Academic literature on the topic 'Nuclear DNA. eng'
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Journal articles on the topic "Nuclear DNA. eng"
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Marini, N. J., and R. M. Benbow. "Differential compartmentalization of plasmid DNA microinjected into Xenopus laevis embryos relates to replication efficiency." Molecular and Cellular Biology 11, no. 1 (January 1991): 299–308. http://dx.doi.org/10.1128/mcb.11.1.299.
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Circular plasmid DNA molecules and linear concatemers formed from the same plasmid exhibit strikingly different fates following microinjection into Xenopus laevis embryos. In this report, we prove quantitatively that only a minority of small, circular DNA molecules were replicated (mean = 14%) from fertilization through the blastula stage of development. At all concentrations tested, very few molecules (approximately 1%) underwent more than one round of DNA synthesis within these multiple cell cycles. In addition, unlike endogenous chromatin, the majority of circular templates became resistant to cleavage by micrococcal nuclease. The extent of nuclease resistance was similar for both replicated and unreplicated templates. Sequestration of circular molecules within a membranous compartment (pseudonucleus), rather than the formation of nucleosomes with abnormal size or spacing, apparently conferred the nuclease resistance. In contrast, most linearly concatenated DNA molecules (derived from end-to-end joining of microinjected monomeric plasmid DNA) underwent at least two rounds of DNA replication during this same period. Linear concatemers also exhibited micrococcal nuclease digestion patterns similar to those seen for endogenous chromatin yet, as judged by their failure to persist in later stages of embryogenesis, were likely to be replicated and maintained extrachromosomally. We propose, therefore, that template size and conformation determine the efficiency of replication of microinjected plasmid DNA by directing DNA to a particular compartment within the cell following injection. Template-dependent compartmentalization may result from differential localization within endogenous nuclei versus extranuclear compartments or from supramolecular assembly processes that depend on template configuration (e.g., association with nuclear matrix or nuclear envelope).
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Marini, N. J., and R. M. Benbow. "Differential compartmentalization of plasmid DNA microinjected into Xenopus laevis embryos relates to replication efficiency." Molecular and Cellular Biology 11, no. 1 (January 1991): 299–308. http://dx.doi.org/10.1128/mcb.11.1.299-308.1991.
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Circular plasmid DNA molecules and linear concatemers formed from the same plasmid exhibit strikingly different fates following microinjection into Xenopus laevis embryos. In this report, we prove quantitatively that only a minority of small, circular DNA molecules were replicated (mean = 14%) from fertilization through the blastula stage of development. At all concentrations tested, very few molecules (approximately 1%) underwent more than one round of DNA synthesis within these multiple cell cycles. In addition, unlike endogenous chromatin, the majority of circular templates became resistant to cleavage by micrococcal nuclease. The extent of nuclease resistance was similar for both replicated and unreplicated templates. Sequestration of circular molecules within a membranous compartment (pseudonucleus), rather than the formation of nucleosomes with abnormal size or spacing, apparently conferred the nuclease resistance. In contrast, most linearly concatenated DNA molecules (derived from end-to-end joining of microinjected monomeric plasmid DNA) underwent at least two rounds of DNA replication during this same period. Linear concatemers also exhibited micrococcal nuclease digestion patterns similar to those seen for endogenous chromatin yet, as judged by their failure to persist in later stages of embryogenesis, were likely to be replicated and maintained extrachromosomally. We propose, therefore, that template size and conformation determine the efficiency of replication of microinjected plasmid DNA by directing DNA to a particular compartment within the cell following injection. Template-dependent compartmentalization may result from differential localization within endogenous nuclei versus extranuclear compartments or from supramolecular assembly processes that depend on template configuration (e.g., association with nuclear matrix or nuclear envelope).
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Franks, R. R., B. R. Hough-Evans, R. J. Britten, and E. H. Davidson. "Direct introduction of cloned DNA into the sea urchin zygote nucleus, and fate of injected DNA." Development 102, no. 2 (February 1, 1988): 287–99. http://dx.doi.org/10.1242/dev.102.2.287.
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A method is described for microinjection of cloned DNA into the zygote nucleus of Lytechinus variegatus. Eggs of this species are unusually transparent, facilitating visual monitoring of the injection process. The initial fate of injected DNA fragments appears similar to that observed earlier for exogenous DNA injected into unfertilized egg cytoplasm. Thus after end-to-end ligation, it is replicated after a lag of several hours to an extent indicating that it probably participates in most of the later rounds of DNA synthesis undergone by the host cell genomes during cleavage. The different consequences of nuclear versus cytoplasmic injection are evident at advanced larval stages. Larvae descendant from eggs in which exogenous DNA was injected into the nuclei are four times more likely (32% versus 8%) to retain this DNA in cell lineages that replicate very extensively during larval growth, i.e. the lineages contributing to the imaginal rudiment, and thus to display greatly enhanced contents of the exogenous DNA. Similarly, 36% of postmetamorphic juveniles from a nuclear injection sample retained the exogenous DNA sequences, compared to 12% of juveniles from a cytoplasmic injection sample. However, the number of copies of the exogenous DNA sequences retained per average genome in postmetamorphic juveniles was usually less than 0.1 (range 0.05-50), and genome blot hybridizations indicate that these sequences are organized as integrated, randomly oriented, end-to-end molecular concatenates. It follows that only a small fraction of the cells of the average juvenile usually retains the exogenous sequences. Thus, even when introduced by nuclear microinjection, the stable incorporation of exogenous DNA in the embryo occurs in a mosaic fashion, although in many recipients the DNA enters a wider range of cell lineages than is typical after cytoplasmic injection. Nuclear injection would probably be the route of choice for studies of exogenous DNA function in the postembryonic larval rudiment.
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Meng, Yuan, Changwei Liu, Lei Shen, Mian Zhou, Wenpeng Liu, Claudia Kowolik, Judith L. Campbell, Li Zheng, and Binghui Shen. "TRAF6 mediates human DNA2 polyubiquitination and nuclear localization to maintain nuclear genome integrity." Nucleic Acids Research 47, no. 14 (June 19, 2019): 7564–79. http://dx.doi.org/10.1093/nar/gkz537.
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Abstract The multifunctional human DNA2 (hDNA2) nuclease/helicase is required to process DNA ends for homology-directed recombination repair (HDR) and to counteract replication stress. To participate in these processes, hDNA2 must localize to the nucleus and be recruited to the replication or repair sites. However, because hDNA2 lacks the nuclear localization signal that is found in its yeast homolog, it is unclear how its migration into the nucleus is regulated during replication or in response to DNA damage. Here, we report that the E3 ligase TRAF6 binds to and mediates the K63-linked polyubiquitination of hDNA2, increasing the stability of hDNA2 and promoting its nuclear localization. Inhibiting TRAF6-mediated polyubiquitination abolishes the nuclear localization of hDNA2, consequently impairing DNA end resection and HDR. Thus, the current study reveals a mechanism for the regulation of hDNA2 localization and establishes that TRAF6-mediated hDNA2 ubiquitination activates DNA repair pathways to maintain nuclear genome integrity.
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Liang, Li, Li Deng, Yanping Chen, Gloria C. Li, Changshun Shao, and Jay A. Tischfield. "Modulation of DNA End Joining by Nuclear Proteins." Journal of Biological Chemistry 280, no. 36 (July 11, 2005): 31442–49. http://dx.doi.org/10.1074/jbc.m503776200.
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Irianto, Jerome, Charlotte R. Pfeifer, Rachel R. Bennett, Yuntao Xia, Irena L. Ivanovska, Andrea J. Liu, Roger A. Greenberg, and Dennis E. Discher. "Nuclear constriction segregates mobile nuclear proteins away from chromatin." Molecular Biology of the Cell 27, no. 25 (December 15, 2016): 4011–20. http://dx.doi.org/10.1091/mbc.e16-06-0428.
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As a cell squeezes its nucleus through adjacent tissue, penetrates a basement membrane, or enters a small blood capillary, chromatin density and nuclear factors could in principle be physically perturbed. Here, in cancer cell migration through rigid micropores and in passive pulling into micropipettes, local compaction of chromatin is observed coincident with depletion of mobile factors. Heterochromatin/euchromatin was previously estimated from molecular mobility measurements to occupy a volume fraction f of roughly two-thirds of the nuclear volume, but based on the relative intensity of DNA and histones in several cancer cell lines drawn into narrow constrictions, f can easily increase locally to nearly 100%. By contrast, mobile proteins in the nucleus, including a dozen that function as DNA repair proteins (e.g., BRCA1, 53BP1) or nucleases (e.g., Cas9, FokI), are depleted within the constriction, approaching 0%. Such losses—compounded by the occasional rupture of the nuclear envelope—can have important functional consequences. Studies of a nuclease that targets a locus in chromosome-1 indeed show that constricted migration delays DNA damage.
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Ma, Hong, Alan J. Siegel, and Ronald Berezney. "Association of Chromosome Territories with the Nuclear Matrix." Journal of Cell Biology 146, no. 3 (August 9, 1999): 531–42. http://dx.doi.org/10.1083/jcb.146.3.531.
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To study the possible role of the nuclear matrix in chromosome territory organization, normal human fibroblast cells are treated in situ via classic isolation procedures for nuclear matrix in the absence of nuclease (e.g., DNase I) digestion, followed by chromosome painting. We report for the first time that chromosome territories are maintained intact on the nuclear matrix. In contrast, complete extraction of the internal nuclear matrix components with RNase treatment followed by 2 M NaCl results in the disruption of higher order chromosome territory architecture. Correlative with territorial disruption is the formation of a faint DNA halo surrounding the nuclear lamina and a dispersive effect on the characteristically discrete DNA replication sites in the nuclear interior. Identical results were obtained using eight different human chromosome paints. Based on these findings, we developed a fractionation strategy to release the bulk of nuclear matrix proteins under conditions where the chromosome territories are maintained intact. A second treatment results in disruption of the chromosome territories in conjunction with the release of a small subset of acidic proteins. These proteins are distinct from the major nuclear matrix proteins and may be involved in mediating chromosome territory organization.
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Meier, J., K. H. Campbell, C. C. Ford, R. Stick, and C. J. Hutchison. "The role of lamin LIII in nuclear assembly and DNA replication, in cell-free extracts of Xenopus eggs." Journal of Cell Science 98, no. 3 (March 1, 1991): 271–79. http://dx.doi.org/10.1242/jcs.98.3.271.
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Xenopus egg extracts, which support nuclear assembly and DNA replication, were functionally depleted of lamin LIII by inoculating them with monoclonal anti-lamin antibodies. Phase-contrast microscopy and electron-microscopy studies indicated that lamin-depleted extracts supported efficient chromatin decondensation, and assembly of double membrane structures and nuclear pores on demembranated sperm heads. Immunofluorescence microscopy suggests that lamin-antibody complexes are transported across the nuclear membrane but do not assemble into a lamina. These findings were confirmed by immunoblotting analysis of isolated nuclei. Metabolic labelling studies with either biotin-11-dUTP or [32P]dCTP, revealed that nuclei lacking a lamina were unable to initiate DNA replication and that, although such nuclei could import proteins required for DNA replication (e.g. PCNA), these proteins were apparently not organized into replicon clusters.
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Büsse, Sebastian, Philipp von Grumbkow, Janine Mazanec, Gert Tröster, Susanne Hummel, and Thomas Hörnschemeyer. "Note on using nuclear 28S rDNA for sequencing ancient and strongly degraded insect DNA." Entomological Science 20, no. 1 (January 2017): 137–41. http://dx.doi.org/10.1111/ens.12242.
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Ceppi, Ilaria, Sean M. Howard, Kristina Kasaciunaite, Cosimo Pinto, Roopesh Anand, Ralf Seidel, and Petr Cejka. "CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection." Proceedings of the National Academy of Sciences 117, no. 16 (April 2, 2020): 8859–69. http://dx.doi.org/10.1073/pnas.2001165117.
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To repair a DNA double-strand break by homologous recombination, 5′-terminated DNA strands must first be resected to reveal 3′-overhangs. This process is initiated by a short-range resection catalyzed by MRE11-RAD50-NBS1 (MRN) stimulated by CtIP, which is followed by a long-range step involving EXO1 or DNA2 nuclease. DNA2 is a bifunctional enzyme that contains both single-stranded DNA (ssDNA)-specific nuclease and motor activities. Upon DNA unwinding by Bloom (BLM) or Werner (WRN) helicase, RPA directs the DNA2 nuclease to degrade the 5′-strand. RPA bound to ssDNA also represents a barrier, explaining the need for the motor activity of DNA2 to displace RPA prior to resection. Using ensemble and single-molecule biochemistry, we show that CtIP also dramatically stimulates the adenosine 5′-triphosphate (ATP) hydrolysis-driven motor activity of DNA2 involved in the long-range resection step. This activation in turn strongly promotes the degradation of RPA-coated ssDNA by DNA2. Accordingly, the stimulatory effect of CtIP is only observed with wild-type DNA2, but not the helicase-deficient variant. Similarly to the function of CtIP to promote MRN, also the DNA2 stimulatory effect is facilitated by CtIP phosphorylation. The domain of CtIP required to promote DNA2 is located in the central region lacking in lower eukaryotes and is fully separable from domains involved in the stimulation of MRN. These results establish how CtIP couples both MRE11-dependent short-range and DNA2-dependent long-range resection and define the involvement of the motor activity of DNA2 in this process. Our data might help explain the less severe resection defects of MRE11 nuclease-deficient cells compared to those lacking CtIP.
Dissertations / Theses on the topic "Nuclear DNA. eng"
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Cavalcante, Neto Aderbal. "Origem do suíno casco-de-burro e sua relação genética com populações ibéricas e americanas /." Jaboticabal : [s.n.], 2010. http://hdl.handle.net/11449/102799.
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Resumo: Com os objetivos de elucidar a origem genética do suíno casco-de-burro e de contribuir para sua conservação, realizou-se uma caracterização genética em 110 animais, oriundos das regiões Nordeste (NE), Centro-Oeste (CO) e Sudeste (SE), usando-se duas classes de marcador molecular e análises citogenéticas. Foram encontrados 13 haplótipos mitocondriais entre os cascos-de-burro, sendo que apenas um foi comum às três subpopulações (NE, CO e SE). O valor médio da diversidade haplotípica e o da nucleotídica na população total foram 0,61 e 0,05 respectivamente. Por meio do DNA mitocondrial, as subpopulações de casco-de-burro apresentaram menor distância genética da população da raça portuguesa bísara. No entanto o haplótipo mais frequente nos cascos-de-burro e o único comum a todas as subpopulações pertence à raça ibérica. A variabilidade genética média obtida por meio dos 25 microssatélites na população total foi: número de alelo = 9,8; conteúdo de informação polimórfica = 0,73; heterozigose esperada = 0,69; heterozigose observada = 0,58; consaguinidade (Fis) = 0,15; e apenas seis loci apresentaram-se em equilíbrio de Hardy-Weinberg. Considerando-se a divisão da população nas três subpopulações que, por meio do DNA nuclear, estiveram mais próximas da população duroc e da bísara , os valores observados para os índices de fixação foram: 0,10 para Fis, 0,09 para Fst e 0,18 para Fit. Os cascos-de-burro possuem o número diploide 2n = 38, não sendo verificado miscigenação com o javali. Os resultados demonstram origem genética ibérica para os cascos-de-burro, com posterior introgressão alélica das raças internacionais importadas no século passadoAbstract: With the purpose of elucidating the genetic origin of Brazilian Mulefoot pigs and to contribute to their conservation, 110 animals from Northeast (NE), Central- West (CW), and Southeast (SE) Brazil were characterized using two molecular marker classes and cytogenetic analysis. A total of 13 mitochondrial haplotypes was found, but only one was common to the three subpopulations (NE, CW, SE) of Brazilian Mulefoot pigs. The total population presented mean haplotype and nucleotide diversity values of 0.61 and 0.05, respectively. Mitochondrial DNA analysis showed that the Brazilian Mulefoot pig subpopulations presented the shortest genetic distance from the Portuguese Bísara breed. However, the most frequent haplotype found in the Brazilian Mulefoot population, and the only one common to all subpopulations belongs to the Ibérica breed. The mean genetic variability of the total population, obtained using 25 microsatellites, was: allele number = 9.8; polymorphic information content = 0.73; expected heterozygosity = 0.69; observed heterozygosity = 0.58; inbreeding = 0.15; and only six loci displayed Hardy-Weinberg equilibrium. Considering the three studied subpopulations which were closer to the Bísara and Duroc populations, based on nuclear DNA the values observed for the fixation indexes were: 0.09 for Fis, 0.10 for Fst, and 0.18 for Fit. Brazilian Mulefoot pigs have a diploid number of 2n = 38, which indicates that there is no interbreeding with wild boars. The results demonstrate that the genetic origin of Brazilian Mulefoot pigs is Iberian, with later allele introgression from foreign breeds imported during the 20th century
Orientador: Jeffrey Frederico Lui
Coorientador:Carlos Manuel M. Santos Fonseca
Coorientador: Maria Aparecida Cassiano Lara
Banca: Sandra Aidar de Queiroz
Banca: Vera Fernanda Martins Hossepian de Lima
Banca: Samuel Rezende Paiva
Banca: Eucleia Primo Betioli Contel
Doutor
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Mariguela, Tatiane Casagrande. "Análise das relações filogenéticas entre os gêneros de Cheirodontinae (Ostariophysi: Characiformes: Charasidae) utilizando sequências de DNA mitocondrial e nuclear /." Botucatu : [s.n.], 2010. http://hdl.handle.net/11449/106510.
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Orientador: Claudio de OliveiraBanca: Guaracy Tadeu Rocha
Banca: Daniela Calcagnotto
Banca: Anderson Luis Alves
Banca: Ricardo Cardoso Benine
Resumo: Os Characiformes são peixes exclusivamente de água doce e encontram-se distribuídos nas Américas e na África, atingindo maior diversidade nas principais drenagens neotropicais. A família Characidae é o grupo mais especioso entre os Characiformes, porém, a relação dessa família com outras famílias é ainda incerta. São conhecidas cerca de 1000 espécies de Characidae das quais cerca de um terço estão distribuídas em 14 subfamílias, e as demais não tem uma posição filogenética clara, sendo incluídas em um grande grupo considerado incertae sedis em Characidae. A subfamília Cheirodontinae compreende cerca de 60 espécies, sendo um grupo de characídeos amplamente distribuídos nas bacias hidrográficas da América do Sul e Central, incluindo espécies trans-andinas. Os gêneros de Cheirodontinae atualmente estão divididos e, três tribos: Cheirodontini, Compsurini e Odontostilbini. No presente estudo, o principal objetivo foi investigar as relações de Cheirodontinae com as subfamílias de Characidae e as relações internas dos membros de Cheirodontinae através da análise de sequências de DNA mitocondrial (16S e Citocromo b) e nuclear (RAG1, RAG2 e Myh6). As análises mostraram que Spintherobolus não pertence à subfamília e Cheirodon stenodon, que era considerado incertae sedis em Characidae, deve fazer parte da mesma. Diversos gêneros apareceram polifiléticos, principalmente Odontostilbe. As espécies trans-andinas e andinas, são as espécies mais antigas da subfamília. As relações observadas nas análises são bastante diferentes das correntemente aceitas para Cheirodontinae e assim é proposta uma nova classificação para o grupo. O gênero Holoshesthes é considerado válido e pertencente a um clado juntamente com o gênero Aphyocheirodon e Acinocheirodon. Odontostilbe forma um clado monofilético com as espécies antes pertencentes à Serrapinnus... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The Characiformes are exclusively freshwater fishes and they are found distributed in Americas and Africa, reaching more diversity in the major Neotropical drainages. The family Characidae is the most specious group among characiforms, but the relationships among this family and other families remains unclear. It is known about 1,000 species belonging to Characidae, one third distributed in 14 subfamilies, and the remaining does not have a clear phylogenetic position, and currently are included in a large group considered incertae sedis in Characidae. The subfamily Cheirodontinae comprises about 60 species, being a characid group widely distributed in the South and Central America hydrographic basins, including trans-Andean species. The genera of Cheirodontinae are currently divided in three tribes: Cheirodontini, Compsurini, and Odontostilbini. In the present work, the main goal was investigate the internal relationships of the members of Cheirodontinae through sequencing and analysis of mitochondrial (16S rRNA and Cytochrome b) and nuclear (RAG1, RAG2, and Myh6) genes. These analyses shown that Spintherobolus does not belong to the subfamily and Cheirodon stenodon, which was considered incertae sedis in Characidae, belongs to the same. Several genera are polyphyletic, mainly Odontostilbe. The trans-Andean and Andean species are the older species of the subfamily. The relationships observed in the analyses are very different of the currently accepted to Cheirodontinae and thereby it is suggested a new classification to the group. The genus Holoshesthes is considered valid and belonging to a clade jointly with the genus Aphyocheirodon and Acinocheirodon. Odontostilbe form a monophyletic clade with the species currently belonging to Serrapinnus, a new species, and Compsura heterura. The tribes Cheirodontini, Compsurini and Odontostilbini are preserved, with different compositions and a new tribe is suggested (Pseudocheirodontini)
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Perecin, Felipe. "Epigenética do desenvolvimento em bovinos : DNA metiltransferases e genes "imprinted" em embriões, fetos e placentas /." Jaboticabal : [s.n.], 2007. http://hdl.handle.net/11449/105948.
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Orientador: Joaquim Mansano GarciaBanca: César Roberto Esper
Banca: Paulo Henrique Franceschini
Banca: Flávio Vieira Meirelles
Banca: Maria Angélica Miglino
Resumo: A clonagem por transferência de núcleo é freqüentemente associada a resultados insatisfatórios devido à reprogramação nuclear anormal da célula somática doadora de núcleo e à expressão gênica alterada. O primeiro objetivo deste trabalho foi estudar a freqüência dos RNAs mensageiros das DNA metiltransferases (DNMT) 1, 3A e 3B, e do gene de expressão constitutiva gliceraldeído 3-fosfato desidrogenase (GAPDH) em blastocistos bovinos isolados produzidos in vivo e in vitro por transferência nuclear (TN) de célula somática, ativação partenogenética e fertilização in vitro (FIV). O segundo objetivo foi avaliar a expressão das DNMTs e dos genes "imprinted" IGF2, IGF2R e H19 em membranas cório-alantóide e fetos bovinos produzidos in vivo e in vitro por TN, ativação partenogenética e FIV e recuperados entre os dias 33 e 36 de gestação. Houve decréscimo (P<0,05) na freqüência do GAPDH nos blastocistos TN e partenogenéticos quando comparados aos embriões fertilizados, e também diferença entre blastocistos TN produzidos com diferentes protocolos de sincronização celular (células em G0 ou G1 do ciclo celular). Com relação às DNMTs, não foram identificados transcritos da DNMT1 nos blastocistos do grupo TN-G0; ocorreu diminuição na freqüência dos transcritos da DNMT3B nos embriões TN quando comparados aos partenotos. Não se observou diferença na freqüência relativa das DNA metiltransferases em membranas cório-alantóide e fetos. Com relação aos genes "imprinted", o grupo partenogenético apresentou menor nível de expressão de IGF2 em relação aos os demais grupos; baixos níveis de expressão de IGF2 e IGF2R foram observados, respectivamente, em amostras de feto e de cório-alantóide derivadas de animais clonados por TN, quando comparadas aos grupos fertilizados in vivo e in vitro.
Abstract: Cloning by nuclear transfer is often associated with poor results due to abnormal nuclear reprogramming of somatic cell donor and altered gene expression. The first objective of this study was to evaluate the frequency of DNA methyltranferases (DNMT) 1, 3A and 3B, and the housekeeping glyceraldehyde 3- phosphate dehydrogenase (GAPDH) mRNAs in single bovine blastocysts produced in vivo or in vitro by somatic cell nuclear transfer (SCNT), parthenogenetic activation and in vitro fertilization (IVF). The second objective was to evaluate the expression of DNMTs and imprinted genes IGF2, IGF2R and H19 in chorio-alantois membrane of bovine fetuses produced in vivo or in vitro by SCNT, parthenogenetic activation and IVF, and recovered between days 33 and 36 of gestation. There was strong GAPDH downregulation (P<0.05) in parthenogenetic and cloned by SCNT blastocysts when compared to fertilized ones, and also differences between cloned blastocysts produced with different cell synchronization (G0 or G1) protocol. Regarding DNMTs expression, we did not identify DNMT1 transcrips in SCNT-G0 derived blastocysts, and observed DNMT3B downregulation in SCNT-derived embryos when compared to parthenotes. No differences in DNA methyltransferase relative frequency were seen in chorio-alantois membrane and fetuses. Regarding imprinted genes expression, downregulation of IGF2 in the parthenogenetic group was observed in comparision to all other groups, and also, downregulation of IGF2 and IGF2R in the cloned-derived fetuses and chorio-alantois samples, respectively, were observed comparing to in vivo and in vitro fertilized groups.
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Abe, Kelly Terumi. "Análise das relações filogenéticas entre espécies da subfamília Bryconinae (Ostariophysi: Characiformes: Characidae) utilizando sequências de DNA mitocrondrial e nuclear /." Botucatu : [s.n.], 2011. http://hdl.handle.net/11449/106497.
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Orientador: Claudio de OliveiraBanca: Adriane Pinto Wasko
Banca: Daniela Calcagnotto
Banca: Flávio César Thadeo de Lima
Banca: Ricardo Cardoso Benine
Resumo: A família Characidae é o grupo mais especioso entre os Characiformes, abrangendo cerca de 1100 espécies válidas, divididas em 14 subfamílias e com diversos gêneros considerados incertae sedis. A subfamília Bryconinae incluí 43 espécies válidas sendo que 41 pertencem ao gênero Brycon, uma ao gênero Henochilus e uma ao gênero Chilobrycon. Os peixes do gênero Brycon estão entre os mais importantes na pesca amadora e profissional de água doce da América do Sul. Apesar da importância econômica e ecológica das espécies dessa subfamília, ainda há resultados controversos presentes na literatura quanto à sua composição, conhecimento da relação entre seus componentes e de seu relacionamento com outros Characiformes. Para tentar resolver essas questões, o presente trabalho tem como objetivo elaborar e testar hipóteses de relacionamento das espécies dos diferentes gêneros dessa subfamília e desta com outros grupos de Characidae e Characiformes. Sequências parciais de dois genes mitocondriais (16S RNA e Citocromo b) e três genes nucleares (Myh6, Rag1 e Rag2) foram obtidas de 231 espécies, incluindo 230 Characiformes e 1 Cypriniformes, totalizando uma matriz total de 4684pb. As análises filogenéticas foram conduzidas pelo método de Máxima Parcimônia, Máxima Verossimilhança e Análise Bayesiana. Todos os métodos filogenéticos apontaram para o mesmo resultado: Bryconinae mais os representantes do gênero Salminus formaram o grupo irmão de Gasteropelecidae, diretamente relacionados às subfamílias de Characidae: Agoniatinae, Clupeacharacinae e Triportheinae e também aos gêneros Engraulisoma e Lignobrycon. A subfamília Bryconinae e o gênero Brycon não são monofiléticos, assim como os grupos cis e transandinos de Brycon. Salminus apareceu entre as amostras de Brycon. Chilobrycon pertence a um clado formado por espécies de Brycon trans-andinas... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The family Characidae is the richest group among Characiformes, comprising about 1100 valid species, divided in 14 subfamilies and several genera considered incertae sedis. Among Characidae, the subfamily Bryconinae includes 43 valid species; among which 41 belong to the genus Brycon, one to the genus Henochilus and one to the genus Chilobrycon. In spite of the economic and ecological importance of the species of the subfamily Bryconinae, its phylogeny, classification and composition are not yet well solved. The main objective of this study was to test the hypothesis of relationship of the Bryconinae with other group of Characidae and Characiformes. Partial sequences of two mitochondrial genes (cytochrome b and 16S RNA) and three nuclear genes (Myh6, RAG1 and RAG2) were obtained from 231 species, including 230 Characiformes and one Cypriniformes, resulting in a matrix of 4684 pb. Phylogenetic analysis were conducted by the methods of Maximum Parsimony, Maximum Likelihood and Bayesian analysis. In all phylogenetic analysis we achieved the same result: Bryconinae and the genus Salminus formed the sister group of Gasteropelecidae directly related to the Characidae subfamilies Agoniatinae, Clupeacharacinae, and Triportheinae and also to the genera Engraulisoma and Lignobrycon. The subfamily Bryconinae and Brycon are not monophyletic, as well as the cis- and trans-Andean groups. Salminus appeared between samples of Brycon. Chilobrycon is related to some trans-Andean species of Brycon. B. moorei (trans-Andean) is related of the species found in the Amazonas, São Francisco and Paraná Basis. Henochilus wheatlandii is sister-group of species of the coastal rivers of eastern Brazil. Some aspects related to the composition of Bryconinae as well as the groups distribution are discussed in the text
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Rytkönen, A. (Anna). "The role of human replicative DNA polymerases in DNA repair and replication." Doctoral thesis, University of Oulu, 2006. http://urn.fi/urn:isbn:9514281381.
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Abstract
The maintenance of integrity of the genome is essential for a cell. DNA repair and faithful DNA replication ensure the stability of the genome. DNA polymerases (pols) are the enzymes that synthesise DNA, a process important both in DNA replication and repair. In DNA replication DNA polymerases duplicate the genome during S phase prior to cell division. Pols α, δ, and ε are implicated in chromosomal DNA replication, but their exact function in replication is not yet completely clear. The mechanisms of different repair pathways and proteins involved are not yet completely characterised either. The deeper understanding of DNA repair and replication mechanisms is crucial for our understanding on the function of the cell.
The mechanism of repair of DNA double strand breaks (DSBs) by non-homologous end joining (NHEJ) was studied with an in vitro assay. DNA polymerase activity was found to be involved in NHEJ and important in stabilising DNA ends. Antibodies against pol α, but not pol β or ε, decreased NHEJ significantly, which indicates the involvement of pol α in NHEJ. In addition, the removal of proliferating cell nuclear antigen (PCNA) slightly decreased NHEJ activity.
The division of labour between pols α, δ, and ε during DNA replication was studied. Results from UV-crosslinking, chromatin association, replication in isolated nuclei, and immunoelectron microscopy (IEM) studies showed that there are temporal differences between the activities and localisations of the pols during S phase. Pol α was active throughout S phase, pol ε was more active at early S phase, whereas the activity of pol δ increased as S phase advanced. These results suggest that pols δ and ε function independently during DNA replication.
Pol ε could be crosslinked to nascent RNA, and this labelling was not linked to DNA replication, but rather to transcription. Immunoprecipitation studies indicated that pol ε, but not pols α and δ, associated with RNA polymerase II (RNA pol II). Only the hyperphosphorylated, transcriptionally active RNA pol II was found to associate with pol ε. A large proportion of pol ε and RNA pol II colocalised in cells as determined with immunoelectron microscopy. The interaction between pol ε and RNA pol II suggests that they are involved in a global regulation of transcription and DNA replication.
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Sun, Wei-Hsin. "The induction of DNA replication in quiescent mammalian nuclei by Xenopus egg extracts." Thesis, King's College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314371.
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Mendonça, Priscila Pasqüetto. "Estudo comparativo das características citogenéticas e moleculares de Triatoma maculata e Triatoma pseudomaculata (Triatominae, Heteroptera) /." São José do Rio Preto : [s.n.], 2010. http://hdl.handle.net/11449/92477.
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Resumo: Os triatomíneos são insetos hematófagos de grande importância para a parasitologia humana, pois são transmissores do Trypanosoma cruzi, protozoário causador da doença de Chagas. Além de sua importância médico-sanitária, os triatomíneos destacam-se pela sua citogenética, pois possuem cromossomos holocêntricos e um modelo de meiose incomum, com meiose invertida para os cromossomos sexuais. Recentes pesquisas com marcadores moleculares em triatomíneos tentam compreender a ancestralidade do grupo. Uma das formas de se compreender a evolução entre espécies é a partir da análise de seqüências do DNA ribossômico (DNAr). Por pertencer a famílias multigênicas, cópias individuais do DNAr não acumulam mutações independentemente, resultando em pequena variação intra-específica e relevante diferenciação interespecífica. No presente trabalho foi realizado um estudo comparativo entre as espécies Triatoma maculata e Triatoma pseudomaculata, com base no uso das técnicas citogenéticas convencionais de orceína lacto-acética, impregnação por íons prata, bandamento-C, reação de Feulgen; da técnica de citogenética molecular de bandamento- C CMA/DAPI; e também por meio da análise da região ITS-1 do DNAr, com base no sequenciamento, com o objetivo de avaliar o grau de homologia entre as espécies estudadas. Os cariogramas das duas espécies indicaram dez pares de autossomos (um deles de tamanho maior) e um par de cromossomos sexuais (2n = 22). No ciclo meiótico foi possível observar a fragmentação da região nucleolar no final do estágio difuso. Corpúsculos nucleolares foram observados em alguns dos núcleos em metáfases meióticas de T. pseudomaculata, evidenciando a persistência nucleolar. A técnica de bandamento-C revelou que o cromossomo Y é heterocromático em ambas as espécies. O sequencimento da região ITS-1, indicou que as espécies apresenta... (Resumo completo, clicar acesso eletrônico abaixo)Abstract: The triatomines are hematophagous insects of great concern in public health because they are vectors of Trypanosoma cruzi, a protozoan that causes Chagas disease. Triatomines are also of great genetic interest, because that they present holocentric chromosomes and an unusual form of meiosis with post-reductional segregation of sex chromosomes. Recent studies based on molecular markers try to understand the evolutionary history of triatomines. To understand the evolution of a given species, ribosomal DNA (rDNA) analyses are frequently used, which can help to infer evolutionary relationships among species. Individual copies of rDNA do not accumulate mutations independently because they belong to multigene families, resulting in slight intraspecific and important interspecific variation. In this study, a comparative analysis was performed between the species Triatoma maculata and Triatoma pseudomaculata, based on the cytogenetic techniques of lacto-acetic orcein, silver ion impregnation, Cbanding, Feulgen reaction; and CMA/DAPI C-banding. We also compared the species by sequencing the ITS-1 rDNA internal transcribed region in order to evaluate the degree of homology among the studied species. The cariograms of the two species revealed ten autosomes and one pair of sexual chromosomes (2n= 22). In the meiotic cycle, nucleolar fragmentation during the final stages of meiotic prophase I was found. Nucleolar corpuscles were found in some meiotic metaphases of T. pseudomaculata, which is evidence of nucleolar persistence. The C-banding technique revealed that the Y chromosome is heterochromatic in both species. The ITS-1 rDNA sequences showed that the species presented a discharge proximity to each other, and had a high degree of homology (98.5%). The knowledge obtained in this study contributes to the understanding of the interrelation and distribution of those species, and offers... (Complete abstract click electronic access below)
Orientador: Maria Tercília Vilela de Azeredo Oliveira
Coorientador: Lilian Castiglioni
Banca: João Aristeu da Rosa
Banca: Carlos Roberto Ceron
Mestre
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Shaw, Alexander George. "Developing models of the mammalian cell S phase." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/developing-models-of-the-mammalian-cell-s-phase(3df7caaf-fd64-4bd2-b500-802f1a2c8ce2).html.
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The accurate replication of the mammalian genome is a complex and logistically challenging process. The entirety of the genome must undergo a single duplication with as little error as possible. This must occur in a coordinated fashion and over suitably short time scale so as to allow timely cellular division within a cell cycle that is typically around 24 hours in a human cell. A great wealth of knowledge already exists describing various aspects of the S phase, during which this replication of the genome occurs. This data has been gathered over a variety of model systems, ranging from inferences from the replicative mechanics of SV40 through to direct observations of replication in mammalian cells.In order integrate this data and determine the value of inferences from different data sources, quantitative models of the mammalian cell S phase are required. This study documents the development of several such models and the exploration of the influences that experimentally determined parameters and different mechanistic theories can have on the behaviour of a simulated S phase. Of particular exploratory interest were the modes of activating replication of replicon clusters, with the aim of simulating experimentally observed dynamics. Additionally, the study also aimed to investigate the variation of replication fork rates and the density of origins of replication, along with the relationship that occurs between the two during both replicational stress and during a normal S phase. Through an iterative series of models, relevant parameters and key theories are sequentially explored so as to better understand the S phase. Particularly influential parameters were identified and studied in detail, with experimental determination where necessary in order to more accurately inform the model system. Conclusions concerning the behaviour of the system and the potential impact of the results were drawn upon the completion of each level of modelling and experimental work.To conclude the study, a linear model simulating the genome of the MRC5 cell line was used to estimate the modes activation of DNA replication along chromosomes in order to recreate experimentally observed replication dynamics. Experimentally determined profiles of replication fork rates and the density of origin firing were also determined for the MRC5 cell line, and were used to populate the model with accurate and appropriate data. Using the model to simulate S phase through a variety of behavioural parameters, realistic S phase dynamics were found to occur through a combination of de novo activation of replicon clusters and a specific probability of neighbour activation by completed clusters. These derived mechanics, when performed on a system correctly parameterised with suitable data, can simulate experimentally observed phenomena. The development of the model highlighted the requirements of data fit for purpose, and the study also stresses the need for critical consideration of inferences made between different model systems.
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Genet, Diane. "Impact de la surexpression de la lamine B1 sur la réparation des cassures double-chaîne de l’ADN." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112204.
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De nombreuses études montrent un rôle important de l'architecture du noyau sur la stabilité du génome. Les lamines sont les constituants majeurs de l’enveloppe nucléaire et sont impliquées dans de nombreux processus, notamment, la régulation génique, la réplication et le maintien de la structure du noyau. Il en existe 2 types, les lamines A/C et les lamines B. Certaines mutations des lamines A/C sont à l’origine de syndromes progéroïdes, classés jusqu’à présents en deux catégories : ceux associés à une dérégulation des lamines (laminopathies) et ceux associés à un défaut de réparation de l’ADN, dont l’Ataxie Télangiectasie (A-T). Il est proposé que le vieillissement prématuré observé dans les laminopathies est dû à un défaut de réparation de l’ADN, qui serait alors la voie commune d’induction de sénescence des syndromes progéroïdes. Ceci est appuyé par le fait que de plus en plus de données associent les mutations des lamines A/C à des défauts de réparation de l’ADN. La mise en évidence, par notre laboratoire d’une accumulation de lamine B1 dans A-T et dans deux autres syndromes progéroïdes, pose la question de l’impact de la surexpression de la lamine B1 sur la réparation de l’ADN, d’autant plus que de plus en plus de données associent une augmentation de la lamine B1 à de nombreux cancers, bien que le mécanisme moléculaire ne soit pas connu. Au cours de ma thèse, j’ai donc pu montrer, notamment à l’aide de substrats intra-Chromosomiques, qu’une surexpression de lamine B1 entraînait un défaut de réparation des cassures double-Brin par NHEJ associé à un défaut de recrutement de 53BP1 à la cassure. La mise en évidence d’une interaction entre 53BP1 et la lamine B1, rompue après dommages permet de suggérer un nouveau rôle de la lamine B1 comme réservoir de 53BP1, régulant son recrutement aux cassures. De plus, d’autres résultats suggèrent que la lamine B1 agirait également au niveau de la signalisation du dommage en altérant l’activation d’ATM par un mécanisme qu’il reste à caractériser. L’ensemble de ces résultats montrent un nouveau rôle très important de la lamine B1 dans la signalisation des dommages et la régulation du recrutement des protéines de réparation, ouvrant la voie à une meilleure compréhension de l’implication de la lamine B1 dans la sénescence et le cancerMany studies show an important role of nuclear shape on genome stability. Lamins are the major components of the nuclear envelope and are implicated in numerous processes like gene regulation, DNA replication and the maintenance of nuclear structure. There are 2 types of lamins : lamin A/C and lamin B. Some mutations of lamin A/C cause progeroid syndromes, which are classified untill now in two categories : those due to lamins deregulation and those due to DNA repair defects, including Ataxia Telangiectasia (A-T). Accelerated aging observed in laminopathies is proposed to be due to a DNA repair defect, which would be the common pathway leading to senescence in progeroid syndromes. This is supported by many data linking lamin A mutations to DNA repair defects. Our laboratory reported that lamin B1 accumulates in A-T and Fanconi and another study showed also an accumulation in Werner syndrome, which is another progeroïd syndrome. This discovery raises a question about the impact of lamin B1 overexpression on DNA repair, especially as more and more data show an increase of lamin B1 in several cancers, although the molecular mechanism is still unclear. During my thesis, I showed, in particular with intrachromosomal substrates, that lamin B1 overexpression leads to an NHEJ double-Strand break (DSB) repair defect associated with a defect of 53BP1 recruitment to the break. The discovery of an interaction between 53BP1 and lamin B1, which is broken after damage, suggests a new role of lamin B1 as a « reservoir » of 53BP1, regulating its recruitment to the break. In addition, we obtained results suggesting that lamin B1 could also act in the DSB signalisation pathway by affecting ATM activation through a mechanism that we still have to characterize.All together, these datas show a new important role of lamin B1 in DSB signalisation and in the regulation of the recruitment of repair proteins, paving the way to a better understanding of the implication of lamin B1 in senescence and cancer
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Raoul, Sébastien. "Réactions d'oxydation des bases puriques des acides nucléiques." Université Joseph Fourier (Grenoble), 1995. http://www.theses.fr/1995GRE10178.
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Les modifications des bases de l'adn, support de l'information genetique, sont une des causes possibles de la mutagenese et la cancerogenese. Bien souvent ces modifications sont de type oxydatives. Elles sont induites par les especes reactives de l'oxygene, formees lors du metabolisme cellulaire et/ou par l'action de divers rayonnements (ionisants, uv, visible). Les mecanismes d'oxydation des deux bases puriques de l'adn, l'adenine et la guanine, ont ete etudies en identifiant et caracterisant les produits finals resultant de l'oxydation des nucleosides correspondants, pris comme systemes modeles. Les produits principaux de modification radio-induite de la 2'-desoxyadenosine en solution aqueuse ainsi que ceux provenant de l'oxydation photosensibilisee ont ete isoles par clhp puis caracterises par diverses methodes spectroscopiques dont notamment la rmn mono- et bi-dimensionnelle heteronucleaire #1h-#1#3c et #1h-#1#5n. L'analyse quantitative de la formation de ces produits dans differentes conditions a permis de proposer un schema de mecanismes coherent. La caracterisation du produit majoritaire de l'oxydation photosensibilisee de la 2'-desoxyguanosine, forme par un mecanisme radicalaire (type i), a ete realisee par les techniques pre-citees. La mise au point d'une methode de detection sensible et specifique de ce nucleoside oxyde, basee sur ses proprietes physico-chimiques, a permis de le rechercher dans un adn irradie. En outre, un schema du mecanisme rendant compte de sa formation est propose. La detection de ce produit, alliee a l'identification et la detection des produits formes par l'intermediaire de l'oxygene singulet (type ii) ont permis l'etude du mode d'action de divers photosensibilisateurs et de determiner pour chacun d'eux la contribution relative du mecanisme de desexcitation (type i/type ii). Enfin, nous avons etudie l'oxydation photosensibilisee de la 8-oxo-7,8-dihydro-2'-desoxyguanosine en identifiant les produits d'oxydation. En effet, ce nucleoside oxyde est un meilleur substrat que la 2'-desoxyguanosine pour l'oxygene singulet
Books on the topic "Nuclear DNA. eng"
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Laurella, Sergio Luis. Resonancia magnética nuclear. Editorial de la Universidad Nacional de La Plata (EDULP), 2017. http://dx.doi.org/10.35537/10915/62803.
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En el estudio de la Química existe una sección muy interesante que consiste en develar cómo están formadas las moléculas que componen los diferentes compuestos. La determinación de estructuras moleculares es un trabajo creativo en el que hay que poner en juego todas nuestras habilidades de deducción, dado que (como las moléculas no se ven) debemos usar herramientas que nos den pistas sobre su constitución. En este sentido, la Resonancia Magnética Nuclear es una técnica que aporta mucha información al respecto: puede decirnos cuáles son los diferentes tipos de átomos presentes, cómo están conectados entre sí, su orientación en el espacio, su cercanía con otros átomos, etcétera. Uno de los desafíos más interesantes es aprender a leer las pistas que las moléculas nos dan y el objetivo principal de este libro es, justamente, aprender a observarlas por medio de sus espectros de RMN. A través de los diferentes capítulos, aprenderemos los fundamentos de la técnica de RMN, la lectura de los espectros que aportan los diferentes elementos presentes (hidrógeno, carbono, flúor, fósforo, entre otros), la corroboración de las estructuras propuestas y diferentes aspectos experimentales que atañen a la técnica. Presentamos ejemplos resueltos de lectura de espectros y postulación de estructuras y, además, problemas propuestos que ayuden a consolidar los conceptos trabajados.
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Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. Single-Molecule Studies of Nucleic Acids and Their Proteins. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.001.0001.
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This book presents a comprehensive overview of the foundations of single-molecule studies, based on manipulation of the molecules and observation of these with fluorescent probes. It first discusses the forces present at the single-molecule scale, the methods to manipulate them, and their pros and cons. It goes on to present an introduction to single-molecule fluorescent studies based on a quantum description of absorption and emission of radiation due to Einstein. Various considerations in the study of single molecules are introduced (including signal to noise, non-radiative decay, triplet states, etc.) and some novel super-resolution methods are sketched. The elastic and dynamic properties of polymers, their relation to experiments on DNA and RNA, and the structural transitions observed in those molecules upon stretching, twisting, and unzipping are presented. The use of these single-molecule approaches for the investigation of DNA–protein interactions is highlighted via the study of DNA and RNA polymerases, helicases, and topoisomerases. Beyond the confirmation of expected mechanisms (e.g., the relaxation of DNA torsion by topoisomerases in quantized steps) and the discovery of unexpected ones (e.g., strand-switching by helicases, DNA scrunching by RNA polymerases, and chiral discrimination by bacterial topoII), these approaches have also fostered novel (third generation) sequencing technologies.
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J, Harwood Adrian, ed. Basic DNA and RNA protocols. Totowa, N.J: Humana Press, 1996.
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L, Macario Alberto J., and Conway de Macario Everly, eds. Gene probes for bacteria. San Diego: Academic Press, 1990.
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Hall, Andrew, and Shamima Rahman. Mitochondrial diseases and the kidney. Edited by Neil Turner. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199592548.003.0340.
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Mitochondrial disease can affect any organ in the body including the kidney. As increasing numbers of patients with mitochondrial disease are either surviving beyond childhood or being diagnosed in adulthood, it is important for all nephrologists to have some understanding of the common renal complications that can occur in these individuals. Mitochondrial proteins are encoded by either mitochondrial or nuclear DNA (mtDNA and nDNA, respectively); therefore, disease causing mutations may be inherited maternally (mtDNA) or autosomally (nDNA), or can arise spontaneously. The commonest renal phenotype in mitochondrial disease is proximal tubulopathy (Fanconi syndrome in the severest cases); however, as all regions of the nephron can be affected, from the glomerulus to the collecting duct, patients may also present with proteinuria, decreased glomerular filtration rate, nephrotic syndrome, water and electrolyte disorders, and renal tubular acidosis. Understanding of the relationship between underlying genotype and clinical phenotype remains incomplete in mitochondrial disease. Proximal tubulopathy typically occurs in children with severe multisystem disease due to mtDNA deletion or mutations in nDNA affecting mitochondrial function. In contrast, glomerular disease (focal segmental glomerulosclerosis) has been reported more commonly in adults, mainly in association with the m.3243A<G point mutation. Co-enzyme Q10 (CoQ10) deficiency has been particularly associated with podocyte dysfunction and nephrotic syndrome in children. Underlying mitochondrial disease should be considered as a potential cause of unexplained renal dysfunction; clinical clues include lack of response to conventional therapy, abnormal mitochondrial morphology on kidney biopsy, involvement of other organs (e.g. diabetes, cardiomyopathy, and deafness) and a maternal family history, although none of these features are specific. The diagnostic approach involves acquiring tissue (typically skeletal muscle) for histological analysis, mtDNA screening and oxidative phosphorylation (OXPHOS) complex function tests. A number of nDNA mutations causing mitochondrial disease have now been identified and can also be screened for if clinically indicated. Management of mitochondrial disease requires a multidisciplinary approach, and treatment is largely supportive as there are currently very few evidence-based interventions. Electrolyte deficiencies should be corrected in patients with urinary wasting due to tubulopathy, and CoQ10 supplementation may be of benefit in individuals with CoQ10 deficiency. Nephrotic syndrome in mitochondrial disease is not typically responsive to steroid therapy. Transplantation has been performed in patients with end-stage kidney disease; however, immunosuppressive agents such as steroids and tacrolimus should be used with care given the high incidence of diabetes in mitochondrial disease.
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PCR protocols: A guide to methods and applications. San Diego: Academic Press, 1990.
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(Editor), Michael A. Innis, David H. Gelfand (Editor), John J. Sninsky (Editor), and Thomas J. White (Editor), eds. PCR Protocols: A Guide to Methods and Applications. Academic Press, 1989.
Find full textBook chapters on the topic "Nuclear DNA. eng"
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Lebofsky, Ronald, Tatsuro Takahashi, and Johannes C. Walter. "DNA Replication in Nucleus-Free Xenopus Egg Extracts." In Methods in Molecular Biology, 229–52. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-815-7_13.
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Parsons, Jason L., Emma Boswell, and Grigory L. Dianov. "Processing of 3′-End Modified DNA Strand Breaks Induced by Oxidative Damage." In Oxidative Damage to Nucleic Acids, 81–90. New York, NY: Springer New York, 2007. http://dx.doi.org/10.1007/978-0-387-72974-9_6.
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Lucchesi, John C. "Aging, cellular senescence and cancer: the role of genomic instability, cellular homeostasis and telomeres." In Epigenetics, Nuclear Organization & Gene Function, 227–37. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0020.
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Aging hallmarks are causative factors of oncogenesis. Genomic instability results from the accumulation of errors that occur during DNA replication or from exposure to endogenous or environmental insults. The genome contains genes responsible for normal cell division and differentiation (oncogenes), and genes that regulate cell division and limit cell growth and proliferation (tumor suppressor genes). Over-expression of oncogenes or inactivation of tumor suppressors results in cancer. During aging, alterations in proteostasis result in the disruption of metabolic pathways that connect with environmental factors. Telomeres are terminal regions of chromosomes that protect the DNA from attack by exonucleases, prevent end-to-end fusions and prevent the shortening of the DNA molecules at each replication cycle. Using RNA as a template, telomerase synthesizes telomeric DNA. Telomerase is absent in most adult human tissues, resulting in a progressive shortening of all telomeres and causing cells to senesce. Cancer cells must activate telomerase to gain “immortality.”
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Lucchesi, John C. "DNA repair and genomic stability." In Epigenetics, Nuclear Organization & Gene Function, 173–83. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0015.
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A number of pathways have evolved in order to repair DNA. Mismatch repair (MMR) operates when an improper nucleotide is used or when an insertion or deletion occurs during replication. Nucleotide excision repair (NER) repairs damage that distorts the DNA helix such as the presence of pyrimidine dimers induced by ultraviolet light. Base excision repair (BER) removes damaged or altered DNA bases that do not result in a conformational change in the chromatin. Single-strand break repair (SSBR) uses the same enzymatic steps as BER. Double-strand break (DSB) repair can involve either non-homologous end-joining (NHEJ) or homologous recombination (HR). In NHEJ, the broken DNA ends are joined directly. HR requires that one of the strands of the broken DNA molecule participates in the strand invasion of the sister chromatid. The site of the DSB must be modified to allow access to the repair machinery. This modification involves remodeling complexes, as well as histone-modifying enzymes.
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Lucchesi, John C. "Epigenetic phenomena in fungi, plants and animals." In Epigenetics, Nuclear Organization & Gene Function, 3–6. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0001.
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DNA does not exist in pure form and is associated with a variety of proteins and RNA to form a complex referred to as chromatin. The individualization of cell types during development requires the differential activation of genes, a process that is initiated by the uneven distribution of morphogens such as transcription factors in the fertilized egg. The transcription of selected genes involves modifications of the proteins that are associated with the DNA and a remodeling of this association. These alterations do not modify the DNA sequence proper and are referred to as epigenetic modifications. Cell types are characterized by different distributions of epigenetic modifications and can be said to exhibit their own particular epigenome. As cells divide, they must transmit to their daughter cells the information necessary to maintain their particular distribution of active genes. This epigenetic memory may involve the transmission of transcription factors as well as the transmission of epigenetic modifications present in the parent cell’s chromatin.
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Lucchesi, John C. "The basic mechanism of gene transcription." In Epigenetics, Nuclear Organization & Gene Function, 17–32. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0003.
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Transcription is initiated by factors that interact with RNA polymerases and recruit them to specific sites, unwind the DNA molecules and allow the synthesis of RNA transcripts complementary to one of the single DNA strands. RNA polymerase II (RNAPII) transcribes genes that encode proteins and some non-coding RNAs; RNAPI transcribes ribosomal RNA genes; RNAPIII transcribes genes that encode tRNAs and other non-coding RNAs. The transcription process starts with a pre-initiation complex (PIC), its activation and promoter clearance. Activation involves chromatin looping, usually promoted by the large multiprotein Mediator complex. RNAPII often makes a promoter-proximal pause, then resumes productive elongation of the transcript. Transition through the different phases of transcription is orchestrated by the phosphorylation of the main subunit of RNAPII. The 5´ end of many transcripts is protected by a methylated guanosine “cap,” and the 3´ end by the addition of a chain of adenosine monophosphates (polyadenylation). Many transcripts undergo splicing to remove regions that interrupt the coding sequence.
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Wong, Agnes. "Disorders Affecting the Extraocular Muscles." In Eye Movement Disorders. Oxford University Press, 2008. http://dx.doi.org/10.1093/oso/9780195324266.003.0023.
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Chronic progressive external ophthalmoplegia (CPEO) occurs in 90% of patients with mitochondrial myopathy. It is characterized by a slowly progressive ptosis and ophthalmoplegia. The ophthalmoplegia is usually preceded by ptosis for months to years, and downgaze is usually intact. Kearns-Sayre Syndrome is a subtype of chronic progressive external ophthalmoplegia. Most cases are sporadic and associated with single deletions of mitochondrial DNA. Ragged-red fibers are seen on light microscopy (using modified Gomori trichrome stain). ■ Due to accumulation of enlarged mitochondria under the sarcolemma of affected muscles ■ Found in skeletal muscles, orbicularis, and extraocular muscles ■ On electron microscopy, the mitochondria contain paracrystalline (“parking lot”) inclusions and disorganized cristae that are sometimes arranged concentrically. 1. Muscle biopsy (e.g., deltoid) 2. ERG 3. Electrocardiogram (EKG) 4. Genetic testing There is no effective treatment for CPEO. Maintaining a high-lipid, low-carbohydrate diet, taking co-enzyme Q10, biotin, or thiamine, and avoiding medications such as valproate and phenobarbital may be helpful. ■ MELAS stands for mitochondrial encephalomyopathy, lactic acidosis, and strokelike episodes. ■ Maternally inherited; caused by point mutations of mitochondrial DNA (A3243G mutation accounts for about 80% of all cases) ■ Clinical features 1. Strokelike episodes before age 40 (hallmark feature) 2. Encephalopathy characterized by developmental delay, seizures, or dementia 3. Mitochondrial dysfunction manifested as lactic acidosis or ragged-red fibers 4. Ophthalmoplegia 5. Optic atrophy and pigmentary retinopathy 6. Diabetes mellitus and hearing loss ■ MNGIE stands for mitochondrial neuro-gastrointestinal encephalomyopathy. ■ Autosomal recessive; caused by mutations in the nuclear gene ECGF1, resulting in thymidine phosphorylase deficiency, which in turn causes deletions, duplications, and depletion of mitochondrial DNA ■ Clinical features: ophthalmoplegia, peripheral neuropathy, leukoencephalopathy, and gastrointestinal symptoms (recurrent nausea, vomiting, or diarrhea) with intestinal dysmotility SANDO stands for sensory ataxic neuropathy, dysarthria, and ophthalmoplegia. It is sporadic and is caused by multiple deletions of mitochondrial DNA.
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Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. "Manipulating DNA." In Single-Molecule Studies of Nucleic Acids and Their Proteins, 11–26. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.003.0002.
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This chapter describes the various methods used to manipulate single DNA molecules and the considerations in the choice of one particular method. It starts with a description of DNA end-labelling, necessary to anchor the molecule to surfaces or beads that can be manipulated. A particular application of DNA anchoring is molecular combing, whereby the molecule is stretched on a surface by a receding meniscus. DNA rearrangements and replication bubbles can then be observed by fluorescence on these straightened molecules. It then looks at the forces at the molecular scale, which range from the smallest one due to thermal agitation, to the largest associated with breaking a covalent bond, via entropic and non-covalent bonding forces. It describes the tools used to manipulate single molecules (micro-needles, AFM cantilevers, optical, magnetic, and acoustic tweezers and traps, etc.), comparing their performances in terms of bandwidth and signal to noise (i.e., force and extension resolutions).
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White, Perrin C. "Genes and Hormones." In Textbook of Endocrine Physiology. Oxford University Press, 2011. http://dx.doi.org/10.1093/oso/9780199744121.003.0005.
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Much of the knowledge presented in the following chapters has been gained using molecular genetic techniques to analyze the structure, synthesis, regulation, and effects of hormones. This chapter provides an overview of some of the relevant techniques and associated concepts. To allow the reader to understand older experiments, we have tried to include techniques that are now of mainly historical interest as well as current concepts. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) consist of nucleotides . A nucleotide consists of a base , a sugar moiety (either deoxyribose or ribose), and a phosphate group. The sugars and phosphates alternate in the backbone of a nucleic acid strand. In general, there are four possible bases. In DNA, these are adenine ( A ), cytosine ( C ), guanine ( G ), and thymine ( T ). Adenine and guanine are purines , whereas cytosine and thymine are pyrimidines . The corresponding nucleotides are adenosine , cytidine , guanosine , and thymidine. In RNA, uracil (uridine) is substituted for thymine (thymidine). DNA is double stranded. Each strand has a direction because the deoxyribose molecules forming the backbone are asymmetrical, with the phosphate bonds linking each two sugar molecules going from the 3’ position of one to the 5’ position of the next. Thus, the 5’ position of a sugar molecule is free at one end (the 5’ end) of the strand, and the 3’ position is free at the other. The two strands of a DNA molecule run in opposite directions, so that the 5’ end of one strand is opposed to the 3’ end of the complementary strand. The DNA strands interact with each other through complementary (Watson-Crick) base pairing , in which A and T, or C and G, are paired through hydrogen bonds. Thus, the sequence of one DNA strand unambiguously determines the sequence of the complementary strand during DNA replication. The length of a DNA segment is typically given in bases or nucleotides (nt) or, if double stranded, base pairs (bp).
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Provan, Drew. "Rheumatology." In Oxford Handbook of Clinical and Laboratory Investigation, edited by Drew Provan, 741–64. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198766537.003.0012.
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This chapter examines the role of investigations in diagnosis, assessing disease activity, and monitoring treatment in rheumatic disease. It reviews the relevance of haematology and biochemistry tests in clinical context, including differential diagnosis of anaemia and cytopenia which may reflect the disease process, co-morbidity, or adverse drug effects. Bone biochemistry and markers are also described. Autoantibodies are important in diagnosis and prognosis in rheumatology. Interpretation of rheumatoid factor, anti-cyclic citrullinated peptide (CCP) antibodies, antinuclear antibodies (ANA), antineutrophil cytoplasmic antibodies (ANCA), extractable nuclear antigens (ENA), antiphospholipid antibodies, and also HLA-B27 is discussed. Arthrocentesis is a technique specific to rheumatology, and neurophysiology is useful in distinguishing neurological versus inflammatory muscle disease, in addition to nerve entrapment syndromes and neuropathies. The chapter also introduces the use of diagnostic imaging and early identification of inflammatory arthritis, including X-ray, ultrasound, magnetic resonance imaging (MRI), positron emission tomography-computed tomography (PET-CT), nuclear medicine bone scintigraphy, and dual-energy X-ray absorptiometry (DXA).
Conference papers on the topic "Nuclear DNA. eng"
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Osawa, Naoki, Yoshinobu Yamamoto, and Tomoaki Kunugi. "Investigation of MHD RANS Modeling Base on DNS Database Under the Advanced Blanket Design Conditions Utilized Molten Salt." In 2014 22nd International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/icone22-30653.
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In this study, validations of Reynolds Averaged Navier-Stokes Simulation (RANS) based on Kenjeres & Hanjalic MHD turbulence model (Int. J. Heat & Fluid Flow, 21, 2000) coupled with the low-Reynolds number k-epsilon model have been conducted with the usage of Direct Numerical Simulation (DNS) database. DNS database of turbulent channel flow imposed wall-normal magnetic field on, are established in condition of bulk Reynolds number 40000, Hartmann number 24, and Prandtl number 5. As the results, the Nagano & Shimada model (Trans. JSME series B. 59, 1993) coupled with Kenjeres & Hanjalic MHD turbulence model has the better availability compared with Myong & Kasagi model (Int. Fluid Eng, 109, 1990) in estimation of the heat transfer degradation in MHD turbulent heat transfer.
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Osawa, Naoki, Yoshinobu Yamamoto, and Tomoaki Kunugi. "Investigation of MHD RANS Modeling Base on DNS Database Under the Advanced Blanket Design Conditions Utilized Molten Salt." In 2014 22nd International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/icone22-30712.
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In this study, validations of Reynolds Averaged Navier-Stokes Simulation (RANS) based on Kenjeres & Hanjalic MHD turbulence model (Int. J. Heat & Fluid Flow, 21, 2000) coupled with the low-Reynolds number k-epsilon model have been conducted with the usage of Direct Numerical Simulation (DNS) database. DNS database of turbulent channel flow imposed wall-normal magnetic field on, are established in condition of bulk Reynolds number 40000, Hartmann number 24, and Prandtl number 5. As the results, the Nagano & Shimada model (Trans. JSME series B. 59, 1993) coupled with Kenjeres & Hanjalic MHD turbulence model has the better availability compared with Myong & Kasagi model (Int. Fluid Eng, 109, 1990) in estimation of the heat transfer degradation in MHD turbulent heat transfer.
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Shin, C. H., T. H. Chun, D. S. Oh, and W. K. In. "Evaluation of Entrance Blockage of Inner Channel in Dual-Cooled Annular Nuclear Fuel." In ASME-JSME-KSME 2011 Joint Fluids Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/ajk2011-18006.
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The Korea Atomic Energy Research Institute (KAERI) has been developing a dual-cooled annular fuel for the power uprate of 20% in an optimized pressurized water reactor (PWR) in Korea, OPR1000. The dual-cooled annular fuel is configured to allow the coolant flow through the inner channel as well as the outer channel. Several thermal-hydraulic issues exist for the application of the dual-cooled annular fuel to OPR1000. One of the key issues is the hypothetical event of inner channel blockage because the inner channel is an isolated flow channel without the coolant mixing between the neighboring flow channels. The inner channel blockage could cause the Departure from Nucleate Boiling (DNB) in the inner channel that eventually results in a fuel failure. A long lower end cap for the annular fuel was invented to provide flow holes by perforating the side surface of the end cap body. The side holes in the lower end cap are expected to supply a minimum coolant in the inner channel in order to prevent the DNB occurrence in the event of partial or even complete blockage of the inner channel entrance. But due to very unusual shape of the lower end cap, it is difficult to estimate the flow resistance of the side flow holes using empirical equations available in the open literatures. Experimental and computational fluid dynamics (CFD) study were performed to investigate the bypass flow through the side holes of the end cap in the case of complete entrance blockage of the inner channel. The form loss coefficient in the side holes was also estimated by using the pressure drop along the bypass flow path.
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Standen, G., P. Moodie, H. Pannekoek, C. L. Verweij, and I. R. Peake. "ANALYSIS OF THE VON WILLEBRAND FACTOR (vWF) GENE IN 6 PATIENTS WITH SEVERE TYPE III VON WILLEBRANDS DISEASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644641.
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DNA from 6 unrelated patients with severe type III von Willebrands disease (vWF antigen < 0.01u/dl) was studied with a cDNA probe for the 3' end of the vWF gene. DNA was extracted from peripheral blood leucocytes using standard techniques and was digested with a range of restriction enzymes. DNA fragments were separated by electrophoresis in 0.7% agarose and were southern blotted onto hybond-N (Amersham). The probe used was pvWF1100, a 1.1kb PstI fragment derived from the 2.28kb vWFcDNA insert of pvWF2280 isolated from a human endothelial cell cDNA expression library (Verweij et al, Nucleic Acids Res 13 (1985) 4699-4717). The probe corresponds to nucleotides 7083 to 8191 of the vWF cDNA (first nucleotide of initiator methionine as 1).When digested with Bglll and probed with pvWF11000, normal DNA showed two invariant bands (13 and 4.9kb) and polymorphic bands of 9 and/or 7.4kb. This pattern was also seen in 5 of the 6 severe vWD patients DNA suggesting that in this 3' area of the gene they had no major deletions or rearrangements. In the 6th case however the band of 4.9kb was not seen and did not appear to be replaced by any novel fragments, suggesting a partial deletion including some of the 3' end of the gene. This patient had the clinically severest form of the condition in that the patient had developed, some 10 years ago, an antibody (inhibitor) to vWF as detected by the ability of the patients plasma to inhibit restocetin cofactor activity in normal plasma. His parents were related (his mother was his father's second cousin) and had levels of vWFAg, considerably lower than those of factor VIII activity. This situation has been previously reported in carriers of recessive severe vWD. vWD was also present in a second family member, but in a less severe form (vWFAg 3u/dl). This patient and all other members of the family have, to date, given normal restriction fragment patterns with the vWF probe and several enzymes, including BgIII.
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Yeo, Woon-Hong, Jae-Hyun Chung, and Kyong-Hoon Lee. "Tuberculosis Diagnostics Using a Nanotip Sensor." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13065.
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Tuberculosis (TB) is one of the most widely spread diseases. In 2006, 9.2 million new TB cases were reported with 1.7 million victims [1]. To diagnose TB, Mycobacterium tuberculosis (MTB) is identified in clinical samples. The challenge of TB diagnostics is high-performance screening conducted by nontrained personnel. Currently, nucleic acid testing with target-amplification strategy such as polymerase chain reaction (PCR) is available for detection of TB. However, this entails cumbersome procedures run by skilled operators with expensive instrumentation and reagents. To overcome these challenges, this paper presents a nanotip sensor to diagnose TB rapidly without target-amplification. The proposed methodology uses a nanostructured tip as a biosensor to detect target analytes. The novelty of this approach is in the superior concentration and detection mechanisms of nucleic acids on the terminal end of a nanotip using an alternating current (AC) electric field, specific chemical binding, and capillary action. Confirmatory identification of MTB is achieved by detecting MTB strains on a nanostructured tip through DNA hybridization. In this paper, the working principle is presented with the demonstration of amplification-free detection of MTB genomic DNA using the nanotip sensor. The performance of the tip sensor is characterized.
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Bosma, P. J., E. A. van den Berg, and T. Kooistra. "ISOLATION OF THE GENE CODING FOR HUMAN PLASMINOGEN ACTIVATOR INHIBITOR TYPE 1 (PAI-1)." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644440.
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A human placenta genomic DNA cosmid library was screened for the presence of the PAI-1 gene using a cDNA probe coding for PAI-1. Two overlapping recombinant cosmids were obtained that contain human DNA spanning 55 kb. The cosmids were mapped using 3' and 5' end probes isolated from an almost full-length cDNA clone of 2.5 kb. The two cosmids were found to contain the entire structural PAI-1 gene (approximately 15 kb) and also included 25 kb 5' flanking sequences. The transcription initiation site was identified by SI nuclease protection experiments and the promotor region was sequenced. Further experiments will be directed at characterizing the regulatory elements of the PAI-1 gene.In order to determine the chromosomal localization of the PAI-1 gene we have hybridized our genomic clones in situ to metaphase chromosomes of a human blood cell culture. Preliminary experiments show a specific hybridization signal which will enable us to sublocalize the chromosomal position of the PAI-1 gene.
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Jamet, Didier. "Fundamental Issues Related to the Numerical Simulation of Two-Phase Flows With Phase-Change." In ASME 2006 2nd Joint U.S.-European Fluids Engineering Summer Meeting Collocated With the 14th International Conference on Nuclear Engineering. ASMEDC, 2006. http://dx.doi.org/10.1115/fedsm2006-98376.
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In direct numerical simulation (DNS) of two-phase flows, all the interfaces of the two-phase system are tracked individually. If this technique is computationally expensive, it is also very powerful, especially to study basic phenomena. In particular, it helped to better understand fundamental issues such as the forces acting on a single bubble (e.g. [1]) or the interaction of a couple of bubbles in a bubbly flow (e.g. [2,3]) and it now begins to be used to assess average models in detail ([4]). Currently, most of the basic phenomena studied involve non-miscible fluids, where no mass transfer between the phases occurs (air and water for instance). However, in many applications of industrial interest, phase-change phenomena are very important because high heat flux can be achieved with moderate temperature gradients (since the energy exchange through latent heat occurs at a constant temperature). It is thus widely used in the energy industry (nuclear energy in particular) and it is used to design compact heat exchangers (e.g. heat pipes for space or electronic devices). Moreover, basic phenomena related to phase-change are, to a large extent, still misunderstood, which make phase-change phenomena of fundamental interest as well. For instance, despite several decades of valuable scientific studies, the boiling crisis, which is an instability of the nucleate boiling regime, is still misunderstood from a fundamental point of view. It is one of the very few fundamental issues that are still open in fluid mechanics. Since DNS has already been successful to study fundamental issues in two-phase flows of non-miscible fluids, it should be successful to study these issues as well. However, the DNS of two-phase flows with phase-change is more difficult than that of two-phase flows involving non-miscible phases. These issues are both numerical and physical and some of them are discussed in this paper.
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Kraus, Adam, Elia Merzari, Thomas Norddine, Oana Marin, and Sofiane Benhamadouche. "Direct Numerical Simulation of Fluid Flow in a 5x5 Square Rod Bundle Using Nek5000." In 2020 International Conference on Nuclear Engineering collocated with the ASME 2020 Power Conference. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/icone2020-16643.
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Abstract Rod bundle flows are commonplace in nuclear engineering, and are present in light water reactors (LWRs) as well as other more advanced concepts. Inhomogeneities in the bundle cross section can lead to complex flow phenomena, including varying local conditions of turbulence. Despite the decades of numerical and experimental investigations regarding this topic, and the importance of elucidating the physics of the flow field, to date there are few publicly available direct numerical simulations (DNS) of the flow in multiple-pin rod bundles. Thus a multiple-pin DNS study can provide significant value toward reaching a deeper understanding of the flow physics, as well as a reference simulation for development of various reduced-resolution analysis techniques. To this end, DNS of the flow in a square 5 × 5 rod bundle at Reynolds number of 19,000 has been performed using the highly-parallel spectral element code Nek5000. The geometrical dimensions were representative of typical LWR fuel designs. The DNS was designed using microscales estimated from an advanced Reynolds-Averaged Navier-Stokes (RANS) model. Characteristics of the velocity field, Reynolds stresses, and anisotropy are presented in detail for various regions of the bundle. The turbulent kinetic energy budget is also presented and discussed.
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Linn, Paul A., Harold V. Julian, James R. Chapman, Alexander Trifanov, Oleg Zhabin, Sergey Fedorchenko, and Alexander Rybchuk. "Applying U.S. EOP Analytical Justification Experience for VVER Plants in the Ukraine." In 10th International Conference on Nuclear Engineering. ASMEDC, 2002. http://dx.doi.org/10.1115/icone10-22640.
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The foundation for new Emergency Operating Instructions (EOIs) being developed at several plants in the Ukraine is the Westinghouse Owners Group (WOG) Emergency Response Guidelines (ERGs) developed in the U.S. The ERGs were chosen as a base for the new EOIs for several reasons. First the overall structure and format was adaptable to VVER Pressurized Water Reactor (PWR) designs. Second, the ERGs have served as a base for many plant EOIs in both the U.S. and internationally. Third, key information supporting the ERGs was available. This paper describes the method used at one of the Ukrainian plants to provide an analytical justification for their EOIs. The method being employed by a second plant is very similar, differing only slightly in how it is implemented. The WOG ERG development program, which started shortly after the accident at Three Mile Island Unit 2, used many sources of technical information on plant and system transient response, which were available in support of the plant design and licensing efforts. In addition, operating experience from many operating PWR plants in the U.S. and around the world was used. For example, design basis accident (DBA) analyses, documented in a plant’s Safety Analysis Report (SAR) and other design documents, had been performed by Nuclear Steam Supply System (NSSS) vendors, utilities, or the Architect/Engineer. All relevant sources were considered in the development of the ERGs. Limited Probabilistic Risk Assessment (PRA) analyses were available during that time period. When a technical basis for a recovery strategy and associated operator actions was not available, an analysis was defined and performed. In general, these analyses were performed on a generic basis, and addressed the different categories of design (e.g., number of reactor coolant loops and/or low/high pressure safety injection system design). U.S. Nuclear Power plants that were in the WOG program were responsible for implementing the generic ERGs. This required the utilities to review the generic analyses to ensure that they were applicable and to justify any deviations from the ERG methodology. Modern PRA analyses are similar to the analyses supporting the ERGs since they address multiple failures and assume better estimate or expected assumptions for equipment availability and operator performance. The process being employed by Ukrainian plants is similar to the WOG. That is, available analyses and operating experience are being reviewed and pertinent information extracted to assist in the analytical justification of the EOIs. This includes the use of recently updated PRA and DBA analyses, other “original” design information and operating experience. A systematic review of the EOIs is being conducted to identify items requiring analytical justification. For each analysis identified, the specific purpose of the analysis is being documented. The analysis needs are then compared to the available analyses and operating experience. From this review, new analyses needed to justify the EOIs are developed, and a basis for using existing analyses is established. The work is being conducted in two phases. The first phase performs all of the reviews and assessments necessary to determine the new analyses required to justify the EOIs. In the second phase, these new analyses will be conducted and documented, and the EOI Analytical Justification (AJ) report will be written.
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Ito, Tatsuo, Shigehisa Kitano, Hediye Erdjument-Bromage, and Marc Ladanyi. "Abstract 437: Novel function of the BAP1 nuclear deubiquitinase in the non-homologous end joining (NHEJ) pathway of double strand DNA repair." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-437.
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