Relevant bibliographies by topics / Nuclear introns

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  2. Dissertations / Theses
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Academic literature on the topic 'Nuclear introns'

Author: Grafiati
Published: 4 June 2021
Last updated: 3 February 2022

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Journal articles on the topic "Nuclear introns"

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Mukhopadhyay, Jigeesha, and Georg Hausner. "Organellar Introns in Fungi, Algae, and Plants." Cells 10, no. 8 (August 6, 2021): 2001. http://dx.doi.org/10.3390/cells10082001.

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Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.
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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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Wiebauer, K., J. J. Herrero, and W. Filipowicz. "Nuclear pre-mRNA processing in plants: distinct modes of 3'-splice-site selection in plants and animals." Molecular and Cellular Biology 8, no. 5 (May 1988): 2042–51. http://dx.doi.org/10.1128/mcb.8.5.2042.

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The report that human growth hormone pre-mRNA is not processed in transgenic plant tissues (A. Barta, K. Sommergruber, D. Thompson, K. Hartmuth, M.A. Matzke, and A.J.M. Matzke, Plant Mol. Biol. 6:347-357, 1986) has suggested that differences in mRNA splicing processes exist between plants and animals. To gain more information about the specificity of plant pre-mRNA processing, we have compared the splicing of the soybean leghemoglobin pre-mRNA with that of the human beta-globin pre-mRNA in transfected plant (Orychophragmus violaceus and Nicotiana tabacum) protoplasts and mammalian (HeLa) cells. Of the three introns of leghemoglobin pre-mRNA, only intron 2 was correctly and efficiently processed in HeLa cells. The 5' splice sites of the remaining two introns were faithfully recognized, but correct processing of the 3' sites took place only rarely (intron 1) or not at all (intron 3); cryptic 3' splice sites were used instead. While the first intron in human beta-globin pre-mRNA was not spliced in transfected plant protoplasts, intron 2 processing occurred at a low level, indicating that some mammalian introns can be recognized by the plant intron-splicing machinery. However, excision of intron 2 proved to be incorrect, involving the authentic 5' splice site and a cryptic 3' splice site. Our results indicate that the mechanism of 3'-splice-site selection during intron excision differs between plants and animals. This conclusion is supported by analysis of the 3'-splice-site consensus sequences in animal and plant introns which revealed that polypyrimidine tracts, characteristic of animal introns, are not present in plant pre-mRNAs. It is proposed that an elevated AU content of plant introns is important for their processing.
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Wiebauer, K., J. J. Herrero, and W. Filipowicz. "Nuclear pre-mRNA processing in plants: distinct modes of 3'-splice-site selection in plants and animals." Molecular and Cellular Biology 8, no. 5 (May 1988): 2042–51. http://dx.doi.org/10.1128/mcb.8.5.2042-2051.1988.

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The report that human growth hormone pre-mRNA is not processed in transgenic plant tissues (A. Barta, K. Sommergruber, D. Thompson, K. Hartmuth, M.A. Matzke, and A.J.M. Matzke, Plant Mol. Biol. 6:347-357, 1986) has suggested that differences in mRNA splicing processes exist between plants and animals. To gain more information about the specificity of plant pre-mRNA processing, we have compared the splicing of the soybean leghemoglobin pre-mRNA with that of the human beta-globin pre-mRNA in transfected plant (Orychophragmus violaceus and Nicotiana tabacum) protoplasts and mammalian (HeLa) cells. Of the three introns of leghemoglobin pre-mRNA, only intron 2 was correctly and efficiently processed in HeLa cells. The 5' splice sites of the remaining two introns were faithfully recognized, but correct processing of the 3' sites took place only rarely (intron 1) or not at all (intron 3); cryptic 3' splice sites were used instead. While the first intron in human beta-globin pre-mRNA was not spliced in transfected plant protoplasts, intron 2 processing occurred at a low level, indicating that some mammalian introns can be recognized by the plant intron-splicing machinery. However, excision of intron 2 proved to be incorrect, involving the authentic 5' splice site and a cryptic 3' splice site. Our results indicate that the mechanism of 3'-splice-site selection during intron excision differs between plants and animals. This conclusion is supported by analysis of the 3'-splice-site consensus sequences in animal and plant introns which revealed that polypyrimidine tracts, characteristic of animal introns, are not present in plant pre-mRNAs. It is proposed that an elevated AU content of plant introns is important for their processing.
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Furulund, Betty M. N., Bård O. Karlsen, Igor Babiak, and Steinar D. Johansen. "A Phylogenetic Approach to Structural Variation in Organization of Nuclear Group I Introns and Their Ribozymes." Non-Coding RNA 7, no. 3 (July 22, 2021): 43. http://dx.doi.org/10.3390/ncrna7030043.

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Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evolution. The ribosomal DNA of the myxomycete Mucilago crustacea was investigated and found to contain seven group I introns, including a direct repeat-containing intron at insertion site S1389 in the small subunit ribosomal RNA gene. We collected, analyzed, and compared 72 S1389 group IC1 introns representing diverse myxomycete taxa. The consensus secondary structure revealed a conserved ribozyme core, but with surprising sequence variations in the guanosine binding site in segment P7. Some S1389 introns harbored large extension sequences in the peripheral region of segment P9 containing direct repeat arrays. These repeats contained up to 52 copies of a putative internal guide sequence motif. Other S1389 introns harbored homing endonuclease genes in segment P1 encoding His-Cys proteins. Homing endonuclease genes were further interrupted by small spliceosomal introns that have to be removed in order to generate the open reading frames. Phylogenetic analyses of S1389 intron and host gene indicated both vertical and horizontal intron transfer during evolution, and revealed sporadic appearances of direct repeats, homing endonuclease genes, and guanosine binding site variants among the myxomycete taxa.
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Takahashi, Y., S. Urushiyama, T. Tani, and Y. Ohshima. "An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene." Molecular and Cellular Biology 13, no. 9 (September 1993): 5613–19. http://dx.doi.org/10.1128/mcb.13.9.5613.

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Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.
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Takahashi, Y., S. Urushiyama, T. Tani, and Y. Ohshima. "An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene." Molecular and Cellular Biology 13, no. 9 (September 1993): 5613–19. http://dx.doi.org/10.1128/mcb.13.9.5613-5619.1993.

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Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.
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Guo, M., P. C. Lo, and S. M. Mount. "Species-specific signals for the splicing of a short Drosophila intron in vitro." Molecular and Cellular Biology 13, no. 2 (February 1993): 1104–18. http://dx.doi.org/10.1128/mcb.13.2.1104.

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The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3' splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5' splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species.
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Guo, M., P. C. Lo, and S. M. Mount. "Species-specific signals for the splicing of a short Drosophila intron in vitro." Molecular and Cellular Biology 13, no. 2 (February 1993): 1104–18. http://dx.doi.org/10.1128/mcb.13.2.1104-1118.1993.

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The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3' splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5' splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species.
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Lee, Sujin, and Scott W. Stevens. "Spliceosomal intronogenesis." Proceedings of the National Academy of Sciences 113, no. 23 (May 23, 2016): 6514–19. http://dx.doi.org/10.1073/pnas.1605113113.

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The presence of intervening sequences, termed introns, is a defining characteristic of eukaryotic nuclear genomes. Once transcribed into pre-mRNA, these introns must be removed within the spliceosome before export of the processed mRNA to the cytoplasm, where it is translated into protein. Although intron loss has been demonstrated experimentally, several mysteries remain regarding the origin and propagation of introns. Indeed, documented evidence of gain of an intron has only been suggested by phylogenetic analyses. We report the use of a strategy that detects selected intron gain and loss events. We have experimentally verified, to our knowledge, the first demonstrations of intron transposition in any organism. From our screen, we detected two separate intron gain events characterized by the perfect transposition of a reporter intron into the yeast genes RPL8B and ADH2, respectively. We show that the newly acquired introns are able to be removed from their respective pre-mRNAs by the spliceosome. Additionally, the novel allele, RPL8Bint, is functional when overexpressed within the genome in a strain lacking the Rpl8 paralogue RPL8A, demonstrating that the gene targeted for intronogenesis is functional.
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Dissertations / Theses on the topic "Nuclear introns"

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Chen, Xing. "EVOLUTION OF GROUP I INTRONS IN THE NUCLEAR RIBOSOMAL RNA GENES OF DOTHIDEOMYCETES." Bowling Green State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1288376350.

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Cooper, Lizette. "Evolutionary investigation of group I introns in nuclear ribosomal internal transcribed spacers in Neoselachii." Bowling Green State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu154229759945368.

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Benavides, Edgar. "Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1652.pdf.

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Vogel, Laura Sanders. "The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies." ScholarWorks@UNO, 2007. http://scholarworks.uno.edu/td/579.

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Two of the most pervasive threats to species biodiversity are invasive species and habitat loss and degradation. Invasive species are often relatively insensitive to disturbance and many expand their range into disturbed and fragmented habitats. This dissertation uses an interdisciplinary approach to investigate how anthropogenic habitat disturbance is precipitating a range expansion in an invasive toad species, Bufo nebulifer, which is driving a decline in its native congener, B. fowleri. I employed a remote sensing and GIS study using historical data to compare changes in the two species distributions and habitat changes, a molecular genetic study to identify interspecific hybrids and their potential effects on the parental species, and an experimental ecology study to look at the effects of competition and predation on the two species. The results of the landscape level analyses of species' distributional changes in different disturbance levels showed that both species' distributions have changed significantly. The distributions of the two species are inversely affected by habitat disturbance; the distribution of B. fowleri in highly degraded habitat has contracted while the expansion of B. nebulifer increased substantially. The molecular genetic study successfully demonstrated the use of nuclear and mitochondrial markers to identify cryptic hybrids and their maternal lineage. Three hybrids were detected using nuclear introns and a morphologically cryptic hybrid was identified using mitochondrial DNA as the progeny of a cross that was previously thought to be inviable. Although relatively few hybrids were currently found, the identification of a cryptic hybrid implies that the rate of historical hybridization may have been drastically underestimated. Ecological studies showed that competition with B. nebulifer tadpoles had a negative effect on both body size measures and survival to metamorphosis for B. fowleri tadpoles. The addition of predators to experiment did not favor the survival of B. fowleri over B. nebulifer. Bufo fowleri's inability to compete with its invasive congener could be a driving mechanism for the decline of B. fowleri and the expansion of B. nebulifer. The methods discussed in this dissertation offer promising and practical new approaches for evaluating and managing changes in the distribution of species of conservation concern.
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Till, Bradley J. "A nucleus-encoded protein required for the splicing of the maize chloroplast atpF group II intron /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9998022.

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Thesis (Ph. D.)--University of Oregon, 2000.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 56-59). Also available for download via the World Wide Web; free to University of Oregon users.
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Jenkins, Bethany Diane. "Identification of nucleus-encoded factors required for group II intron splicing in chloroplasts /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9963446.

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Thesis (Ph. D.)--University of Oregon, 2000.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 110-117). Also available for download via the World Wide Web; free to University of Oregon users. Address: http://wwwlib.umi.com/cr/uoregon/fullcit?p9963446.
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Aggarwal, Neha. "Characterization of a microRNA Harboring Intron for pre-mRNA Splicing and microRNA Processing." Cleveland State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=csu1275407397.

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Baboo, Sabyasachi. "Nuclear translation." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:5266f049-d576-44fd-ab26-11cf7a27f678.

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In bacteria, protein synthesis can occur tightly coupled to transcription. In eukaryotes, it is believed that translation occurs solely in the cytoplasm; I test whether some occurs in nuclei and find: (1) L-azidohomoalanine (Aha) – a methionine analogue (detected by microscopy after attaching a fluorescent tag using ‘click’ chemistry) – is incorporated within 5 s into nuclei in a process sensitive to the translation inhibitor, anisomycin. (2) Puromycin – another inhibitor that end-labels nascent peptides (detected by immuno-fluorescence) – is similarly incorporated in a manner sensitive to a transcriptional inhibitor. (3) CD2 – a non-nuclear protein – is found in nuclei close to the nascent RNA that encodes it (detected by combining indirect immuno-labelling with RNA fluorescence in situ hybridization using intronic probes); faulty (nascent) RNA is destroyed by a quality-control mechanism sensitive to translational inhibitors. I conclude that substantial translation occurs in the nucleus, with some being closely coupled to transcription and the associated proof-reading. Moreover, most peptides made in both the nucleus and cytoplasm are degraded soon after they are made with half-lives of about one minute. I also collaborated on two additional projects: the purification of mega-complexes (transcription ‘factories’) containing RNA polymerases I, II, or III (I used immuno-fluorescence to confirm that each contained the expected constituents), and the demonstration that some ‘factories’ specialize in transcribing genes responding to tumour necrosis factor α – a cytokine that signals through NFκB (I used RNA fluorescence in situ hybridization coupled with immuno-labelling to show active NFκB is found in factories transcribing responsive genes).
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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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Hushek, Stephen Gerard. "Quantitative analysis of intro-operative magnetic resonance images and tissue survival for laserthermia of 9L gliosarcoma." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/28078.

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Book chapters on the topic "Nuclear introns"

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Heinze, B. "PCR-RFLP analysis of introns of nuclear genes in Populus and Prunus." In Genetic Response of Forest Systems to Changing Environmental Conditions, 117–27. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-015-9839-2_10.

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Pyle, A. M. "Catalytic Reaction Mechanisms and Structural Features of Group II Intron Ribozymes." In Nucleic Acids and Molecular Biology, 75–107. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-61202-2_5.

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Been, M. D., and M. Puttaraju. "Circular RNAs: Generation of Small RNAs with Unique Properties by Splicing Permuted Intron-Exon Sequences." In Nucleic Acids and Molecular Biology, 145–59. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-61202-2_8.

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Limborska, S. A., A. N. Fedorov, V. L. Bukhman, and M. I. Prosniak. "Detection of a β-Globin Intron Mutation in a β-Thalas Semic Patient from Azerbaijan." In Metabolism and Enzymology of Nucleic Acids, 197–201. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4613-0749-5_30.

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Westrich, Kathleen M., Nick R. Konkol, Makoto P. Matsuoka, and Ruth B. Phillips. "Interspecific relationships among charrs based on phylogenetic analysis of nuclear growth hormone intron sequences." In Ecology, behaviour and conservation of the charrs, genus Salvelinus, 217–22. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-017-1352-8_19.

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Lucchesi, John C. "DNA methylation and gene expression." In Epigenetics, Nuclear Organization & Gene Function, 93–103. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0008.

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DNA methylation is an epigenetic modification that consists of the addition of a methyl, or of a hydroxyl and a methyl group, to the cytosine of CpG dinucleotides. Some gene promoters are rich in CpGs that are predominantly not modified; other promoters and most enhancers are poor in CpGs. These elements, as well as most exons, introns and intergenic regions, tend to be methylated. CpG methylation plays an important role in maintaining transposable elements and tandem arrays of repetitive sequences in a repressed state. CpG methylation is also responsible for the uniparental silencing of imprinted alleles, allowing the monoallelic expression of some genes, and for the silencing and clonal transmission of the inactive X chromosome in mammals. The use of this modification as a means of dynamically turning individual genes on or off, illustrated by the activation of individual odorant receptor genes, is less common.
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"Black Bass Diversity: Multidisciplinary Science for Conservation." In Black Bass Diversity: Multidisciplinary Science for Conservation, edited by Michael D. Tringali, Brandon L. Barthel, Seifu Seyoum, and John R. Knight. American Fisheries Society, 2015. http://dx.doi.org/10.47886/9781934874400.ch33.

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<em>Abstract</em>.—While investigating hybridization in Shoal Bass <em>Micropterus cataractae</em> in the Chipola River, Florida, we encountered a distinctive genetic signature from an unknown taxon. We soon determined that the signature originated from a novel bass that inhabits Gulf Coastal Plain rivers and streams in Florida. Superficially, these bass resemble Spotted Bass <em>M. punctulatus</em> and historically have been considered as such. Cladistically, they are diagnosable through four autapomorphies at two nuclear gene introns and one mitochondrial DNA gene; phenetically, by various clustering techniques using 17 microsatellite loci. In nuclear-gene phylogenies based on 10 sequenced introns, this taxon is reciprocally monophyletic and shares a common ancestor with a clade comprising Spotted Bass and Guadalupe Bass <em>M. treculii</em>. Morphologically, its members differ from Spotted Bass, Alabama Bass <em>M. henshalli</em>, and Guadalupe Bass in mean/modal counts of soft anal-fin and dorsal-fin rays. They further appear to differ from Guadalupe Bass in mean/modal counts of scales above and below the lateral line and around the caudal peduncle. Little is known yet about the biology and life history of this new taxon. It appears to occupy different mesohabitats than those occupied by sympatric congeners, although its habitat preferences seem to be most similar to those of the Guadalupe Bass. Operational requirements were satisfied for 11 of 15 applicable species concepts, providing a foundation for taxonomic recognition under the fundamental evolutionary species concept. For operational concepts in which requirements were not satisfied, analogous shortfalls occur in all recognized micropterids. We therefore recommend that this taxon, designated herein as the Choctaw Bass, be elevated to species rank. Undetected, native populations of Choctaw Bass could be susceptible to negative ecological and genetic impacts and/or serve as vectors of similar damage to congeneric populations.
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Dock-Bregeon, A. C., and D. Moras. "Nucleic Acids and Their Complexes." In Crystallization of Nucleic Acids and Proteins. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199636792.003.0012.

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At first glance crystallizing nucleic acids poses the same problems as crystallizing proteins since most of the variables to investigate are alike. It is thus astonishing that crystallization data banks (1) that describe so many successful protein crystallizations are so poor in information on nucleic acids. This relies on the physico-chemical and biochemical characteristics of nucleic acids distinguishing them from proteins. The aim of this chapter is to underline features explaining the difficulties often encountered in nucleic acid crystallization and to discuss strategies that could help to crystallize them more readily, either as free molecules or as complexes with proteins. Other general principles, in particular for RNA crystallization, are discussed in ref. 2. Among natural nucleic acids only the smaller ones provide good candidates for successful crystallizations. Large DNAs or RNAs can a priori be excluded because of their flexibility that generates conformational heterogeneity not compatible with crystallization. Thus the smaller RNAs with more compact structures (with 75-120 nt), especially transfer RNAs (tRNAs), but also 5S RNA, were the first natural nucleic acids to be crystallized (3, 4). At present attempts are being made with other RNA systems, such as ribozymes and introns, fragments of mRNA, viroids, viral and other tRNA-like RNAs, SELEX-evolved RNAs, and crystallization successes leading to X-ray structure determinations were reported for RNA domains of up to 160 nt long, with the resolution of the P4-P6 domain of the self-splicing Tetrahymena intron (5). The recent excitement in nucleic acid crystallography, and particularly in RNA crystallography, have partly been due to technological improvements in the preparation methods of the molecules. Advances in oligonucleotide chemical synthesis provide opportunity for making large amounts of pure desoxyribo- and more recently of ribo-oligomers of any desired sequence. This led to the crystallization of a number of DNA and RNA fragments and was followed by the co-crystallization of complexes between proteins and such synthetic fragments. Transcription methods of RNAs from synthetic DNA templates were also essential for rejuvenating the structural biology of RNAs. In the case of complexes of proteins with RNAs, the main difficulty was to purify large quantities of homogeneous biological material with well defined physico-chemical properties.
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Sinibaldi, Ralph M., and Irvin J. Mettler. "Intron Splicing and Intron-mediated Enhanced Expression in Monocots." In Progress in Nucleic Acid Research and Molecular Biology, 229–57. Elsevier, 1992. http://dx.doi.org/10.1016/s0079-6603(08)60577-2.

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Berger, Shelby L. "[23] Nuclease digestion: A method for mapping introns." In Methods in Enzymology, 325–34. Elsevier, 1989. http://dx.doi.org/10.1016/0076-6879(89)80109-0.

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Conference papers on the topic "Nuclear introns"

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Ostersetzer-Biran, Oren. "PLANT MITOCHONDRIA GROUP INTRONS SPLICING: A WINDOW INTO THE EVOLUTION OF THE NUCLEAR SPLICEOSOMAL MACHINERIES." In The Second All-Russian Scientific Conference with international participation "Regulation Mechanisms of Eukariotic Cell Organelle Functions". SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/978-5-94797-318-1-83-83.

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Martins, Letícia, Marianny Rodrigues Costa Amorim, and Andreia Juliana Rodrigues Caldeira. "ORIGEM E IMPORTÂNCIA FILOGENÉTICA DO DNA MITOCONDRIAL." In I Congresso Nacional On-line de Biologia Celular e Estrutural. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/1942.

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Introdução: A molécula do DNA mitocondrial (mtDNA) é muito utilizada em estudos envolvendo estrutura populacional, relações filogenéticas e o entendimento de vários aspectos biológicos e evolutivos de uma grande variedade de organismos. Mas, apesar desse destaque em estudos moleculares, ainda existem muitas dúvidas sobre a organela. Objetivo: Realizar uma revisão bibliográfica sobre a origem e importância filogenética do mtDNA.Material e método: Foi realizada uma busca de artigo embase dados como SciELO Brasil e Web of Science. Resultados: A mitocôndria é uma organela responsávelpela respiração celular e tem origem endossimbiótica, que pode ser evidenciada pela presença de um DNA própriocircular, semelhante à células ancestrais procariotas. O mtDNA é pequeno (aproximadamente 16 kb nos animais), com raras exceções; possui poucos genes, 37 no total, que codifica para apenas 5% dos produtos necessários para o funcionamento da mitocôndria. É considerado como um genoma compacto, com poucas seqüências espaçadoras, seqüências repetitivas, pseudogenes e introns e aindaausência de recombinação, embora exceções sejam descritas. O conteúdo gênico é conservado, e a ordem em que esses genes se encontram organizados no genomacostuma ser também conservada. A taxa evolutiva do mtDNA é alta, quando comparada a do genoma nuclear. O mtDNA é capaz de ligar pessoas à sua linhagem materna, já que este possui herança exclusivamente materna além disso, é considerado um marcador genético, pois apresenta mais de 5 mil cópias numa única célula. Conclusão: A análise desse tipo de DNA é excepcional em estudo de tecidos antigos e até arqueológicos, como dentes e ossos epodem ser amplamente usados em estudo de evolução e antropologia. Na atualidade, o mtDNA ganhou destaque na área forense, favorecendo a coleta evidencias que elucidam as situações de crimes.
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Melia, U. S. P., F. Claria, J. J. Gallardo, P. Caminal, A. Perera, and M. Vallverdu. "Exons and introns characterization in nucleic acid sequences by time-frequency analysis." In 2010 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2010). IEEE, 2010. http://dx.doi.org/10.1109/iembs.2010.5626756.

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Lönnberg, Tuomas, Johanna Kiiski, Jonna Korhonen, and Satu Mikkola. "The 2'-OH group as a hydrogen bond donor in the reactions of group I introns." 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/css200507269.

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Reports on the topic "Nuclear introns"

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Hastings, Michelle, and Adrian Krainer. Mechanism of Splicing of Unusual Intron in Human Proliferating Cell Nucleolar P120. Fort Belvoir, VA: Defense Technical Information Center, December 1999. http://dx.doi.org/10.21236/ada384086.

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