebacterium halobacterium volcanii /." The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487681788253537.

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Wu, Jingyan. "A Genome-wide Analysis to Identify and Characterize Novel Genes Involved in tRNA Biology in Saccharomyces cerevisiae." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429197786.

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Mayer, Margit [Verfasser]. "Transfer-RNAs mit Intron und ihre Reifung durch die tRNA-Spleiß-Endonuklease in Spalthefe / Margit Mayer." Ulm : Universität Ulm. Fakultät für Naturwissenschaften, 2001. http://d-nb.info/1015269400/34.

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Book chapters on the topic "TrnL intron"

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Schomburg, Dietmar, and Dörte Stephan. "tRNA-intron endonuclease." In Enzyme Handbook 15, 221–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-642-58948-5_51.

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Rould, M. A., J. J. Perona, and T. A. Steitz. "Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase." In Structural Insights into Gene Expression and Protein Synthesis, 395–400. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0046.

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"Genomics and Genetic Testing." In Examining the Causal Relationship Between Genes, Epigenetics, and Human Health, 269–87. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-8066-9.ch012.

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This chapter focuses on the Human Genome Project (HGP), which determined that humans have between 20,000 to 25,000 protein-coding genes and only about 1.5% of the genome codes for proteins, rRNA, and tRNA. The remainder once referred as “junk DNA” is today known to be crucial to survival of the species. Research indicates that genes are not contiguous, and some genes occur within the introns of other genes; some genes can overlap with each other either on the same or on different DNA strands with shared coding and/or regulatory elements; plus, the vast majority of human genes undergo alternative splicing leading to different proteins being encoded by the same gene. Advances in genomics and gene sequencing technologies have created exceptional opportunities for the delivery of personalized medical care. Clinical genetic testing has been helpful in identifying gene variants associated with risks for a number of diseases and health conditions.
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Perona, John J., Mark A. Rould, and Thomas A. Steitz. "Structural Basis for Transfer RNA Aminoacylation by Escherichia coli Glutaminyl-tRNA Synthetase." In Structural Insights into Gene Expression and Protein Synthesis, 401–14. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0047.

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Silvian, Laura F., Jimin Wang, and Thomas A. Steitz. "Insights into Editing from an Ile-tRNA Synthetase Structure with tRNAIle and Mupirocin." In Structural Insights into Gene Expression and Protein Synthesis, 415–18. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0048.

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Lucchesi, John C. "The role of non-coding RNAs." In Epigenetics, Nuclear Organization & Gene Function, 69–79. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0006.

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Most of the genome is transcribed into non-coding transcripts that far exceed in number the transcripts of protein-coding genes. These RNAs are subdivided into different classes. Long non-coding RNAs (lncRNAs) are at least 200 nucleotides in length and are transcribed from promoter, coding, intergenic or enhancer regions (eRNAs). These RNAs repress or enhance the transcription of target genes by facilitating the interaction between promoters and enhancers or by interacting with transcription factors and targeting histone-modifying enzymes. Short non-coding RNAs include a diverse group of functional types: miRNAs (micro RNAs) and siRNAs (small interfering RNAs) are negative regulators of gene expression; piRNAs (Piwi-interacting RNAs) suppress the action of transposable elements in the germline; snRNAs (small nuclear RNAs) are involved in mRNA splicing and rRNA maturation; tRNA-derived non-coding RNAs are involved in the cellular reaction to stress and in the repression of gene function. Additional short RNAs are rasiRNAs (repeat-associated small interfering RNAs) that appear to be involved in centromeric heterochromatin formation.
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Schmeing, T. Martin, Kevin S. Huang, Scott A. Strobel, and Thomas A. Steitz. "An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA." In Structural Insights into Gene Expression and Protein Synthesis, 552–56. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0065.

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Shapiro, Bruce A., and Wojciech Kasprzak. "RNA Structure Analysis: A Multifaceted Approach." In Pattern Discovery in Biomolecular Data. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195119404.003.0018.

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Genomic information (nucleic acid and amino acid sequences) completely determines the characteristics of the nucleic acid and protein molecules that express a living organism’s function. One of the greatest challenges in which computation is playing a role is the prediction of higher order structure from the one-dimensional sequence of genes. Rules for determining macromolecule folding have been continually evolving. Specifically in the case of RNA (ribonucleic acid) there are rules and computer algorithms/systems (see below) that partially predict and can help analyze the secondary and tertiary interactions of distant parts of the polymer chain. These successes are very important for determining the structural and functional characteristics of RNA in disease processes and hi the cell life cycle. It has been shown that molecules with the same function have the potential to fold into similar structures though they might differ in their primary sequences. This fact also illustrates the importance of secondary and tertiary structure in relation to function. Examples of such constancy in secondary structure exist in transfer RNAs (tRNAs), 5s RNAs, 16s RNAs, viroid RNAs, and portions of retroviruses such as HIV. The secondary and tertiary structure of tRNA Phe (Kim et al., 1974), of a hammerhead ribozyme (Pley et al., 1994), and of Tetrahymena (Cate et al., 1996a, 1996b) have been shown by their crystal structure. Currently little is known of tertiary interactions, but studies on tRNA indicate these are weaker than secondary structure interactions (Riesner and Romer, 1973; Crothers and Cole, 1978; Jaeger et al., 1989b). It is very difficult to crystallize and/or get nuclear magnetic resonance spectrum data for large RNA molecules. Therefore, a logical place to start in determining the 3D structure of RNA is computer prediction of the secondary structure. The sequence (primary structure) of an RNA molecule is relatively easy to produce. Because experimental methods for determining RNA secondary and tertiary structure (when the primary sequence folds back on itself and forms base pairs) have not kept pace with the rapid discovery of RNA molecules and their function, use of and methods for computer prediction of secondary and tertiary structures have increasingly been developed.
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ROULD, MARK A., JOHN J. PERONA, DIETER SÖLL, and THOMAS A. STEITZ. "Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNAGln and ATP at 2.8 Å Resolution." In Structural Insights into Gene Expression and Protein Synthesis, 387–94. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0045.

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Schmeing, T. Martin, Kevin S. Huang, David E. Kitchen, Scott A. Strobel, and Thomas A. Steitz. "Structural Insights into the Roles of Water and the 2′ Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction." In Structural Insights into Gene Expression and Protein Synthesis, 557–68. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0066.

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Conference papers on the topic "TrnL intron"

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Vladimirova, Mariia, Alexey Afonin, Virtoria Muntyan, Boris Simarov, and Marina Roumiantseva. "Evaluation of Sinorhizobium meliloti Genomic Islands Inserted into the tRNA-Thr." In 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB). IEEE, 2020. http://dx.doi.org/10.1109/csgb51356.2020.9214720.

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Drutarovsky, M., M. Varchola, and M. Petrvalsky. "Remotely testable setup of soft CPU with cryptographic TRNG coprocessor extension embedded into Altera FPGA." In 2013 23rd International Conference Radioelektronika (RADIOELEKTRONIKA 2013). IEEE, 2013. http://dx.doi.org/10.1109/radioelek.2013.6530904.

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Mikhailov, Sergey N., Ekaterina V. Efimtseva, Alexandra A. Shelkunova, Jef Rozenski, Gert Emmerechts, Arthur Van Aerschot, and Piet Herdewijn. "Chemical incorporation of minor tRNA component O-β-D-ribofuranosyl-(1''-2')-adenosine-5''-phosphate into oligoribonucleotides." In XIIIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2005. http://dx.doi.org/10.1135/css200507333.

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Kestner, Brian K., Jeff S. Schutte, Jonathan C. Gladin, and Dimitri N. Mavris. "Ultra High Bypass Ratio Engine Sizing and Cycle Selection Study for a Subsonic Commercial Aircraft in the N+2 Timeframe." In ASME 2011 Turbo Expo: Turbine Technical Conference and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/gt2011-45370.

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This paper presents an engine sizing and cycle selection study of ultra high bypass ratio engines applied to a subsonic commercial aircraft in the N+2 (2020) timeframe. NASA has created the Environmentally Responsible Aviation (ERA) project to serve as a technology transition bridge between fundamental research (TRL 1–4) and potential users (TRL 7). Specifically, ERA is focused on subsonic transport technologies that could reach TRL 6 by 2020 and are capable of integration into an advanced vehicle concept that simultaneously meets the ERA project metrics for noise, emissions, and fuel burn. An important variable in exploring the trade space is the selection of the optimal engine cycle for use on the advanced aircraft. In this paper, two specific ultra high bypass engine cycle options will be explored: advanced direct drive and geared turbofan. The advanced direct drive turbofan is an improved version of conventional turbofans. In terms of both bypass ratio and overall pressure ratio, the advanced direct turbofan benefits from improvements in aerodynamic design of its components, as well as material stress and temperature properties. By putting a gear between the fan and the low pressure turbine, a geared turbo fan allows both components to operate at optimal speeds, thus further improving overall cycle efficiency relative to a conventional turbofan. In this study, sensitivity of cycle design with level of technology will be explored, in terms of both cycle parameters (such as specific thrust consumption (TSFC) and bypass ratio) and aircraft mission parameters (such as fuel burn and noise). To demonstrate this sensitivity, engines will be sized for optimal performance on a 300 passenger class aircraft for a 2010 level technology tube and wing airframe, a N+2 level technology tube and wing air-frame, and finally on a N+2 level technology blended wing body airframe with and without boundary layer ingestion (BLI) engines.
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Niemeyer, Jonathan K., and Daniel E. Whitney. "Risk Reduction of Jet Engine Product Development Using Technology Readiness Metrics." In ASME 2002 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2002. http://dx.doi.org/10.1115/detc2002/dtm-34000.

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This paper looks at the product development process as an exercise in risk reduction and performs a critical analysis of how gas turbine engine manufacturers weigh the competing risks associated with on-time delivery, product quality, and development costs. Three frameworks are used to focus the analysis: • Iteration by using multiple attempts to converge to an acceptable solution. • Maintaining options in development, and delaying convergence to a single design. • Improving the organization’s predictive capability prior to committing to a particular set of performance goals, designs, or technologies for a product. This is explored from the perspective of “technology readiness”. For six gas turbine engine development programs, case studies were performed to assess the effectiveness of the product development process by measuring how well the engine met its guaranteed level of fuel consumption. For each development program, performance against guarantees was compared against technology readiness levels (TRL) at program launch when performance was guaranteed by contract to customers, and against the degree of flexibility provided to designers to react once performance shortfalls were known. Decomposition of the engine system into sub-systems was necessary to specifically define TRL, parallel efforts, and iteration. Risk strategies were compared in light of the time sensitivity of the quality of information, the cost of engineering changes, contractual penalties, and lead times associated with implementing improvements.
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Kestner, Brian, Jeff S. Schutte, Jimmy C. M. Tai, Christopher A. Perullo, and Dimitri N. Mavris. "Surrogate Modeling for Simultaneous Engine Cycle and Technology Optimization for Next Generation Subsonic Aircraft." In ASME Turbo Expo 2012: Turbine Technical Conference and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/gt2012-68724.

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This paper presents an engine sizing and cycle selection study of ultra high bypass ratio engines applied to a subsonic commercial aircraft in the N+2 (2025) timeframe. NASA has created the Environmentally Responsible Aviation (ERA) project to serve as a technology transition bridge between fundamental research (TRL 1–4) and potential commercial application (TRL 7). Specifically, ERA is focused on subsonic transport technologies that could reach TRL 6 by 2020 and can be integrated into an advanced vehicle concept to simultaneously meet the ERA project metrics for noise, emissions, and fuel burn. An important variable in exploring the technology trade space is the selection of the optimal engine cycle for use on the advanced aircraft. Previous literature demonstrated the cycle optimization using a design of experiments (DOE) to explore the engine cycle design space for a pre-defined technology package. However, since the optimal engine cycle is dependent upon the specific technology package, this process would have to be repeated to ensure optimal performance for each technology package. With more than 80 technologies to be analyzed, the combinatorial space of technology packages is enormous. As a result, executing a DOE to find the optimum engine cycle for each technology package is infeasible. To address this issue, it is proposed to use surrogate models that encompass the engine cycle and technology design space to enable fast and accurate optimization of the engine cycle for any given technology package. This paper describes the generation and analysis of surrogate models used for technology assessment and cycle optimization of an ultra high bypass geared turbofan engine architecture. The first study in the paper shows that a single surrogate model can be used to accurately simulate both a technology and cycle design space. To demonstrate the proposed surrogate modeling approach, the cycle design space for three different technology packages was analyzed. This study demonstrated that when an optimal cycle is found within the constrained interior of a design space, the surrogate modeling approach is quite accurate. The study also established that the surrogate models can also be used to assess potential cycles at the boundaries or even outside of the region for which they were trained.
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Calkins, F. T., and J. H. Mabe. "Flight Test of a Shape Memory Alloy Actuated Adaptive Trailing Edge Flap." In ASME 2016 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/smasis2016-9141.

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The Boeing Company has a goal of creating aircraft that are capable of continuous optimization for all flight conditions. Recent advances in SMA actuation and a detailed understanding of wing design were combined to design, build, and safely demonstrate small trailing edge flaps driven by SMA actuation. As part of a 2012 full-scale flight test program a lightweight and compact Shape Memory Alloy (SMA) rotary actuator was integrated into the hinge line of a small flap on the trailing edge of a commercial aircraft wing. This Adaptive Trailing Edge program was part of a Boeing and Federal Aviation Administration (FAA) collaboration. Aerodynamic studies of these small trailing edge flaps show that improved performance requires multiple flap configurations that vary with flight regime. Configurations include small angles of deployment for reduced fuel burn and emissions during high speed cruise and larger angles of deployment for increased lift and lower noise during takeoff and approach. SMA actuation is an ideal compact solution to position these small flaps and increase aircraft performance by simply and efficiently altering the wings aerodynamic characteristics for each flight segment. Closed loop control of the flap’s position, using the SMA actuator, was demonstrated at multiple flight conditions during flight tests. Results of the successful flight test on a 737–800 commercial airplane and the significantly improved performance benefits will be presented. This is the first flight test of an SMA rotary actuator system, which was matured from TRL 4 to TRL 7 during the program.
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Pilatis, Nick, Michael Whiteman, Paul Madden, Michael A. Macquisten, and A. John Moran. "Forced Combustion Experiments on Aero Combustors." In ASME 2011 Turbo Expo: Turbine Technical Conference and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/gt2011-45235.

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In the world of gas turbine combustion there is always the spectre of thermo-acoustic instability. Over the past few decades there has been significant effort afforded to researching the phenomenon of thermo-acoustics. The results of the research have produced numerous mathematical models and at system level these models have been used to predict and postdict where noise is likely to occur in a given system. The models also allow the combustion system to be numerically tested through the flight or operational envelope to identify areas where instability may occur before testing is carried out, thus reducing the risk of unexpected noise occurring. The weakness of many of these models is that they require, what is known as a flame transfer function. The flame transfer function is normally measured after the combustor has been fully designed and at a high TRL (Technology Readiness Level) so significant investment in time and money are already baked into the design. Remedial action if required can result in a significant loss of time and money in the development of the combustor. This paper describes the design and use of a test rig that allows combustion systems to be tested at much lower TRL. A ‘siren’ rig has been developed and used to identify what particular design changes in either combustor flow field or fuel delivery systems have effects on the thermo-acoustics. The exit boundary of the unit has a representative choked end point. This end point has the ability to be modulated in time, thus forcing the whole system. How the system reacts to the forcing is measured over a range of frequencies. The rig has been successfully used to influence design changes required to avoid combustion driven oscillations within the next generation of aero gas turbine combustors. The rig is not a representation of a complete 360 degree annular combustor system, but of a smaller sector. The objective is to isolate the Fuel Spray Nozzle (FSN) and corresponding combustor sector from acoustic resonances and derive functions expressing the relationship between unsteady heat release rate and unsteady aerodynamics for a range of operating conditions by controlling the modulation of air mass flow rate. Such functions can be used in conjunction with acoustic linear theory to predict wave modes and growth rates in combustor geometries.
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Grönstedt, Tomas, Carlos Xisto, Vishal Sethi, Andrew Rolt, Nicolás García Rosa, Arne Seitz, Kyros Yakinthos, et al. "Ultra Low Emission Technology Innovations for Mid-Century Aircraft Turbine Engines." In ASME Turbo Expo 2016: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/gt2016-56123.

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Commercial transport fuel efficiency has improved dramatically since the early 1950s. In the coming decades the ubiquitous turbofan powered tube and wing aircraft configuration will be challenged by diminishing returns on investment with regards to fuel efficiency. From the engine perspective two routes to radically improved fuel efficiency are being explored; ultra-efficient low pressure systems and ultra-efficient core concepts. The first route is characterized by the development of geared and open rotor engine architectures but also configurations where potential synergies between engine and aircraft installations are exploited. For the second route, disruptive technologies such as intercooling, intercooling and recuperation, constant volume combustion as well as novel high temperature materials for ultra-high pressure ratio engines are being considered. This paper describes a recently launched European research effort to explore and develop synergistic combinations of radical technologies to TRL 2. The combinations are integrated into optimized engine concepts promising to deliver ultra-low emission engines. The paper discusses a structured technique to combine disruptive technologies and proposes a simple means to quantitatively screen engine concepts at an early stage of analysis. An evaluation platform for multidisciplinary optimization and scenario evaluation of radical engine concepts is outlined.
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Maung, Yuzana, Sutartinah Sri Handayani, and Lukman Aryoseto. "Effect of Drumstick (Moringa Oleifera Lam) Leaves Ethanol Extract on Anopheles Aconitus L. Third Instar Larvae Mortality." In The 7th International Conference on Public Health 2020. Masters Program in Public Health, Universitas Sebelas Maret, 2020. http://dx.doi.org/10.26911/the7thicph.05.59.

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Background: Synthetic insecticides may have the negative effect to nature. Many studies suggested the applications of botanical larvicides as an alternative replacement for synthetic insecticides. This study aimed to examine the effect of Moringa oleifera Lam leaves ethanol extract on the Anopheles aconitus L. third instar larvae mortality. Subjects and Method: This was a laboratory experimental with post-test only con-trol group design conducted at Salatiga, Central Java, in November 2016. A total of 150 Anopheles aconitus L. third instar larvae was selected by convenience sampling method and divided into 6 groups in which contained replication of 25 larvae. One negative control group was added 100 ml distilled water. The other treatment groups were 1 mg/ 100 ml, 10 mg/ 100 ml, 20 mg/ 100 ml, 30 mg/ 100 ml, and 40 mg/ 100 ml of Moringa oleifera Lam leaves ethanol extract. Each test group was repeated four times. The dependent variable was mortality of the larvae. The independent variable was different concentrations of Moringa oleifera Lam leaves ethanol extract. The observation of larvae mortality was conducted after 48 hours of exposure with extract. The data were analyzed by Kruskal-Wallis. Results: Mean of the mortality of Anopheles aconitus L. third instar larvae was dif-ferent in each group, and it was statistically significant (p= 0.008). Conclusion: Moringa oleifera Lam leaves ethanol extract has effect on mortality of Anopheles aconitus L. third instar larvae. Keywords: Moringa oleifera Lam, Anopheles aconitus L., ethanol extract, mortality Correspondence: Yuzana Maung. Masters Program in Public Health, Universitas Sebelas Maret. Jl. Ir. Sutami 36A, Surakarta, 57126, Central Java, Indonesia. Email: yuzmg5699@student.-uns.ac.id. Mobile: +6281295346614. DOI: https://doi.org/10.26911/the7thicph.05.59
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Reports on the topic "TrnL intron"

1

Daniels, Charles J. Processing of Archaebacterial Intron-Containing tRNA Gene Transcripts. Fort Belvoir, VA: Defense Technical Information Center, July 1988. http://dx.doi.org/10.21236/ada197868.

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