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Sample records for 4n dna content

  1. Repairing DNA damage in xeroderma pigmentosum: T4N5 lotion and gene therapy.

    PubMed

    Zahid, Sarwar; Brownell, Isaac

    2008-04-01

    Patients with xeroderma pigmentosum (XP) have defective DNA repair and are at a high risk for cutaneous malignancies. Standard treatments for XP are limited in scope and effectiveness. Understanding the molecular etiology of XP has led to the development of novel therapeutic approaches, including enzyme and gene therapies. One new topical treatment utilizing bacteriophage T4 endonuclease 5 (T4N5) in a liposomal lotion is currently in clinical trials and has received a Fast Track designation from the FDA. Gene therapy for XP, while making leaps in preclinical studies, has been slower to develop due to tactical hurdles, but seems to have much potential for future treatment. If these treatments prove effective in lowering the risk of cancer in patients with XP, they may also be found useful in reducing skin cancers in other at-risk patient populations.

  2. [Contents of nutrient elements in NH4(+)-N fertilizer and urea].

    PubMed

    Wang, Zheng-Rui; Qu, Gui-Qin; Rui, Yu-Kui; Shen, Jian-Bo; Zhang, Fu-Suo

    2009-03-01

    Fertilizer contains not only one compound or one element, so it is important to determine the contents of other elements necessitous and beneficial to plant. All the other nutrient elements for plant, including necessitous elements and beneficial elements in ammonia nitrogen fertilizer ((NH4)2SO4) and CO(NH2)2, were analyzed by method of ICP-MS. The results showed that ammonia nitrogen fertilizer ((NH4)2SO4) and CO(NH2)2 both contain many necessitous elements, Mg, P, K, Ca, Mn, Fe, Ni, Cu, Zn and Mo, thereinto the contents of Mg, P, K, Ca, Mn and Fe were on microg x g(-1) the level, and Ni, Cu, Zn and Mo were on the ng x g(-1) level; compared with CO(NH2)2, ammonia nitrogen fertilizer ((NH4)2SO4) contains more necessitous elements and beneficial elements except Mo and Si. All the above elements could influence the results of nitrogen fertilizer efficiency experiments, so pure fertilizer should be used in the future nitrogen fertilizer efficiency experiments and the comparative experiments of different form nitrogen fertilizer.

  3. DNA replication checkpoint signaling depends on a Rad53-Dbf4 N-terminal interaction in Saccharomyces cerevisiae.

    PubMed

    Chen, Ying-Chou; Kenworthy, Jessica; Gabrielse, Carrie; Hänni, Christine; Zegerman, Philip; Weinreich, Michael

    2013-06-01

    Dbf4-dependent kinase (DDK) and cyclin-dependent kinase (CDK) are essential to initiate DNA replication at individual origins. During replication stress, the S-phase checkpoint inhibits the DDK- and CDK-dependent activation of late replication origins. Rad53 kinase is a central effector of the replication checkpoint and both binds to and phosphorylates Dbf4 to prevent late-origin firing. The molecular basis for the Rad53-Dbf4 physical interaction is not clear but occurs through the Dbf4 N terminus. Here we found that both Rad53 FHA1 and FHA2 domains, which specifically recognize phospho-threonine (pT), interacted with Dbf4 through an N-terminal sequence and an adjacent BRCT domain. Purified Rad53 FHA1 domain (but not FHA2) bound to a pT Dbf4 peptide in vitro, suggesting a possible phospho-threonine-dependent interaction between FHA1 and Dbf4. The Dbf4-Rad53 interaction is governed by multiple contacts that are separable from the Cdc5- and Msa1-binding sites in the Dbf4 N terminus. Importantly, abrogation of the Rad53-Dbf4 physical interaction blocked Dbf4 phosphorylation and allowed late-origin firing during replication checkpoint activation. This indicated that Rad53 must stably bind to Dbf4 to regulate its activity.

  4. Influence of terminal substitution on structural, DNA, protein binding, anticancer and antibacterial activities of palladium(II) complexes containing 3-methoxy salicylaldehyde-4(N) substituted thiosemicarbazones.

    PubMed

    Kalaivani, P; Prabhakaran, R; Ramachandran, E; Dallemer, F; Paramaguru, G; Renganathan, R; Poornima, P; Vijaya Padma, V; Natarajan, K

    2012-02-28

    The variable chelating behavior of 3-methoxysalicylaldehyde-4(N)-substituted thiosemicarbazones was observed in equimolar reactions with [PdCl(2)(PPh(3))(2)]. The new complexes were characterized by various analytical, spectroscopic techniques (mass, (1)H-NMR, absorption, IR). All the new complexes were structurally characterized by single crystal X-ray diffraction. Crystallographic results showed that the ligands H(2)L(1) and H(2)L(4) are coordinated as binegative tridentate ONS donor ligands in the complexes 1 and 4 by forming six and five member rings. However, the ligands H(2)L(2) and H(2)L(3) bound to palladium in 2 and 3 as uninegative bidentate NS donors by forming a five member chelate ring. From this study, it was found that the substitution on terminal 4(N)-nitrogen may have an influence on the chelating ability of thiosemicarbazone. The presence of hydrogen bonding in 2 and 3 might be responsible for preventing the coordination of phenolic oxygen to the metal ion. The interaction of the complexes with calf-thymus DNA (CT-DNA) has been explored by absorption and emission titration methods. Based on the observations, an electrostatic binding mode of DNA has been proposed. The protein binding studies were monitored by quenching of tryptophan and tyrosine residues in the presence of complexes using Lysozyme as model protein. Antibacterial activity studies of the complexes have been screened against pathogenic bacteria such as Enterococcus faecalis, Staphylococcus aureus, Escherichia coli, Klebsiella pneumonia and Pseudomonas aeruginosa. MIC50 values of the complexes showed that they exhibited significant activity against the pathogens and among them, 3 exhibited higher activity. Further, anticancer activity of the complexes on the lung cancer cell line A549 has also been studied. PMID:22222360

  5. Content and persistence of extracellular DNA in native soils

    NASA Astrophysics Data System (ADS)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Anderson, Traute-Heidi; Kuzyakov, Yakov

    2014-05-01

    The long-term persistence of soil extracellular DNA is questionable because of high potential activity of nucleases produced by soil microorganisms. By the other hand, the relative persistence of DNA-like biopolymers could be due to their adsorption on clay minerals and humus substances in soil. High-specific and ultra sensitive reagent PicoGreenTM (Molecular Probes) permits the quantitative assessment of microbial dsDNA in diluted soil extracts giving a good tool for tracing the DNA fate in soil. Our goal was to determine intracellular and extracellular DNA content in cambisol (loamy sand) and in chernozem (silty loam) soils and to investigate the possible adsorption and degradation of extracellular DNA in soil. Optimized procedure of mechanical and enzymatic destruction of cell walls was used for direct extraction of microbial DNA with Tris-EDTA buffer (Blagodatskaya et al., 2003). Extracellular dsDNA was determined in distilled water and in Tris-EDTA extracts without enzymatic or mechanical treatments. DNA content was determined after addition of PicoGreen to diluted soil extracts. Degradation of extracellular DNA was traced during 24 h incubation of 2 µg lambda-phage DNA in soil. Possible DNA adsorption to soil matrix was determined by recovery of lambda -phage DNA added to autoclaved soil. Extracellular dsDNA was absent in water extracts of both soils. The content of extracellular dsDNA extracted by Tris-EDTA buffer was 0.46 µg/g in chernozem and 1.59 µg/g in cambisol amounting 0.43 and 2.8% of total dsDNA content in these soils, respectively. 100% and 64.8% of added extracellular lambda -phage dsDNA was found in cambisol and chernozem soils, respectively, in 5 h after application. 39% and 73.5% of added DNA disappeared in cambisol and in chernozem, respectively, during 24 h incubation. Degradation rate of extracellular DNA depended on microbial biomass content, which was 2.5 times higher in chernozem as compared to cambisol. Maximum adsorption of DNA by

  6. Mitochondrial DNA content increase in response to cigarette smoking.

    PubMed

    Masayesva, Brett G; Mambo, Elizabeth; Taylor, Rodney J; Goloubeva, Olga G; Zhou, Shaoyu; Cohen, Yoram; Minhas, Khalid; Koch, Wayne; Sciubba, James; Alberg, Anthony J; Sidransky, David; Califano, Joseph

    2006-01-01

    An increase in mitochondrial DNA (mtDNA) content and decline in mitochondrial function occurs with aging and in response to DNA-damaging agents, including tobacco smoke. We did a cross-sectional study and quantified changes in mtDNA content in a population of individuals with varied smoking and alcohol exposure. Age, smoking history, ethanol intake, and other demographic data were characterized for 604 individuals participating in a screening study for smoking-related upper aerodigestive malignancy. Total DNA was extracted from exfoliated cells in saliva. DNA from a nuclear gene, beta-actin, and two mitochondrial genes, cytochrome c oxidase I and II (Cox I and Cox II), were quantified by real-time PCR. mtDNA content was correlated with age, exposure history, and other variables using multivariate regression analyses. A significant increase (P<0.001) in mtDNA content was noted in smokers (31% and 29% increase for Cox I and Cox II, respectively) and former smokers (31% and 34%) when compared with never smokers. This association persisted after adjustment for other significant factors including age, alcohol drinking, and income (P<0.001). Increased mtDNA content was positively associated with pack-years of smoking (P=0.02). Despite an average smoking cessation interval of 21 years in former smokers, tobacco cessation interval was not statistically significantly associated with mtDNA content. Smoking is associated with increased mtDNA content in a dose-dependent fashion. Mitochondrial DNA alterations in response to smoking persist for several decades after smoking cessation, consistent with long-term, smoking-related damage.

  7. Measuring DNA content by flow cytometry in fission yeast.

    PubMed

    Sabatinos, Sarah A; Forsburg, Susan L

    2015-01-01

    Flow cytometry is an essential tool to monitor DNA content and determine cell cycle distribution. Its utility in fission yeast reflects the ease of sample preparation, the stochiometric binding of the most popular DNA dyes (propidium iodide and Sytox Green), and ability to monitor cell size. However, the study of DNA replication with multicolour flow analysis has lagged behind its use in mammalian cells. We present basic and advanced protocols for analysis of DNA replication in fission yeast by flow cytometry including whole cell, nuclear "ghosts," two-color imaging with BrdU, and estimates of DNA synthesis using EdU.

  8. DNA content of a functioning chicken kinetochore.

    PubMed

    Ribeiro, Susana Abreu; Vagnarelli, Paola; Earnshaw, William C

    2014-04-01

    In order to understand the three-dimensional structure of the functional kinetochore in vertebrates, we require a complete list and stoichiometry for the protein components of the kinetochore, which can be provided by genetic and proteomic experiments. We also need to know how the chromatin-containing CENP-A, which makes up the structural foundation for the kinetochore, is folded, and how much of that DNA is involved in assembling the kinetochore. In this MS, we demonstrate that functioning metaphase kinetochores in chicken DT40 cells contain roughly 50 kb of DNA, an amount that corresponds extremely closely to the length of chromosomal DNA associated with CENP-A in ChIP-seq experiments. Thus, during kinetochore assembly, CENP-A chromatin is compacted into the inner kinetochore plate without including significant amounts of flanking pericentromeric heterochromatin. PMID:24633498

  9. Radiation-induced DNA content variability in mouse sperm

    SciTech Connect

    Pinkel, D.; Gledhill, B.L.; van Dilla, M.A.; Lake, S.; Wyrobek, A.J.

    1983-09-01

    Mouse sperm collected from the cauda epididymidis 35 days after acute testicular x-ray exposure and fluorescently stained for DNA show dose-dependent increases in the coefficient of variation (CV) of flow cytometrically obtained fluorescence distributions. By comparing dose-response curves obtained with three protocols which overcome the optical and cytochemical difficulties of sperm measurement in different ways we conclude the response is due to x-ray-induced DNA content variability. Computer modeling of the shapes of the fluorescence distributions show that at 600 rad 30 to 40% of the sperm have abnormal DNA content. Some have errors as large as two whole chromosomes, but it is not clear whether they are due to whole chromosome nondisjunction or a finer fragmentation of the genome. Exposures to benzo(a)pyrene and mitomycin C cause no detectable DNA content variability. We conclude mouse sperm DNA content measurements are not sensitive to small amounts of aneuploidy and as such will only be useful in detecting agents that produce substantial DNA content variability. Another animal with a smaller number of chromosomes might be more favorable. These sperm measurement techniques may find additional application in other areas of reproductive biology, such as the determination of the relative numbers of X and Y chromosome-bearing sperm in semen that may be artifically enriched in one population.

  10. DNA analysis of digested tomato seeds in stomach contents.

    PubMed

    Lee, Cheng-Lung; Coyle, Heather Miller; Carita, Eric; Ladd, Carll; Yang, Nicholas C S; Palmbach, Timothy M; Hsu, Ian C; Lee, Henry C

    2006-06-01

    Examination of stomach contents is one of the important steps in medical legal autopsy. Vegetative materials such as stems, roots, and seeds in stomach contents can be valuable evidence for providing investigative leads in death investigation. Currently, the identification of plant materials relies on microscopic and morphologic examination. We have found that many seeds are often protected from acid degradation during stomach digestion by their tough exterior seed coat. Tomato seeds were selected as a model system to assess DNA analysis and plant variety marker identification. The DNA-amplified fragment length polymorphism method was performed to determine if the DNA obtained from single seeds could be used for PCR analysis. From the amplified fragment length polymorphism results, some candidate markers for individualizing seeds from morphologically distinct tomatoes were identified. These data on DNA analysis of tomato seeds indicate amplified fragment length polymorphism is a viable procedure for the individualization of seeds from stomach contents in forensic investigations.

  11. Estimates of nuclear DNA content in red algal lineages

    PubMed Central

    Kapraun, Donald F.; Freshwater, D. Wilson

    2012-01-01

    Background and aims The red algae are an evolutionarily ancient group of predominantly marine organisms with an estimated 6000 species. Consensus higher-level molecular phylogenies support a basal split between the unicellular Cyanidiophytina and morphologically diverse Rhodophytina, the later subphylum containing most red algal species. The Rhodophytina is divided into six classes, of which five represent early diverging lineages of generally uninucleate species, whose evolutionary relationships are poorly resolved. The remaining species compose the large (27 currently recognized orders), morphologically diverse and typically multinucleate Florideophyceae. Nuclear DNA content estimates have been published for <1 % of the described red algae. The present investigation summarizes the state of our knowledge and expands our coverage of DNA content information from 196 isolates of red algae. Methodology The DNA-localizing fluorochrome DAPI (4′,6-diamidino-2-phenylindole) and RBC (chicken erythrocytes) standards were used to estimate 2C values with static microspectrophotometry. Principal results Nuclear DNA contents are reported for 196 isolates of red algae, almost doubling the number of estimates available for these organisms. Present results also confirm the reported DNA content range of 0.1–2.8 pg, with species of Ceramiales, Nemaliales and Palmariales containing apparently polyploid genomes with 2C = 2.8, 2.3 and 2.8 pg, respectively. Conclusions Early diverging red algal lineages are characterized by relatively small 2C DNA contents while a wide range of 2C values is found within the derived Florideophyceae. An overall correlation between phylogenetic placement and 2C DNA content is not apparent; however, genome size data are available for only a small portion of red algae. Current data do support polyploidy and aneuploidy as pervasive features of red algal genome evolution. PMID:22479676

  12. Radiation-induced DNA content variability in mouse sperm

    SciTech Connect

    Pinkel, D.; Gledhill, B.L.; Van Dilla, M.A.; Lake, S.; Wyrobek, A.J.

    1983-09-01

    Mouse sperm collected from the cauda epididymidis 35 days after acute testicular X-ray exposure and fluorescently stained for DNA show dose-dependent increases in the coefficient of variation (CV) of flow cytometrically obtained fluorescence distributions. By comparing dose-response curves obtained with three protocols which overcome the optical and cytochemical difficulties of sperm measurement in different ways we conclude the response is due to X-ray-induced DNA content variability. In the range between 0 and 600 rad the dose dependence of the square of CV of the DNA content variability, delta CV2D, is described by delta CV2D . Bx + Cx2, with 0 less than or equal to B less than or equal to 0.23 X 10(-2) and C . (0.44 +/- 0.06) X 10(-4). The dose x is measured in rad and delta CVD is expressed in percent. Computer modeling of the shapes of the fluorescence distributions show that at 600 rad 30 to 40% of the sperm have abnormal DNA content. Some have errors as large as two whole chromosomes, but it is not clear whether they are due to whole chromosome nondisjunction or a finer fragmentation of the genome. Exposures to benzo(a)pyrene and mitomycin C cause no detectable DNA content variability. We conclude mouse sperm DNA content measurements are not sensitive to small amounts of aneuploidy and as such will only be useful in detecting agents that produce substantial DNA content variability. Another animal with a smaller number of chromosomes might be more favorable. These sperm measurement techniques may find additional application in other areas of reproductive biology, such as the determination of the relative numbers of X and Y chromosome-bearing sperm in semen that may be artificially enriched in one population.

  13. Nuclear DNA Content Variation among Central European Koeleria Taxa

    PubMed Central

    PECINKA, ALES; SUCHÁNKOVÁ, PAVLA; LYSAK, MARTIN A.; TRÁVNÍČEK, BOHUMIL; DOLEŽEL, JAROSLAV

    2006-01-01

    • Background and Aims Polyploidization plays an important role in the evolution of many plant genera, including Koeleria. The knowledge of ploidy, chromosome number and genome size may enable correct taxonomic treatment when other features are insufficient as in Koeleria. Therefore, these characteristics and their variability were determined for populations of six central European Koeleria taxa. • Methods Chromosome number analysis was performed by squashing root meristems, and ploidy and 2C nuclear DNA content were estimated by flow cytometry. • Key Results Three diploids (K. glauca, K. macrantha var. macrantha and var. pseudoglauca), one tetraploid (K. macrantha var. majoriflora), one decaploid (K. pyramidata) and one dodecaploid (K. tristis) were found. The 2C nuclear DNA content of the diploids ranged from 4·85 to 5·20 pg. The 2C DNA contents of tetraploid, decaploid and dodecaploid taxa were 9·31 pg, 22·89 pg and 29·23 pg, respectively. The DNA content of polyploids within the K. macrantha aggregate (i.e. within K. macrantha and K. pyramidata) was smaller than the expected multiple of the diploid genome (K. macrantha var. macrantha). Geography-correlated variation of DNA content was found for some taxa. Czech populations of K. macrantha var. majoriflora had a 5·06 % smaller genome than the Slovak ones. An isolated eastern Slovakian population of K. tristis revealed 8·04 % less DNA than populations from central Slovakia. In central and north-west Bohemia, diploid and tetraploid cytotypes of K. macrantha were sympatric; east from this region diploid populations, and towards the west tetraploid populations were dominant. • Conclusions Remarkable intra-specific inter-population differences in nuclear DNA content were found between Bohemian and Pannonian populations of Koeleria macrantha var. majoriflora and between geographically isolated central and eastern Slovakian populations of K. tristis. These differences occur over a relatively small

  14. Blood Cell Mitochondrial DNA Content and Premature Ovarian Aging

    PubMed Central

    Cacciatore, Chiara; Busnelli, Marta; Rossetti, Raffaella; Bonetti, Silvia; Paffoni, Alessio; Mari, Daniela; Ragni, Guido; Persani, Luca; Arosio, M.; Beck-Peccoz, P.; Biondi, M.; Bione, S.; Bruni, V.; Brigante, C.; Cannavo`, S.; Cavallo, L.; Cisternino, M.; Colombo, I.; Corbetta, S.; Crosignani, P.G.; D'Avanzo, M.G.; Dalpra, L.; Danesino, C.; Di Battista, E.; Di Prospero, F.; Donti, E.; Einaudi, S.; Falorni, A.; Foresta, C.; Fusi, F.; Garofalo, N.; Giotti, I.; Lanzi, R.; Larizza, D.; Locatelli, N.; Loli, P.; Madaschi, S.; Maghnie, M.; Maiore, S.; Mantero, F.; Marozzi, A.; Marzotti, S.; Migone, N.; Nappi, R.; Palli, D.; Patricelli, M.G.; Pisani, C.; Prontera, P.; Petraglia, F.; Radetti, G.; Renieri, A.; Ricca, I.; Ripamonti, A.; Rossetti, R.; Russo, G.; Russo, S.; Tonacchera, M.; Toniolo, D.; Torricelli, F.; Vegetti, W.; Villa, N.; Vineis, P.; Wasniewsk, M.; Zuffardi, O.

    2012-01-01

    Primary ovarian insufficiency (POI) is a critical fertility defect characterized by an anticipated and silent impairment of the follicular reserve, but its pathogenesis is largely unexplained. The frequent maternal inheritance of POI together with a remarkable dependence of ovarian folliculogenesis upon mitochondrial biogenesis and bioenergetics suggested the possible involvement of a generalized mitochondrial defect. Here, we verified the existence of a significant correlation between blood and ovarian mitochondrial DNA (mtDNA) content in a group of women undergoing ovarian hyperstimulation (OH), and then aimed to verify whether mtDNA content was significantly altered in the blood cells of POI women. We recruited 101 women with an impaired ovarian reserve: 59 women with premature ovarian failure (POF) and 42 poor responders (PR) to OH. A Taqman copy number assay revealed a significant mtDNA depletion (P<0.001) in both POF and PR women in comparison with 43 women of similar age and intact ovarian reserve, or 53 very old women with a previous physiological menopause. No pathogenic variations in the mitochondrial DNA polymerase γ (POLG) gene were detected in 57 POF or PR women with low blood mtDNA content. In conclusion, blood cell mtDNA depletion is a frequent finding among women with premature ovarian aging, suggesting that a still undetermined but generalized mitochondrial defect may frequently predispose to POI which could then be considered a form of anticipated aging in which the ovarian defect may represent the first manifestation. The determination of mtDNA content in blood may become an useful tool for the POI risk prediction. PMID:22879975

  15. Blood cell mitochondrial DNA content and premature ovarian aging.

    PubMed

    Bonomi, Marco; Somigliana, Edgardo; Cacciatore, Chiara; Busnelli, Marta; Rossetti, Raffaella; Bonetti, Silvia; Paffoni, Alessio; Mari, Daniela; Ragni, Guido; Persani, Luca

    2012-01-01

    Primary ovarian insufficiency (POI) is a critical fertility defect characterized by an anticipated and silent impairment of the follicular reserve, but its pathogenesis is largely unexplained. The frequent maternal inheritance of POI together with a remarkable dependence of ovarian folliculogenesis upon mitochondrial biogenesis and bioenergetics suggested the possible involvement of a generalized mitochondrial defect. Here, we verified the existence of a significant correlation between blood and ovarian mitochondrial DNA (mtDNA) content in a group of women undergoing ovarian hyperstimulation (OH), and then aimed to verify whether mtDNA content was significantly altered in the blood cells of POI women. We recruited 101 women with an impaired ovarian reserve: 59 women with premature ovarian failure (POF) and 42 poor responders (PR) to OH. A Taqman copy number assay revealed a significant mtDNA depletion (P<0.001) in both POF and PR women in comparison with 43 women of similar age and intact ovarian reserve, or 53 very old women with a previous physiological menopause. No pathogenic variations in the mitochondrial DNA polymerase γ (POLG) gene were detected in 57 POF or PR women with low blood mtDNA content. In conclusion, blood cell mtDNA depletion is a frequent finding among women with premature ovarian aging, suggesting that a still undetermined but generalized mitochondrial defect may frequently predispose to POI which could then be considered a form of anticipated aging in which the ovarian defect may represent the first manifestation. The determination of mtDNA content in blood may become an useful tool for the POI risk prediction. PMID:22879975

  16. Blood cell mitochondrial DNA content and premature ovarian aging.

    PubMed

    Bonomi, Marco; Somigliana, Edgardo; Cacciatore, Chiara; Busnelli, Marta; Rossetti, Raffaella; Bonetti, Silvia; Paffoni, Alessio; Mari, Daniela; Ragni, Guido; Persani, Luca

    2012-01-01

    Primary ovarian insufficiency (POI) is a critical fertility defect characterized by an anticipated and silent impairment of the follicular reserve, but its pathogenesis is largely unexplained. The frequent maternal inheritance of POI together with a remarkable dependence of ovarian folliculogenesis upon mitochondrial biogenesis and bioenergetics suggested the possible involvement of a generalized mitochondrial defect. Here, we verified the existence of a significant correlation between blood and ovarian mitochondrial DNA (mtDNA) content in a group of women undergoing ovarian hyperstimulation (OH), and then aimed to verify whether mtDNA content was significantly altered in the blood cells of POI women. We recruited 101 women with an impaired ovarian reserve: 59 women with premature ovarian failure (POF) and 42 poor responders (PR) to OH. A Taqman copy number assay revealed a significant mtDNA depletion (P<0.001) in both POF and PR women in comparison with 43 women of similar age and intact ovarian reserve, or 53 very old women with a previous physiological menopause. No pathogenic variations in the mitochondrial DNA polymerase γ (POLG) gene were detected in 57 POF or PR women with low blood mtDNA content. In conclusion, blood cell mtDNA depletion is a frequent finding among women with premature ovarian aging, suggesting that a still undetermined but generalized mitochondrial defect may frequently predispose to POI which could then be considered a form of anticipated aging in which the ovarian defect may represent the first manifestation. The determination of mtDNA content in blood may become an useful tool for the POI risk prediction.

  17. Intra- and interspecific variation in DNA content in Cistus (Cistaceae).

    PubMed

    Ellul, Philippe; Boscaiu, Monica; Vicente, Oscar; Moreno, Vicente; Rosselló, Josep A

    2002-09-01

    Flow cytometry, using propidium iodide and 4',6-diamidano-2-phenylindole staining, was used to estimate the nuclear DNA content (2C) and the proportion of A-T base pairs in 16 species of the Mediterranean genus Cistus. Genome sizes were shown to be constant within species, since no significant intraspecific variation in 2C DNA content was detected. At the genus level, up to about 1.5-fold differences in absolute DNA amounts were observed, ranging from 3.92 pg in C. crispus to 5.88 pg in C. monspeliensis. The (AT) : (GC) ratio was close to 1, and was similar for all species examined, ranging from 47.87% A-T content in C clusii, to 50.67% in C. populifolius. Pink-flowered species (subgenus Cistus) had lower DNA amounts than white-flowered species (subgenera Leucocistus and Halimioides). However, the distribution of DNA amounts in Cistus appeared to be continuous and did not permit a clear separation of infra-generic ranks in the genus. PMID:12234146

  18. Intra‐ and Interspecific Variation in DNA Content in Cistus (Cistaceae)

    PubMed Central

    ELLUL, PHILIPPE; BOSCAIU, MONICA; VICENTE, OSCAR; MORENO, VICENTE; ROSSELLÓ, JOSEP A.

    2002-01-01

    Flow cytometry, using propidium iodide and 4′,6‐diamidano‐2-phenylindole staining, was used to estimate the nuclear DNA content (2C) and the proportion of A–T base pairs in 16 species of the Mediterranean genus Cistus. Genome sizes were shown to be constant within species, since no significant intraspecific variation in 2C DNA content was detected. At the genus level, up to about 1·5‐fold differences in absolute DNA amounts were observed, ranging from 3·92 pg in C. crispus to 5·88 pg in C. monspeliensis. The (AT) : (GC) ratio was close to 1, and was similar for all species examined, ranging from 47·87 % A–T content in C. clusii, to 50·67 % in C. populifolius. Pink‐flowered species (subgenus Cistus) had lower DNA amounts than white‐flowered species (subgenera Leucocistus and Halimioides). However, the distribution of DNA amounts in Cistus appeared to be continuous and did not permit a clear separation of infra‐generic ranks in the genus. PMID:12234146

  19. DNA methylation detection based on difference of base content

    NASA Astrophysics Data System (ADS)

    Sato, Shinobu; Ohtsuka, Keiichi; Honda, Satoshi; Sato, Yusuke; Takenaka, Shigeori

    2016-04-01

    Methylation frequently occurs in cytosines of CpG sites to regulate gene expression. The identification of aberrant methylation of certain genes is important for cancer marker analysis. The aim of this study was to determine the methylation frequency in DNA samples of unknown length and/or concentration. Unmethylated cytosine is known to be converted to thymine following bisulfite treatment and subsequent PCR. For this reason, the AT content in DNA increases with an increasing number of methylation sites. In this study, the fluorescein-carrying bis-acridinyl peptide (FKA) molecule was used for the detection of methylation frequency. FKA contains fluorescein and two acridine moieties, which together allow for the determination of the AT content of double-stranded DNA fragments. Methylated and unmethylated human genomes were subjected to bisulfide treatment and subsequent PCR using primers specific for the CFTR, CDH4, DBC1, and NPY genes. The AT content in the resulting PCR products was estimated by FKA, and AT content estimations were found to be in good agreement with those determined by DNA sequencing. This newly developed method may be useful for determining methylation frequencies of many PCR products by measuring the fluorescence in samples excited at two different wavelengths.

  20. The Nuclear DNA Content and Genetic Diversity of Lampetra morii

    PubMed Central

    Yan, Xinyu; Meng, Wenbin; Wu, Fenfang; Xu, Anlong; Chen, Shangwu; Huang, Shengfeng

    2016-01-01

    We investigated the nuclear DNA content and genetic diversity of a river lamprey, the Korean lamprey Lampetra morii, which is distributed in the northeast of China. L. morii spends its whole life cycle in fresh water, and its adult size is relatively small (~160 mm long) compared with that of other lampreys. The haploid nuclear DNA content of L. morii is 1.618 pg (approximately 1.582 Gb) in germline cells, and there is ~15% germline DNA loss in somatic cells. These values are significantly smaller than those of Petromyzon marinus, a lamprey with a published draft genome. The chromosomes of L. morii are small and acrocentric, with a diploid modal number of 2n = 132, lower than some other lampreys. Sequence and AFLP analyses suggest that the allelic polymorphism rate (~0.14% based on examined nuclear and mitochondrial DNA sequences) of L. morii is much lower than that (~2%) of P. marinus. Phylogenetic analysis based on a mitochondrial DNA fragment confirms that L. morii belongs to the genus Lampetra, which, together with the genus Lethenteron, forms a sister group to P. marinus. These genetic background data are valuable for subsequent genetic and genomic research on L. morii. PMID:27388621

  1. Air-sampled Filter Analysis for Endotoxins and DNA Content.

    PubMed

    Lang-Yona, Naama; Mazar, Yinon; Pardo, Michal; Rudich, Yinon

    2016-01-01

    Outdoor aerosol research commonly uses particulate matter sampled on filters. This procedure enables various characterizations of the collected particles to be performed in parallel. The purpose of the method presented here is to obtain a highly accurate and reliable analysis of the endotoxin and DNA content of bio-aerosols extracted from filters. The extraction of high molecular weight organic molecules, such as lipopolysaccharides, from sampled filters involves shaking the sample in a pyrogen-free water-based medium. The subsequent analysis is based on an enzymatic reaction that can be detected using a turbidimetric measurement. As a result of the high organic content on the sampled filters, the extraction of DNA from the samples is performed using a commercial DNA extraction kit that was originally designed for soils and modified to improve the DNA yield. The detection and quantification of specific microbial species using quantitative polymerase chain reaction (q-PCR) analysis are described and compared with other available methods. PMID:27023725

  2. Nuclear DNA content variation and evolution in liverworts.

    PubMed

    Bainard, Jillian D; Forrest, Laura L; Goffinet, Bernard; Newmaster, Steven G

    2013-09-01

    Across embryophytes there is a significant range in DNA content, both in regards to genome size (total DNA in an unreduced chromosome complement) and degree of endoreduplication (when DNA replication not followed by division resulting in various ploidy levels within the same individual). However, there is little information available on DNA content evolution in liverworts, the likely sister group to all other living plants. This study seeks to detect a phylogenetic structure in the variation in genome size and degree of endopolyploidy within liverworts. Furthermore, we test the hypothesis that shifts in breeding systems and genome size are correlated, as polyploidy is suggested to be a possible mechanism for the evolution of monoecy in liverworts and could therefore be associated with larger genome sizes. Genome size was determined for 67 liverwort species from 33 families using flow cytometry. Estimates for 48 species and 16 families are new to science. A phylogeny was reconstructed using the plastid gene rbcL. Over all taxa analyzed, there was a considerable range in genome size estimates with 1C-values from 0.27 pg (Jungermannia rubra) to 20.46 pg (Phyllothallia fuegiana). Large genome sizes were also found in the Haplomitriopsida. None of the liverwort species showed evidence of endopolyploidy. Although some taxa may be polyploids, a correlation between shifts in genome size and breeding system is lacking. Importantly, genome size variation in liverworts exhibits strong phylogenetic signal (Pagel's λ=0.99955).

  3. Flow cytometry reliability analysis and variations in sugarcane DNA content.

    PubMed

    Oliveira, A C L; Pasqual, M; Bruzi, A T; Pio, L A S; Mendonça, P M S; Soares, J D R

    2015-01-01

    The aim of this study was to evaluate the reliability of flow cytometry analysis and the use of this technique to differentiate species and varieties of sugarcane (Saccharum spp) according to their relative DNA content. We analyzed 16 varieties and three species belonging to this genus. To determine a reliable protocol, we evaluated three extraction buffers (LB01, Marie, and Tris·MgCl2), the presence and absence of RNase, six doses of propidium iodide (10, 15, 20, 25, and 30 μg), four periods of exposure to propidium iodide (0, 5, 10, and 20 min), and seven external reference standards (peas, beans, corn, radish, rye, soybean, and tomato) with reference to the coefficient of variation and the DNA content. For statistical analyses, we used the programs Sisvar(®) and Xlstat(®). We recommend using the Marie extraction buffer and at least 15 μg propidium iodide. The samples should not be analyzed immediately after the addition of propidium iodide. The use of RNase is optional, and tomato should be used as an external reference standard. The results show that sugarcane has a variable genome size (8.42 to 12.12 pg/2C) and the individuals analyzed could be separated into four groups according to their DNA content with relative equality in the genome sizes of the commercial varieties.

  4. A sensitive impedimetric platform biosensing protein: Insoluble precipitates based on the biocatalysis of manganese(III) meso-tetrakis (4-N-methylpyridiniumyl)-porphyrinin in HCR-assisted dsDNA.

    PubMed

    Zhou, Xingxing; Xue, Shuyan; Jing, Pei; Xu, Wenju

    2016-12-15

    In this study, a sensitive biosensing interface for protein was reported based on nonconductive insoluble precipitates (IPs) by the biocatalysis of manganese(III) meso-tetrakis (4-N-methylpyridiniumyl)-porphyrin (MnTMPyP), which was intercalated into formed double-strand DNA (dsDNA) scaffold triggered by hybridization chain reaction (HCR). In the proposed impedimetric aptasensor, carcinoembryonic antigen (CEA) and its aptamer were used as testing model. PtPd nanowires (PtPdNWs) with large surface area and superior conductivity were employed as nanocarriers to greatly immobilize biomolecules (e.g. CEA aptamers). Then, two DNA hairpins H1 and H2 were introduced to trigger HCR with the assistance of DNA initiator, resulting in the formation of a long dsDNA scaffold. Meanwhile, mimicking enzyme MnTMPyP molecules were embedded into the resultant dsDNA, in situ generating the complex MnTMPyP-dsDNA with peroxidase-like activity. Under the biocatalysis of MnTMPyP-dsDNA, 3,3-diaminobenzidine (DAB) was oxidized to form nonconductive IPs. As a result, the electron transfer between electrode interface and redox probe was vastly hindered, leading to the significant amplification of electrochemical impedimetric signal. So, greatly improved analytical performances of the proposed aptasensor were achieved with a detection limit as low as 0.030pgmL(-1). And the successful assay of CEA in human serum samples enabled the developed biosensing platform to have promising potential in bioanalysis.

  5. High resolution DNA content measurements of mammalian sperm

    SciTech Connect

    Pinkel, D.; Lake, S.; Gledhill, B.L.; Van Dilla, M.A.; Stephenson, D.; Watchmaker, G.

    1982-01-01

    The high condensation and flat shape of the mammalian sperm nucleus present unique difficulties to flow cytometric measurement of DNA content. Chromatin compactness makes quantitative fluorescent staining for DNA difficult and causes a high index of refraction. The refractive index makes optical measurements sensitive to sperm head orientation. We demonstrate that the optical problems can be overcome using the commercial ICP22 epiillumination flow cytometer (Ortho Instruments, Westwood, MA) or a specially built cell orientating flow cytometer (OFCM). The design and operation of the OFCM are described. Measurements of the angular dependence of fluorescence from acriflavine stained rabbit sperm show that it is capable of orienting flat sperm with a tolerance of +-7/sup 0/. Differences in the angular dependence for the similarly shaped bull and rabbit sperm allow discrimination of these cells. We show that DNA staining with 4-6 diamidino-2-phenylindole (DAPI) or an ethidium bromide mithramycin combination allows resolution of the X and Y populations in mouse sperm. They have also been successful with sperm from the bull, ram, rabbit, and boar. Reliable results with human sperm are not obtained. The accuracy of the staining and measurement techniques are verified by the correct determination of the relative content of these two populations in sperm from normal mice and those with the Cattanach (7 to X) translocation. Among the potential uses of these techniques are measurement of DNA content errors induced in sperm due to mutagen exposure, and assessment of the fractions of X and Y sperm in semen that may have one population artifically enriched.

  6. Enzyme therapy of xeroderma pigmentosum: safety and efficacy testing of T4N5 liposome lotion containing a prokaryotic DNA repair enzyme.

    PubMed

    Yarosh, D; Klein, J; Kibitel, J; Alas, L; O'Connor, A; Cummings, B; Grob, D; Gerstein, D; Gilchrest, B A; Ichihashi, M; Ogoshi, M; Ueda, M; Fernandez, V; Chadwick, C; Potten, C S; Proby, C M; Young, A R; Hawk, J L

    1996-06-01

    Xeroderma pigmentosum (XP) is a rare genetic disease in which patients are defective in DNA repair and are extremely sensitive to solar UV radiation exposure. A new treatment approach was tested in these patients, in which a prokaryotic DNA repair enzyme specific for UV-induced DNA damage was delivered into the skin by means of topically applied liposomes to supplement the deficient activity. Acute and chronic safety testing in both mice and humans showed neither adverse reactions nor significant changes in serum chemistry or in skin histology. The skin of XP patients treated with the DNA repair liposomes had fewer cyclobutylpyrimidine dimers in DNA and showed less erythema than did control sites. The results encourage further clinical testing of this new enzyme therapy approach.

  7. Synthesis, crystal structure, DNA and protein binding studies of novel binuclear Pd(II) complex of 6-methoxy-2-oxo-1,2-dihydroquinoline-3-carbaldehyde-4(N,N)-dimethylthiosemicarbazone.

    PubMed

    Eswaran, Ramachandran; Bertani, Roberta; Sgarbossa, Paolo; Karuppannan, Natarajan; Nattamai S P, Bhuvanesh

    2016-02-01

    A novel binuclear palladium(II) complex [(AsPh3)2ClPd(L)PdCl] (LPd2) has been synthesized by reacting 2-oxo-1,2-dihydroquinoline-3-carbaldehyde-4(N,N)-dimethylthiosemicarbazone (HL) with [PdCl2(AsPh3)2], and the molecular structure was confirmed by single crystal X-ray diffraction studies. The DNA interactions of the free ligand and of the complex have been evaluated by absorption and ethidium bromide (EB) competitive studies which revealed that the complex could interact with calf thymus DNA (CT-DNA) through intercalation. In addition, the interactions with bovine serum albumin (BSA) were also studied showing that the new binuclear palladium complex had a strong binding affinity with BSA.

  8. Synthesis, crystal structure, DNA and protein binding studies of novel binuclear Pd(II) complex of 6-methoxy-2-oxo-1,2-dihydroquinoline-3-carbaldehyde-4(N,N)-dimethylthiosemicarbazone.

    PubMed

    Eswaran, Ramachandran; Bertani, Roberta; Sgarbossa, Paolo; Karuppannan, Natarajan; Nattamai S P, Bhuvanesh

    2016-02-01

    A novel binuclear palladium(II) complex [(AsPh3)2ClPd(L)PdCl] (LPd2) has been synthesized by reacting 2-oxo-1,2-dihydroquinoline-3-carbaldehyde-4(N,N)-dimethylthiosemicarbazone (HL) with [PdCl2(AsPh3)2], and the molecular structure was confirmed by single crystal X-ray diffraction studies. The DNA interactions of the free ligand and of the complex have been evaluated by absorption and ethidium bromide (EB) competitive studies which revealed that the complex could interact with calf thymus DNA (CT-DNA) through intercalation. In addition, the interactions with bovine serum albumin (BSA) were also studied showing that the new binuclear palladium complex had a strong binding affinity with BSA. PMID:26606287

  9. Development of a method to quantify the DNA content in cationic peptide-DNA nanoparticles.

    PubMed

    Jain, Arvind K; Yusuf, Helmy; Pattani, Aditya; McCarthy, Helen O; McDonald, Denise M; Kett, Vicky L

    2014-11-01

    Gene therapy has the potential to provide safe and targeted therapies for a variety of diseases. A range of intracellular gene delivery vehicles have been proposed for this purpose. Non-viral vectors are a particularly attractive option and among them cationic peptides have emerged as promising candidates. For the pharmaceutical formulation and application to clinical studies it is necessary to quantify the amount of pDNA condensed with the delivery system. There is a severe deficiency in this area, thus far no methods have been reported specifically for pDNA condensed with cationic peptide to form nanoparticles. The current study seeks to address this and describes the evaluation of a range of disruption agents to extract DNA from nanoparticles formed by condensation with cationic fusogenic peptides RALA and KALA. Only proteinase K exhibited efficient and reproducible results and compatibility with the PicoGreen reagent based quantification assay. Thus we report for the first time a simple and reliable method that can quantify the pDNA content in pDNA cationic peptide nanoparticles.

  10. Cytometric analysis of shape and DNA content in mammalian sperm

    SciTech Connect

    Gledhill, B.L.

    1983-10-10

    Male germ cells respond dramatically to a variety of insults and are important reproductive dosimeters. Semen analyses are very useful in studies on the effects of drugs, chemicals, and environmental hazards on testicular function, male fertility and heritable germinal mutations. Sperm were analyzed by flow cytometry and slit-scan flow analysis for injury following the exposure of testes to mutagens. The utility of flow cytometry in genotoxin screening and monitoring of occupational exposure was evaluated. The technique proved valuable in separation of X- and Y-chromosome bearing sperm and the potential applicability of this technique in artificial insemination and a solution, of accurately assessing the DNA content of sperm were evaluated-with reference to determination of X- and Y-chromosome bearing sperm.

  11. [Biological significance of DNA content in parotid carcinoma].

    PubMed

    Yang, B

    1991-09-01

    The DNA content was analysed by flow cytometry in 5 samples of normal salivary tissue, 36 cases of benign salivary gland tumors and 50 cases of parotid carcinoma. It was found that the difference in the DNA index (DI) and proliferative index (PI) in age, sex, tumor size and TNM staging were insignificant (P greater than 0.05). The DI and PI of poorly differentiated parotid carcinoma were much higher than those of well differentiated parotid carcinoma (P less than 0.05). The DI and PI were closely related to the presence of lymph node metastasis (P less than 0.001). The DI and PI of patients with facial nerve paralysis and with disease free period shorter than 5 years were remarkably higher than those with normal facial nerve and disease free survival for more than 5 years (P less than 0.01). The above results indicate that DI and PI, showing cell proliferative kinetic characteristics, can provide reliable and objective parameters for assessing the degree of differentiation, degree of malignancy, biological behavior and prognosis of parotid carcinomas.

  12. Mitochondrial DNA content contributes to climate adaptation using Chinese populations as a model.

    PubMed

    Cheng, Yao-Ting; Liu, Jia; Yang, Li-Qin; Sun, Chang; Kong, Qing-Peng

    2013-01-01

    Maintaining a balance between ATP synthesis and heat generation is crucial for adapting to changes in climate. Variation in the mitochondrial DNA (mtDNA), which encodes 13 subunits of the respiratory chain complexes, may contribute to climate adaptation by regulating thermogenesis and the use of bioenergy. However, studies looking for a relationship between mtDNA haplogroups and climate have obtained mixed results, leaving unresolved the role of mtDNA in climate adaptation. Since mtDNA content can regulate human bioenergy processes and is known to influence many physiological traits and diseases, it is possible that mtDNA content contributes to climate adaptation in human populations. Here, we analyze the distribution of mtDNA content among 27 Chinese ethnic populations residing across China and find a significant association between mtDNA content and climate, with northern populations having significantly higher mtDNA content than southern populations. Functional studies have shown that high mtDNA content correlates with an increase in the expression of energy metabolism enzymes, which may accelerate thermogenesis. This suggests that the significantly higher mtDNA content observed in northern populations may confer a selective advantage in adapting to colder northern climates.

  13. DNA content variation and its significance in the evolution of the genus Micrasterias (Desmidiales, Streptophyta).

    PubMed

    Poulíčková, Aloisie; Poulíèková, Aloisie; Mazalová, Petra; Vašut, Radim J; Šarhanová, Petra; Neustupa, Jiří; Neustupa, Jiøí; Škaloud, Pavel

    2014-01-01

    It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4-30.7 pg in M. truncata and 32.0-64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae.

  14. DNA content variation and its significance in the evolution of the genus Micrasterias (Desmidiales, Streptophyta).

    PubMed

    Poulíčková, Aloisie; Poulíèková, Aloisie; Mazalová, Petra; Vašut, Radim J; Šarhanová, Petra; Neustupa, Jiří; Neustupa, Jiøí; Škaloud, Pavel

    2014-01-01

    It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4-30.7 pg in M. truncata and 32.0-64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae. PMID:24465986

  15. DNA Content Variation and Its Significance in the Evolution of the Genus Micrasterias (Desmidiales, Streptophyta)

    PubMed Central

    Poulíèková, Aloisie; Mazalová, Petra; Vašut, Radim J.; Šarhanová, Petra; Neustupa, Jiøí; Škaloud, Pavel

    2014-01-01

    It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4–30.7 pg in M. truncata and 32.0–64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae. PMID:24465986

  16. Correlates of Peripheral Blood Mitochondrial DNA Content in a General Population

    PubMed Central

    Knez, Judita; Winckelmans, Ellen; Plusquin, Michelle; Thijs, Lutgarde; Cauwenberghs, Nicholas; Gu, Yumei; Staessen, Jan A.; Nawrot, Tim S.; Kuznetsova, Tatiana

    2016-01-01

    Accumulation of mitochondrial DNA (mtDNA) mutations leads to alterations of mitochondrial biogenesis and function that might produce a decrease in mtDNA content within cells. This implies that mtDNA content might be a potential biomarker associated with oxidative stress and inflammation. However, data on correlates of mtDNA content in a general population are sparse. Our goal in the present study was to describe in a randomly recruited population sample the distribution and determinants of peripheral blood mtDNA content. From 2009 to 2013, we examined 689 persons (50.4% women; mean age = 54.4 years) randomly selected from a Flemish population (Flemish Study on Environment, Genes, and Health Outcomes). Relative mtDNA copy number as compared with nuclear DNA was measured by quantitative real-time polymerase chain reaction in peripheral blood. There was a curvilinear relationship between relative mtDNA copy number and age. mtDNA content slightly increased until the fifth decade of life and declined in older subjects (Page2 = 0.0002). mtDNA content was significantly higher in women (P = 0.007) and increased with platelet count (P < 0.0001), whereas it was inversely associated with white blood cell count (P < 0.0001). We also observed lower mtDNA content in women using estroprogestogens (P = 0.044). This study demonstrated in a general population that peripheral blood mtDNA content is significantly associated with sex and age. Blood mtDNA content is also influenced by platelet and white blood cell counts and estroprogestogen intake. Further studies are required to clarify the impact of chronic inflammation and hormone therapy on mitochondrial function. PMID:26702630

  17. Tumor-specific changes in mtDNA content in human cancer.

    PubMed

    Mambo, Elizabeth; Chatterjee, Aditi; Xing, Mingzhao; Tallini, Giovanni; Haugen, Bryan R; Yeung, Sai-Ching J; Sukumar, Saraswati; Sidransky, David

    2005-10-10

    Mitochondrial DNA (mtDNA) alterations are associated with various cancer types, suggesting that the mitochondrial genome may be a critical contributing factor in carcinogenesis. mtDNA alterations have been suggested as a potentially sensitive and specific biomarker for several cancer types. We examined mtDNA content in 25 pairs of normal and tumor breast tissue samples, 37 papillary thyroid carcinoma (PTC), 21 benign thyroid neoplasms and in 20 paired normal and PTC samples. Our results showed that mtDNA content was reduced in 80% of the breast tumors relative to their corresponding normal. mtDNA was increased in papillary thyroid carcinomas, however, when compared to the corresponding normal DNA taken from the same individual. Also, mtDNA content was increased in none-paired PTC samples compared to the normal controls. Our findings indicate that changes in mtDNA content during carcinogenesis may be regulated in a tumor specific manner. Additionally, changes in mtDNA levels did not correlate with tumor grade and metastasis, suggesting that these alterations may occur in the early stages of tumorigenesis. Our findings suggest that mtDNA content can be used as a molecular diagnostic tool to help identify genetic abnormalities in human tumors.

  18. Variation in nuclear DNA content in Malus species and cultivated apples.

    PubMed

    Tatum, Tatiana C; Stepanovic, Svetlana; Biradar, D P; Rayburn, A Lane; Korban, Schuyler S

    2005-10-01

    The nuclear DNA content for a group of 40 Malus species and hybrids has been estimated using flow cytometry. Estimates of nuclear DNA content for this germplasm collection range from 1.45 pg for Malus fusca (diploid) to 2.57 pg for Malus ioensis (triploid). Among diploids, the nuclear (2C) DNA ranges from 1.45 pg for M. fusca to 1.68 pg for Malus transitoria. Among triploids, the nuclear (3C) DNA content ranges from 2.37 pg / 3C for Malus sikkimensis to 2.57 pg / 3C for M. ioensis. Given the complexity of the apple genome and its suggested allopolyploid origin, the results obtained in this study confirm earlier reports that polyploids can easily withstand the loss of a certain amount of DNA, and that there is a slight tendency towards diminished haploid nuclear DNA content with increased polyploidy.

  19. Mitochondrial DNA content contributes to healthy aging in Chinese: a study from nonagenarians and centenarians.

    PubMed

    He, Yong-Han; Lu, Xiang; Wu, Huan; Cai, Wang-Wei; Yang, Li-Qin; Xu, Liang-You; Sun, Hong-Peng; Kong, Qing-Peng

    2014-07-01

    Mitochondrial DNA (mtDNA) content plays an important role in energy production and sustaining normal physiological function. A decline in the mtDNA content and subsequent dysfunction cause various senile diseases, with decreasing mtDNA content observed in the elderly individuals with age-related diseases. In contrast, the oldest old individuals, for example, centenarians, have a delayed or reduced prevalence of these diseases, suggesting centenarians may have a different pattern of the mtDNA content, enabling them to keep normal mitochondrial functions to help delay or escape senile diseases. To test this hypothesis, a total of 961 subjects, consisting of 424 longevity subjects and 537 younger control subjects from Hainan and Sichuan provinces of China, were recruited for this study. The mtDNA content was found to be inversely associated with age among the age of group 40-70 years. Surprisingly, no reduction of mtDNA content was observed in nonagenarians and centenarians; instead, these oldest old showed a significant increase than the elderly people aged between 50 and 70 years. The results suggest the higher mtDNA content may convey a beneficial effect to the longevity of people through assuring sufficient energy supply.

  20. Chromosomal DNA content of sweet pepper determined by association of cytogenetic and cytometric tools.

    PubMed

    de Abreu, Isabella Santiago; Carvalho, Carlos Roberto; Clarindo, Wellington Ronildo

    2008-07-01

    The nuclear DNA content of sweet pepper (Capsicum annuum L. var. annuum, 2n = 24) has been measured by flow and image cytometries but the DNA content of each chromosome of this species has not yet been regarded. DNA content of individual chromosomes has been quantified by the flow karyotyping technique, which requires a great quantity of intact metaphasic chromosomes and methods that allow the characterization of individual chromosomes; however, the obtainment of adequate number of metaphases can be difficult in some species like C. annuum. In order to estimate the DNA content of each C. annuum var. annuum cv. "New Mexican" chromosome, flow and image cytometries were associated with the cytogenetic methodology. First, the DNA amount (2C = 6.90 pg) was established by flow cytometry. Integrated optical density (IOD) values were calculated by image cytometry for each Feulgen stained metaphasic chromosome. Then, by distributing the correspondent metaphasic value (4C = 13.80 pg) proportionally to average IOD values, the following chromosomal DNA contents were obtained in pg: 0.74 (chromosome 1), 0.67 (2), 0.61 (3, 4), 0.60 (5), 0.59 (6, 7), 0.58 (8), 0.57 (9), 0.56 (10) and 0.39 (11, 12). This study reports an alternative and reproducible technique that makes quantifying the chromosomal DNA content possible.

  1. Abnormal DNA content in oral epithelial dysplasia is associated with increased risk of progression to carcinoma

    PubMed Central

    Bradley, G; Odell, E W; Raphael, S; Ho, J; Le, L W; Benchimol, S; Kamel-Reid, S

    2010-01-01

    Background: Oral epithelial dysplasia (OED) is a histologically detectable lesion that may progress to carcinoma but there are no accurate markers that predict progression. This study examined the development of carcinoma from oral dysplastic lesions, and the association between abnormal DNA content and progression to carcinoma. Methods: Epithelial dysplasias from the Oral Pathology Diagnostic Service were matched against the Ontario Cancer Registry database to identify cases that progressed to carcinoma. A case–control study was conducted to compare DNA image cytometry of dysplasias that progressed with those that have not progressed. For a subset of the progressed dysplasias, DNA content of the carcinoma was also analysed. Results: A total of 8% of epithelial dysplasias progressed to carcinoma after 6–131 months. In all, 28 of 99 dysplasias showed abnormal DNA content by image cytometry. In multivariate analysis of time to progression, abnormal DNA content was a significant predictor with hazard ratio of 3.3 (95% confidence interval: 1.5–7.4) corrected for site and grade of dysplasia. Analysis of sequential samples of dysplasia and carcinoma suggested that epithelial cell populations with grossly abnormal DNA content were transient intermediates during oral cancer development. Conclusions: Abnormal DNA content is a significant biomarker of a subset of OED that progress to carcinoma. PMID:20859287

  2. DNA content, kinetic complexity, and the ploidy question in Candida albicans.

    PubMed Central

    Riggsby, W S; Torres-Bauza, L J; Wills, J W; Townes, T M

    1982-01-01

    Candida albicans is a dimorphic fungus that is pathogenic for humans. No sexual cycle has been reported for this fungus, and earlier reports have differed on whether typical strains of C. albicans are haploid or diploid. Previous estimates of the DNA content of C. albicans varied by one order of magnitude. We used three independent methods to measure the kinetic complexity of the single-copy DNA from a typical strain of C. albicans (strain H317) to determine the DNA content per haploid genote; we obtained values of 15 and 20 fg per cell by using S1 nuclease and hydroxyapatite assays, respectively. Optical assays for DNA reassociation kinetics, although not definitive in themselves, yielded values in this range. Chemical measurements of the DNA content of several typical strains, including strain H317, yielded values clustered about a mean of 37 fg per cell. We concluded that these strains are diploid. PMID:6765567

  3. Mechanical Properties of High-G⋅C Content DNA with A-Type Base-Stacking

    PubMed Central

    Hormeño, Silvia; Ibarra, Borja; Carrascosa, José L.; Valpuesta, José M.; Moreno-Herrero, Fernando; Arias-Gonzalez, J. Ricardo

    2011-01-01

    The sequence of a DNA molecule is known to influence its secondary structure and flexibility. Using a combination of bulk and single-molecule techniques, we measure the structural and mechanical properties of two DNAs which differ in both sequence and base-stacking arrangement in aqueous buffer, as revealed by circular dichroism: one with 50% G·C content and B-form and the other with 70% G·C content and A-form. Atomic force microscopy measurements reveal that the local A-form structure of the high-G·C DNA does not lead to a global contour-length decrease with respect to that of the molecule in B-form although it affects its persistence length. In the presence of force, however, the stiffness of high-G·C content DNA is similar to that of balanced-G·C DNA as magnetic and optical tweezers measured typical values for the persistence length of both DNA substrates. This indicates that sequence-induced local distortions from the B-form are compromised under tension. Finally, high-G·C DNA is significantly harder to stretch than 50%-G·C DNA as manifested by a larger stretch modulus. Our results show that a local, basepair configuration of DNA induced by high-G·C content influences the stretching elasticity of the polymer but that it does not affect the global, double-helix arrangement. PMID:21504736

  4. Assessment of Telomere Length, Phenotype, and DNA Content

    PubMed Central

    Kelesidis, Theodoros; Schmid, Ingrid

    2016-01-01

    Telomere sequences at the end of chromosomes control somatic cell division; therefore, telomere length in a given cell population provides information about its replication potential. This unit describes a method for flow cytometric measurement of telomere length in subpopulations using fluorescence in situ hybridization of fluorescently-labeled probes (Flow-FISH) without prior cell separation. After cells are stained for surface immunofluorescence, antigen-antibody complexes are covalently cross-linked onto cell membranes before FISH with a telomere-specific probe. Cells with long telomeres are included as internal standards. Addition of a DNA dye permits exclusion of proliferating cells during data analysis. DNA ploidy measurements of cells of interest and internal standard are performed on separate aliquots in parallel to Flow-FISH. Telomere fluorescence of G0/1 cells of subpopulations and internal standards obtained from Flow-FISH are normalized for DNA ploidy and telomere length in subsets of interest is expressed as a fraction of the internal standard telomere length. PMID:18770803

  5. Increased mitochondrial DNA content in peripheral blood lymphocytes from HIV-infected patients with lipodystrophy.

    PubMed

    Cossarizza, Andrea; Riva, Agostino; Pinti, Marcello; Ammannato, Silvia; Fedeli, Paolo; Mussini, Cristina; Esposito, Roberto; Galli, Massimo

    2003-08-01

    We have evaluated mitochondrial (mt) DNA content in CD4 and CD8 peripheral blood lymphocytes (PBLs) from HIV-infected patients taking highly active antiretroviral therapy (HAART) who display different types of adipose tissue alterations. A cross-sectional study was performed in a total of 23 patients with lipodystrophy (LD): nine patients with fat accumulation, six patients with fat loss, eight patients with combined form, who were compared to 11 individuals infected by HIV without LD (HIV-positive) and 10 seronegative controls (CTRL). PBLs were obtained by standard methods, that is, gradient density centrifugation on Ficoll, and CD4 or CD8 cells were positively isolated by magnetic sorting to eliminate the contamination of platelets. mtDNA content was then measured by an original assay based upon real-time PCR. mtDNA content was significantly increased in CD4 T cells from patients with LD, while no differences were present between CD4 and CD8 cells from HIV-positive and CTRL individuals. Nor were any differences found when comparing LD or HIV-positive patients treated with stavudine or zidovudine, or taking D-drugs or non D-drugs. Patients with fat accumulation had significantly higher mtDNA content compared to HIV-positive and CTRL, this phenomenon regarding both CD4 and CD8 PBLs. Considering all HIV-positive patients (including LD), mtDNA content showed a significant, positive correlation with cholesterolaemia but not with triglyceridaemia and glycaemia. Relatively high mtDNA content in LD patients, as well as the correlation between mtDNA content and cholesterol in all HIV-positive subjects, suggest the involvement of mitochondria in such a pathology. However, further studies are needed to confirm these initial observations and ascertain whether the quantification of mtDNA in PBL is a useful and reliable marker to investigate and monitor HAART-related changes in fat distribution.

  6. Mitochondrial DNA content of mature spermatozoa and oocytes in the genetic model Drosophila.

    PubMed

    Wolff, Jonci Nikolai; Sutovsky, Peter; Ballard, John William Oman

    2013-07-01

    Although crucial to the success of fertilization and embryogenesis, little is known about the mitochondrial DNA (mtDNA) content of mature spermatozoa and oocytes across taxa and across different fertilization systems. Oocytes are assumed to hold a large population of mtDNAs that populate emerging cells during early embryogenesis, whereas spermatozoa harbor only a limited pool of mtDNAs that is believed to sustain functionality but fails to contribute paternal mtDNA to the zygote. Recent work suggests that mature sperm of the genetic model Drosophila melanogaster lack mtDNA, questioning the significance of zygotic mechanisms for the selective elimination of paternal mtDNA and their necessity for fertilization success. This finding further contradicts previous observations of the inheritance of paternal mtDNA in drosophilids. Using quantitative polymerase chain reaction, we estimate the mtDNA content of several laboratory strains of D. melanogaster and D. simulans to shed light on this discrepancy and to describe the mitochondrial/mtDNA load of gametes within this system. These measurements led to an average estimate of 22.91±4.61 mtDNA molecules/copies per spermatozoon across both species and to 1.07E+07±2.71E+06 molecules/copies per oocyte for D. simulans. As a consequence, the ratio of paternal and maternal mtDNA in the zygote was estimated at 1:4.65E+05.

  7. [Cytologic study of glandular tumors in maxillofacial regions-- diagnostic application of nuclear DNA content].

    PubMed

    Kawasaki, T; Kimura, H; Shingaki, S; Saito, R; Nakajima, T; Mizutani, H; Mori, M; Ishiki, T

    1983-12-01

    We studied whether the DNA contents may be useful in the differential diagnosis of glandular tumors in the maxillofacial regions. In 25 of these tumors, the DNA contents were measured by microspectrophotometry, using 4 normal salivary glands as controls. We found that: (1) DNA histgram patterns were useful in differential diagnosis only in special cases. (2) The criteria were based on our decision and these tumors were classified into 3 types (a) Benign, (b) Low-grade malignant, (c) High-grade malignant. Our classification seemed to offer an objective means for differentiating between Benign & Malignant tumors of these types.

  8. Nuclear DNA Content Estimates in Multicellular Green, Red and Brown Algae: Phylogenetic Considerations

    PubMed Central

    KAPRAUN, DONALD F.

    2005-01-01

    • Background and Aims Multicellular eukaryotic algae are phylogenetically disparate. Nuclear DNA content estimates have been published for fewer than 1 % of the described species of Chlorophyta, Phaeophyta and Rhodophyta. The present investigation aims to summarize the state of our knowledge and to add substantially to our database of C-values for theses algae. • Methods The DNA-localizing fluorochrome DAPI (4′, 6-diamidino-2-phenylindole) and RBC (chicken erythrocyte) standard were used to estimate 2C values with static microspectrophotometry. • Key Results 2C DNA contents for 85 species of Chlorophyta range from 0·2–6·1 pg, excluding the highly polyploidy Charales and Desmidiales with DNA contents of up to 39·2 and 20·7 pg, respectively. 2C DNA contents for 111 species of Rhodophyta range from 0·1–2·8 pg, and for 44 species of Phaeophyta range from 0·2–1·8 pg. • Conclusions New availability of consensus higher-level molecular phylogenies provides a framework for viewing C-value data in a phylogenetic context. Both DNA content ranges and mean values are greater in taxa considered to be basal. It is proposed that the basal, ancestral genome in each algal group was quite small. Both mechanistic and ecological processes are discussed that could have produced the observed C-value ranges. PMID:15596456

  9. Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta)

    PubMed Central

    Phillips, Naomi; Kapraun, Donald F.; Gómez Garreta, Amelia; Ribera Siguan, M. Antonia; Rull, Jorde L.; Salvador Soler, Noemi; Lewis, Raymond; Kawai, Hiroshi

    2011-01-01

    Background and aims Brown algae are critical components of marine ecosystems around the world. However, the genome of only one species of the class has so far been sequenced. This contrasts with numerous sequences available for model organisms such as higher plants, flies or worms. The present communication expands our coverage of DNA content information to 98 species of brown algae with a view to facilitating further genomic investigations of the class. Methodology The DNA-localizing fluorochrome DAPI (4′,6-diamidino-2-phenylindole) and the red blood cell (chicken erythrocyte) standard were used to estimate 2C values by static microspectrophotometry. Principal results 2C DNA contents are reported for 98 species of brown algae, almost doubling the number of estimates available for the class. The present results also expand the reported DNA content range to 0.2–3.6 pg, with several species of Fucales and Laminariales containing apparent polyploid genomes with 2C = 1.8–3.6 pg. Conclusions The data provide DNA content values for 12 of the 19 recognized orders of brown algae spanning the breadth of the class. Despite earlier contentions concerning DNA content and the presence of oogamy, the present results do not support a correlation between phylogenetic placement and genome size. The closest sister groups to the brown algae have genome sizes on the order of 0.3 pg (e.g. Schizocladiophyceae), suggesting that this may be the ancestral genome size. However, DNA content ranges widely across the class. PMID:22476472

  10. Increased mitochondrial DNA content in saliva associated with head and neck cancer.

    PubMed

    Jiang, Wei-Wen; Masayesva, Brett; Zahurak, Marianna; Carvalho, Andre Lopes; Rosenbaum, Eli; Mambo, Elizabeth; Zhou, Shaoyu; Minhas, Khalid; Benoit, Nicole; Westra, William H; Alberg, Anthony; Sidransky, David; Koch, Wayne; Califano, Joseph

    2005-04-01

    Alterations of the mitochondrial DNA (mtDNA) have been described in human tumors and in other tissues in association with smoking exposure. We did quantitative PCR of cytochrome c oxidase I (Cox I) and cytochrome c oxidase II (Cox II) genes on oral rinse samples obtained from 94 patients with primary head and neck squamous cell carcinoma (HNSC) and a control group of 656 subjects. Mitochondrial DNA/nuclear DNA in saliva from HNSC patients and controls in relationship to smoking exposure, ethanol intake, and tumor stage were examined. Mean levels of Cox I and Cox II in saliva samples were significantly higher in HNSC patients: Cox I, 0.076 [95% confidence interval (95% CI), 0.06-0.09] and Cox II, 0.055 (95% CI, 0.04-0.07) in comparison with controls Cox I, 0.054 (95% CI, 0.05-0.06), P < 0.0001 and Cox II, 0.046 (95% CI, 0.04-0.05), P = 0.003 (t test). MtDNA levels were elevated in primary tumors when compared with matched, pretreatment saliva and significant correlation was noted (Cox I, r = 0.30, P = 0.005 and Cox II r = 0.33, P = 0.002, respectively, Pearson's correlation). On univariate analysis, smoking, age, HNSC diagnosis, and advanced stage of HNSC were associated with higher level of mtDNA content in saliva. Multivariate analysis showed a significant and independent association of HNSC diagnosis, age, and smoking with increasing mtDNA/nuclear DNA for Cox I and Cox II. mtDNA content alteration is associated with HNSC independently of age and smoking exposure, can be detected in saliva, and may be due to elevation in mtDNA content in primary HNSC.

  11. Decreased Integrity, Content, and Increased Transcript Level of Mitochondrial DNA Are Associated with Keratoconus

    PubMed Central

    Hao, Xiao-Dan; Chen, Zhao-Li; Qu, Ming-Li; Zhao, Xiao-Wen; Li, Su-Xia; Chen, Peng

    2016-01-01

    Oxidative stress may play an important role in the pathogenesis of keratoconus (KC). Mitochondrial DNA (mtDNA) is involved in mitochondrial function, and the mtDNA content, integrity, and transcript level may affect the generation of reactive oxygen species (ROS) and be involved in the pathogenesis of KC. We designed a case-control study to research the relationship between KC and mtDNA integrity, content and transcription. One-hundred ninety-eight KC corneas and 106 normal corneas from Chinese patients were studied. Quantitative real-time PCR was used to measure the relative mtDNA content, transcript levels of mtDNA and related genes. Long-extension PCR was used to detect mtDNA damage. ROS, mitochondrial membrane potential and ATP were measured by respective assay kit, and Mito-Tracker Green was used to label the mitochondria. The relative mtDNA content of KC corneas was significantly lower than that of normal corneas (P = 9.19×10−24), possibly due to decreased expression of the mitochondrial transcription factor A (TFAM) gene (P = 3.26×10−3). In contrast, the transcript levels of mtDNA genes were significantly increased in KC corneas compared with normal corneas (NADH dehydrogenase subunit 1 [ND1]: P = 1.79×10−3; cytochrome c oxidase subunit 1 [COX1]: P = 1.54×10−3; NADH dehydrogenase subunit 1, [ND6]: P = 4.62×10−3). The latter may be the result of increased expression levels of mtDNA transcription-related genes mitochondrial RNA polymerase (POLRMT) (P = 2.55×10−4) and transcription factor B2 mitochondrial (TFB2M) (P = 7.88×10−5). KC corneas also had increased mtDNA damage (P = 3.63×10−10), higher ROS levels, and lower mitochondrial membrane potential and ATP levels compared with normal corneas. Decreased integrity, content and increased transcript level of mtDNA are associated with KC. These changes may affect the generation of ROS and play a role in the pathogenesis of KC. PMID:27783701

  12. Flow-cytometric DNA content of histiocytosis X (Langerhans cell histiocytosis).

    PubMed Central

    Rabkin, M. S.; Wittwer, C. T.; Kjeldsberg, C. R.; Piepkorn, M. W.

    1988-01-01

    Retrospective DNA-content analysis was performed by flow cytometry on formalin-fixed, paraffin-embedded tissue from 36 patients with histiocytosis X (Langerhans cell histiocytosis). Included were 17 patients with solitary bone lesions, 4 patients with multiple bone lesions, 2 patients with solitary extraosseous lesions, 1 patient with congenital self-healing histiocytosis, and 12 patients with disseminated disease. The diagnosis was in each case verified by review of the clinical history and histopathologic material. None of the cases displayed significant cytologic atypia. DNA content analysis failed to reveal additional G0-G1 peaks or "shoulders" suggestive of aneuploid subpopulations in any case. Full-peak coefficients of variation ranged from 3.8 to 8.0. Our data suggest that despite a prior report of a single aneuploid case of histiocytosis X, DNA content analysis may not be useful in predicting clinical stage and outcome in this disease. Images Figure 1 PMID:3258734

  13. [The applying and foreground of quantifying DNA content by image analysis technique in determining postmortem interval].

    PubMed

    Wang, Cheng-yi; Liu, Liang

    2002-02-01

    Image Analysis Technique(IAT) was developed at 1950's, which quantifies the changing all the part of image by sampling, processing, quantifying, computing, analyzing the information of image. And now it has become a normal quantifying technique in biology and medicine research. In the present paper, we reviewed briefly the principium of quantifying the DNA content by IAT, the law of degradation of DNA in nucleus and the foreground of this method in determining PMI in forensic pathology.

  14. Nuclear DNA content in Miscanthus sp. and the geographical variation pattern in Miscanthus lutarioriparius

    NASA Astrophysics Data System (ADS)

    Sheng, Jiajing; Hu, Xiaohu; Zeng, Xiaofei; Li, Ye; Zhou, Fasong; Hu, Zhongli; Jin, Surong; Diao, Ying

    2016-10-01

    The genome sizes of five Miscanthus species, including 79 accessions of M. lutarioriparius, 8 of M. floridulus, 6 of M. sacchariflorus, 7 of M. sinensis, and 4 of M. × giganteus were examined using flow cytometry. The overall average nuclear DNA content were 4.256 ± 0.6 pg/2C in M. lutarioriparius, 5.175 ± 0.3 pg/2C in M. floridulus, 3.956 ± 0.2 pg/2C in M. sacchariflorus, 5.272 ± 0.2 pg/2C in M. sinensis, and 6.932 ± 0.1 pg/2C in M. × giganteus. Interspecific variation was found at the diploid level, suggesting that DNA content might be a parameter that can be used to differentiate the species. Tetraploid populations were found in M. lutarioriparius, M. sacchariflorus, and M. sinensis, and their DNA content were 8.34 ± 1.2, 8.52, and 8.355 pg, respectively. The association between the DNA content of M. lutarioriparius, collected from representative ranges across the Yangtze River, and its geographic distribution was statistically analyzed. A consistent pattern of DNA content variation in 79 M. lutarioriparius accessions across its entire geographic range was found in this study. Along the Yangtze River, the DNA content of M. lutarioriparius tended to increase from the upstream to the downstream areas, and almost all tetraploids gathered in the upstream area extended to coastal regions.

  15. Nuclear DNA content in Miscanthus sp. and the geographical variation pattern in Miscanthus lutarioriparius

    PubMed Central

    Sheng, Jiajing; Hu, Xiaohu; Zeng, Xiaofei; Li, Ye; Zhou, Fasong; Hu, Zhongli; Jin, Surong; Diao, Ying

    2016-01-01

    The genome sizes of five Miscanthus species, including 79 accessions of M. lutarioriparius, 8 of M. floridulus, 6 of M. sacchariflorus, 7 of M. sinensis, and 4 of M. × giganteus were examined using flow cytometry. The overall average nuclear DNA content were 4.256 ± 0.6 pg/2C in M. lutarioriparius, 5.175 ± 0.3 pg/2C in M. floridulus, 3.956 ± 0.2 pg/2C in M. sacchariflorus, 5.272 ± 0.2 pg/2C in M. sinensis, and 6.932 ± 0.1 pg/2C in M. × giganteus. Interspecific variation was found at the diploid level, suggesting that DNA content might be a parameter that can be used to differentiate the species. Tetraploid populations were found in M. lutarioriparius, M. sacchariflorus, and M. sinensis, and their DNA content were 8.34 ± 1.2, 8.52, and 8.355 pg, respectively. The association between the DNA content of M. lutarioriparius, collected from representative ranges across the Yangtze River, and its geographic distribution was statistically analyzed. A consistent pattern of DNA content variation in 79 M. lutarioriparius accessions across its entire geographic range was found in this study. Along the Yangtze River, the DNA content of M. lutarioriparius tended to increase from the upstream to the downstream areas, and almost all tetraploids gathered in the upstream area extended to coastal regions. PMID:27698438

  16. Effect of A-L tonic capsule on DNA content in rat experimental hepatocarcinogenesis.

    PubMed

    Guan, Yang; Zhou, Zebin; Zhang, Chunming; Ruan, Youbing; Wu, Zhongbi

    2002-01-01

    The effects of A-L tonic capsule on DNA content in rat experimental hepatocarcinogenesis induced by diethylnitrosamine (DENA) were observed. The experimental rats were divided into 4 groups. With exception of group D in which the rats were only administered with DENA, the rats in the groups A, B, C were previously, simultaneously and subsequently fed with A-L tonic capsule respectively while they were administered with DENA. The DNA content of all rat livers was measured using automatic image analysis technique 20 weeks after administration of DENA. The results showed that the highest and lowest DNA contents were respectively seen in the groups D and A. There was significant difference in DNA contents between the groups A or B or C and D, and also between the groups A and B or C (both P < 0.01). 4 components (4C) and > or = 5C cells were predominant in the group D, while 2C cells were the minority. The number of 2C cells in the groups A, B, C was significantly higher than that in the group D, and the number of > or = 5C cells in the groups A, B, C was markedly lower than that in the group D (P < 0.01). Also, there was very significant difference in the number of 2C and > or = 5C cells between group A and B or C (P < 0.01). It was concluded that A-L tonic capsule could effectively inhibit the increase of DNA content of hepatocytes and improve the distribution of DNA content in rat hepatocarcinogenesis, especially in group A. PMID:12658771

  17. DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning

    PubMed Central

    Rodsand, Pouria; Hellman, Urban; Waldenström, Anders; Lundholm, Marie; Ahrén, Dag; Biber, Björn; Ronquist, Gunnar; Haney, Michael

    2016-01-01

    Background Extracellular vesicles (EV) are nano-sized membranous structures released from most cells. They have the capacity to carry bioactive molecules and gene expression signals between cells, thus mediating intercellular communication. It is believed that EV confer protection after ischemic preconditioning (IPC). We hypothesize that myocardial ischemic preconditioning will lead to rapid alteration of EV DNA content in EV collected from coronary venous effluent. Materials and Methods In a porcine myocardial ischemic preconditioning model, EV were isolated from coronary venous blood before and after IPC by differential centrifugation steps culminating in preparative ultracentrifugation combined with density gradient ultracentrifugation. The EV preparation was validated, the DNA was extracted and further characterized by DNA sequencing followed by bioinformatics analysis. Results Porcine genomic DNA fragments representing each chromosome, including mitochondrial DNA sequences, were detected in EV isolated before and after IPC. There was no difference detected in the number of sequenced gene fragments (reads) or in the genomic coverage of the sequenced DNA fragments in EV isolated before and after IPC. Gene ontology analysis showed an enrichment of genes coding for ion channels, enzymes and proteins for basal metabolism and vesicle biogenesis and specific cardiac proteins. Conclusions This study demonstrates that porcine EV isolated from coronary venous blood plasma contain fragments of DNA from the entire genome, including the mitochondria. In this model we did not find specific qualitative or quantitative changes of the DNA content in EV collected immediately after an in vivo myocardial IPC provocation. This does not rule out the possibility that EV DNA content changes in response to myocardial IPC which could occur in a later time frame. PMID:27434143

  18. Nuclear DNA Content Variation in Life History Phases of the Bonnemasoniaceae (Rhodophyta)

    PubMed Central

    Salvador Soler, Noemi; Gómez Garreta, Amelia; Ribera Siguan, Mª Antonia; Kapraun, Donald F.

    2014-01-01

    Nuclear DNA content in gametophytes and sporophytes or the prostrate phases of the following species of Bonnemaisoniaceae (Asparagopsis armata, Asparagopsis taxiformis, Bonnemaisonia asparagoides, Bonnemaisonia clavata and Bonnemaisonia hamifera) were estimated by image analysis and static microspectrophotometry using the DNA-localizing fluorochrome DAPI (4′, 6-diamidino-2-phenylindole, dilactate) and the chicken erythrocytes standard. These estimates expand on the Kew database of DNA nuclear content. DNA content values for 1C nuclei in the gametophytes (spermatia and vegetative cells) range from 0.5 pg to 0.8 pg, and for 2C nuclei in the sporophytes or the prostrate phases range from 1.15–1.7 pg. Although only the 2C and 4C values were observed in the sporophyte or the prostrate phase, in the vegetative cells of the gametophyte the values oscillated from 1C to 4C, showing the possible start of endopolyploidy. The results confirm the alternation of nuclear phases in these Bonnemaisoniaceae species, in those that have tetrasporogenesis, as well as those that have somatic meiosis. The availability of a consensus phylogenetic tree for Bonnemaisoniaceae has opened the way to determine evolutionary trends in DNA contents. Both the estimated genome sizes and the published chromosome numbers for Bonnemaisoniaceae suggest a narrow range of values consistent with the conservation of an ancestral genome. PMID:24465835

  19. Nuclear DNA content variation in life history phases of the Bonnemasoniaceae (Rhodophyta).

    PubMed

    Salvador Soler, Noemi; Gómez Garreta, Amelia; Ribera Siguan, Ma Antonia; Kapraun, Donald F

    2014-01-01

    Nuclear DNA content in gametophytes and sporophytes or the prostrate phases of the following species of Bonnemaisoniaceae (Asparagopsis armata, Asparagopsis taxiformis, Bonnemaisonia asparagoides, Bonnemaisonia clavata and Bonnemaisonia hamifera) were estimated by image analysis and static microspectrophotometry using the DNA-localizing fluorochrome DAPI (4', 6-diamidino-2-phenylindole, dilactate) and the chicken erythrocytes standard. These estimates expand on the Kew database of DNA nuclear content. DNA content values for 1C nuclei in the gametophytes (spermatia and vegetative cells) range from 0.5 pg to 0.8 pg, and for 2C nuclei in the sporophytes or the prostrate phases range from 1.15-1.7 pg. Although only the 2C and 4C values were observed in the sporophyte or the prostrate phase, in the vegetative cells of the gametophyte the values oscillated from 1C to 4C, showing the possible start of endopolyploidy. The results confirm the alternation of nuclear phases in these Bonnemaisoniaceae species, in those that have tetrasporogenesis, as well as those that have somatic meiosis. The availability of a consensus phylogenetic tree for Bonnemaisoniaceae has opened the way to determine evolutionary trends in DNA contents. Both the estimated genome sizes and the published chromosome numbers for Bonnemaisoniaceae suggest a narrow range of values consistent with the conservation of an ancestral genome.

  20. DNA content in embryo and endosperm of maize kernel (Zea mays L.): impact on GMO quantification.

    PubMed

    Trifa, Youssef; Zhang, David

    2004-03-10

    PCR-based techniques are the most widely used methods for the quantification of genetically modified organisms (GMOs) through the determination of the ratio of transgenic DNA to total DNA. It is shown that the DNA content per mass unit is significantly different among 10 maize cultivars. The DNA contents of endosperms, embryos, and teguments of individual kernels from 10 maize cultivars were determined. According to our results, the tegument's DNA ratio reaches at maximum 3.5% of the total kernel's DNA, whereas the endosperm's and the embryo's DNA ratios are nearly equal to 50%. The embryo cells are diploid and made of one paternal and one maternal haploid genome, whereas the endosperm is constituted of triploid cells made of two maternal haploid genomes and one paternal haploid genome. Therefore, it is shown, in this study, that the accuracy of the GMO quantification depends on the reference material used as well as on the category of the transgenic kernels present in the mixture.

  1. Identifying X- and Y-chromosome-bearing sperm by DNA content: retrospective perspectives and prospective opinions

    SciTech Connect

    Gledhill, B.L.; Pinkel, D.; Garner, D.L.

    1982-03-05

    Theoretically, since DNA should be the most constant component, quantitatively, of normal sperm, then genotoxic agents arising from energy production and consumption, and chemical and physical mutagens, could be identified by measuring variability in the DNA content of individual sperm from exposed men or test animals. The difference between the DNA content of X and Y sperm seemed a biologically significant benchmark for the measurement technology. Several methods are available for determining the genetic activity of agents in male germ cells, but these tests are generally laborious. Sperm-based methods provide an attractive alternate since they are not invasive, and are directly applicable to the study of human exposure. Slide-based assay of DNA content suggests that human sperm with X, Y, or YY chromosome constitutions can be distinguished by their fluorescence with quinacrine. Subsequent measurement of the dry mass of human sperm heads is performed. Dry mass is proportional to DNA content. While the study showed that human sperm with none and one quinacrine-fluorescent spot are X- and Y-bearing, respectively, the dry mass measurements indicated that many of the sperm with two quinacrine-fluorescent spots are not YY-bearing. While several reports on the initial application of flow cytometry of sperm to the investigation of mammalian infertility have appeared recently, emphasis here has been on the development of an in vivo sperm-based flow cytometric bioassay for mutations, and has not centered on andrological applications. In this review, the ability to differentiate between two equally sized populations of sperm, one bearing X and the other Y chromosomes with mean DNA content differing by about 3 to 4% is described. It has direct application to the preselection of sex of offspring, and could likely have a profound impact on animal improvement. (ERB)

  2. High leukocyte mtDNA content contributes to poor prognosis through ROS-mediated immunosuppression in hepatocellular carcinoma patients

    PubMed Central

    Zhou, Feng; Zhou, Xingchun; Chen, Yibing; Guo, Xu; Li, Jibin; Huang, Qichao; Yang, Yefa; Lyu, Zhuomin; Zhang, Hongxin; Xing, Jinliang

    2016-01-01

    Compelling epidemiological evidences indicate a significant association between leukocyte mitochondrial DNA (mtDNA) content and incidence risk of several malignancies, including hepatocellular carcinoma (HCC). However, whether leukocyte mtDNA content affect prognosis of HCC patients and underlying mechanism has never been explored. In our study, leukocyte mtDNA content was measured in 618 HCC patients and its prognostic value was analyzed. Moreover, we detected the immunophenotypes of peripheral blood mononuclear cells (PBMCs) and plasma concentrations of several cytokines in 40 HCC patients and assessed the modulating effects of mtDNA content on immunosuppression in cell models. Our results showed that HCC patients with high leukocyte mtDNA content exhibited a significantly worse recurrence-free survival (RFS) and overall survival (OS) than those with low leukocyte mtDNA content. Leukocyte mtDNA content and TNM stage exhibited a notable joint effect in prognosis prediction. Furthermore, we found that patients with high leukocyte mtDNA content exhibited a higher frequency of CD4+CD25+FOXP3+ regulatory T (Treg) cells and lower frequency of NK cells in PBMCs and had higher TGF-β1 and lower TNF-α and IFN-γ plasma concentration when compared with those with low leukocyte mtDNA content, which suggests an immunosuppressive status. High leukocyte mtDNA content significantly enhanced the ROS-mediated secretion of TGF-β1, which accounted for higher Treg and lower NK frequency in PBMCs. In a conclusion, our study for the first time demonstrates that leukocyte mtDNA content is an independent prognostic marker complementing TNM stage and associated with an ROS-mediated immunosuppressive phenotype in HCC patients. PMID:26985767

  3. Abnormal DNA content predicts the occurrence of carcinomas in non-dysplastic oral white patches.

    PubMed

    Sudbø, J; Ried, T; Bryne, M; Kildal, W; Danielsen, H; Reith, A

    2001-10-01

    The majority of oral squamous cell carcinomas (OSCCs) are preceded by visible changes in the oral mucosa, most often white patches. Although the histological finding of dysplasia in oral white patches signals increased risk of developing OSCC, this may also occur in non-dysplastic lesions. However, no reliable markers exist to predict the occurrence of OSCC in these patients. From a total of 263 patients diagnosed with oral white patches, biopsies from 45 patients were selected on the criteria that the patients had lesions histologically proven to be non-dysplastic. The lesions were analyzed with respect to their DNA content. The clinical outcome of the patients was known from the Cancer Registry of Norway, and these data were compared to the DNA content of their lesions. Among the 45 patients, five cases (11%) later developed an OSCC. Four of the cases that subsequently developed an OSCC were among the five aneuploid (abnormal) cases (P=0.001). One aneuploid lesion did not develop a carcinoma during a follow-up time of 120 months. The fifth case that subsequently developed an OSCC was diploid (normal), and developed into an OSCC after an observation time of 73 months (P=0.001). In conclusion, aberrant DNA content reliably predicts the occurrence of OSCC in patients that otherwise would be regarded as at very low risk. Normal DNA content indicates low risk. PMID:11564576

  4. Cytometric analysis of mammalian sperm for induced morphologic and DNA content errors

    SciTech Connect

    Pinkel, D.

    1983-06-27

    Some flow-cytometric and image analysis procedures under development for quantitative analysis of sperm morphology are reviewed. The results of flow-cytometric DNA-content measurements on sperm from radiation exposed mice are also summarized, the results related to the available cytological information, and their potential dosimetric sensitivity discussed. (ACR)

  5. Karyotype characterization and nuclear DNA content measurement in Bromeliaceae: state of the art and future perspectives.

    PubMed

    Nunes, Andrei C P; Clarindo, Wellington R

    2014-12-01

    In Bromeliaceae, cytogenetic and flow cytometry analyses have been performed to clarify systematic and evolutionary aspects. Karyotyping approaches have shown the relatively high chromosome number, similar morphology and small size of the chromosomes. These facts have prevented a correct chromosome counting and characterization. Authors have established a basic chromosome number of x = 25 for Bromeliaceae. Recently, one karyomorphological analysis revealed that x = 25 is no longer the basic chromosome number, whose genome may have a polyploid origin. Besides cytogenetic characterization, the 2C DNA content of bromeliads has been measured. Nuclear DNA content has varied from 2C = 0.60 to 2C = 3.34 picograms. Thus, in relation to most angiosperms, the 2C DNA content of Bromeliaceae species as well as their chromosome size can be considered relatively small. In spite of some advances, cytogenetic and flow cytometry data are extremely scarce in this group. In this context, this review reports the state of the art in karyotype characterization and nuclear DNA content measurement in Bromeliaceae, emphasizing the main problems and suggesting prospective solutions and ideas for future research. PMID:25590721

  6. Mucin-producing pancreatic tumors: a study of nuclear DNA content by flow cytometry.

    PubMed

    Murakami, Y; Yokoyama, T; Kodama, T; Takesue, Y; Okita, M; Nakamitsu, A; Imamura, Y; Santo, T; Tsumura, H; Miyamoto, K

    1993-01-01

    Nuclear DNA content in eight surgically resected mucin-producing pancreatic tumors (MPPT) consisting of two mucinous intraductal adenocarcinomas (MIDAC), two mucinous intraductal adenomas (MIDA), one mucinous cyst-adenocarcinoma (MCAC), and three mucinous cystadenomas (MCA) were measured by flow cytometry using paraffin-embedded tissue samples. The technique of Shutte was used for the preparation of paraffin-embedded tissue into single dissociated nuclei, while the method of Vindelov was used for staining the isolated nuclei with propidium iodine. Clinicopathologically, the four patients with MIDAC or MIDA were all male and had cystic lesions with a dilated pancreatic duct at the head of the pancreas, while the four patients with MCAC or MCA were all females and had cystic tumors at either the body or tail of the pancreas. All eight patients with MPPT had no metastasis to the regional lymph nodes and were all still alive without recurrence. In an analysis of nuclear DNA content, seven of eight patients had DNA diploid tumors while one patient with a MIDAC perforating the duodenum and choledochus had a DNA aneuploid tumor. Thus, these findings suggest that DNA diploid patterns in MPPT might be associated with a favorable prognosis in MPPT although some patients whose MPPT invaded the surrounding organs might have DNA aneuploid tumors. PMID:8395265

  7. DAPI-fluorescent fading: a problem in microscopy or a way to measure nuclear DNA content?

    NASA Astrophysics Data System (ADS)

    Gallardo-Escárate, Cristian; Álvarez-Borrego, Josué; Kober, V.; del Río-Portilla, Miguel Á.

    2006-01-01

    In observation by confocal or conventional fluorescence microscopy, the retardation of the lost in fluorescence, from highest signal of fluorescence to lowest intensity are important factors in order to obtain accurate images. This problem is very common in fluorochromes for nuclear DNA and especially for DAPI stain. The fluorescence of DAPI is rapidly lost when it is exposure to excitation by ultra violet (UV) light, and especially under optimal condition of observation. Although the fading process could be retardate by using of mounting medium with antifading solutions, the photochemical process underlying the fluorescence decay has not yet been fully explained. In addiction, neither relationship has been tested between the fluorescence fading and nuclear DNA content. However, the capacity of the DNA to absorb UV light is knows. In order to test this relationship we measured by means of image analysis the fluorescence intensity in several nuclei types during a fading period. The analysis was performed by an algorithm specifically built in MATLAB software. The relationship between nuclear DNA content and DAPI-fluorescence fading was found equal to 99%. This study demonstrates the feasibility for estimates genome size by quantification of fluorescence fading. In this context, the present method allows to measure nuclear DNA content in several medical applications (cancer, HIV, organ transplants, etc). Nowadays, for measuring DNA content, flow cytometry is widely used; however, with the flow cytometry method it is not possible to select a specific group of cells, such as from a specific region of a tumor. Moreover, the using of image analysis allows automatizing diagnostics procedures.

  8. Chromatin organisation in duckweed interphase nuclei in relation to the nuclear DNA content.

    PubMed

    Cao, H X; Vu, G T H; Wang, W; Messing, J; Schubert, I

    2015-01-01

    The accessibility of DNA during fundamental processes, such as transcription, replication and DNA repair, is tightly modulated through a dynamic chromatin structure. Differences in large-scale chromatin structure at the microscopic level can be observed as euchromatic and heterochromatic domains in interphase nuclei. Here, key epigenetic marks, including histone H3 methylation and 5-methylcytosine (5-mC) as a DNA modification, were studied cytologically to describe the chromatin organisation of representative species of the five duckweed genera in the context of their nuclear DNA content, which ranged from 158 to 1881 Mbp. All studied duckweeds, including Spirodela polyrhiza with a genome size and repeat proportion similar to that of Arabidopsis thaliana, showed dispersed distribution of heterochromatin signatures (5mC, H3K9me2 and H3K27me1). This immunolabelling pattern resembles that of early developmental stages of Arabidopsis nuclei, with less pronounced heterochromatin chromocenters and heterochromatic marks weakly dispersed throughout the nucleus.

  9. Effects of reduced mitochondrial DNA content on secondary mitochondrial toxicant exposure in Caenorhabditis elegans.

    PubMed

    Luz, Anthony L; Meyer, Joel N

    2016-09-01

    The mitochondrial genome (mtDNA) is intimately linked to cellular and organismal health, as demonstrated by the fact that mutations in and depletion of mtDNA result in severe mitochondrial disease in humans. However, cells contain hundreds to thousands of copies of mtDNA, which provides genetic redundancy, and creates a threshold effect in which a large percentage of mtDNA must be lost prior to clinical pathogenesis. As certain pharmaceuticals and genetic mutations can result in depletion of mtDNA, and as many environmental toxicants target mitochondria, it is important to understand whether reduced mtDNA will sensitize an individual to toxicant exposure. Here, using ethidium bromide (EtBr), which preferentially inhibits mtDNA replication, we reduced mtDNA 35-55% in the in vivo model organism Caenorhabditis elegans. Chronic, lifelong, low-dose EtBr exposure did not disrupt nematode development or lifespan, and induced only mild alterations in mitochondrial respiration, while having no effect on steady-state ATP levels. Next, we exposed nematodes with reduced mtDNA to the known and suspected mitochondrial toxicants aflatoxin B1, arsenite, paraquat, rotenone or ultraviolet C radiation (UVC). EtBr pre-exposure resulted in mild sensitization of nematodes to UVC and arsenite, had no effect on AfB1 and paraquat, and provided some protection from rotenone toxicity. These mixed results provide a first line of evidence suggesting that reduced mtDNA content may sensitize an individual to certain environmental exposures.

  10. Effects of reduced mitochondrial DNA content on secondary mitochondrial toxicant exposure in Caenorhabditis elegans.

    PubMed

    Luz, Anthony L; Meyer, Joel N

    2016-09-01

    The mitochondrial genome (mtDNA) is intimately linked to cellular and organismal health, as demonstrated by the fact that mutations in and depletion of mtDNA result in severe mitochondrial disease in humans. However, cells contain hundreds to thousands of copies of mtDNA, which provides genetic redundancy, and creates a threshold effect in which a large percentage of mtDNA must be lost prior to clinical pathogenesis. As certain pharmaceuticals and genetic mutations can result in depletion of mtDNA, and as many environmental toxicants target mitochondria, it is important to understand whether reduced mtDNA will sensitize an individual to toxicant exposure. Here, using ethidium bromide (EtBr), which preferentially inhibits mtDNA replication, we reduced mtDNA 35-55% in the in vivo model organism Caenorhabditis elegans. Chronic, lifelong, low-dose EtBr exposure did not disrupt nematode development or lifespan, and induced only mild alterations in mitochondrial respiration, while having no effect on steady-state ATP levels. Next, we exposed nematodes with reduced mtDNA to the known and suspected mitochondrial toxicants aflatoxin B1, arsenite, paraquat, rotenone or ultraviolet C radiation (UVC). EtBr pre-exposure resulted in mild sensitization of nematodes to UVC and arsenite, had no effect on AfB1 and paraquat, and provided some protection from rotenone toxicity. These mixed results provide a first line of evidence suggesting that reduced mtDNA content may sensitize an individual to certain environmental exposures. PMID:27566481

  11. Mitochondrial DNA content in breast cancer: Impact on in vitro and in vivo phenotype and patient prognosis

    PubMed Central

    Weerts, Marjolein J.A.; Sieuwerts, Anieta M.; Smid, Marcel; Look, Maxime P.; Foekens, John A.; Sleijfer, Stefan; Martens, John W.M.

    2016-01-01

    Reduced mitochondrial DNA (mtDNA) content in breast cancer cell lines has been associated with transition towards a mesenchymal phenotype, but its clinical consequences concerning breast cancer dissemination remain unidentified. Here, we aimed to clarify the link between mtDNA content and a mesenchymal phenotype and its relation to prognosis of breast cancer patients. We analyzed mtDNA content in 42 breast cancer cell lines and 207 primary breast tumor specimens using a combination of quantitative PCR and array-based copy number analysis. By associating mtDNA content with expression levels of genes involved in epithelial-to-mesenchymal transition (EMT) and with the intrinsic breast cancer subtypes, we could not identify a relation between low mtDNA content and mesenchymal properties in the breast cancer cell lines or in the primary breast tumors. In addition, we explored the relation between mtDNA content and prognosis in our cohort of primary breast tumor specimens that originated from patients with lymph node-negative disease who did not receive any (neo)adjuvant systemic therapy. When patients were divided based on the tumor quartile levels of mtDNA content, those in the lowest quarter (≤ 350 mtDNA molecules per cell) showed a poorer 10-year distant metastasis-free survival than patients with > 350 mtDNA molecules per cell (HR 0.50 [95% CI 0.29–0.87], P = 0.015). The poor prognosis was independent of established clinicopathological markers (HR 0.54 [95% CI 0.30–0.97], P = 0.038). We conclude that, despite a lack of evidence between mtDNA content and EMT, low mtDNA content might provide meaningful prognostic value for distant metastasis in breast cancer. PMID:27081694

  12. Variation in DNA content of blood cells of largemouth bass from contaminated and uncontaminated waters

    SciTech Connect

    Lingenfelser, S.F.; Dallas, C.E.; Jagoe, C.H.; Smith, M.H.; Brisbin, I.L. Jr.; Chesser, R.K.

    1997-10-01

    Largemouth bass (Micropterus salmoides) were collected from locations with and without documented histories of pollution in Georgia and South Carolina. Whole blood samples were collected from over 3,000 bass and analyzed by flow cytometry to measure changes in cellular DNA content and cell cycle distribution. The coefficient of variation (CV) of the cell cycle phase G{sub 0}G{sub 1} peak was used as a measure of variation in DNA content within an individual. The mean CV varied significantly among locations, and some locations with known chemical or radioactive contaminants had higher CVs. Plotting the frequency distribution of CV values for each site revealed greater skewness and kurtosis in most locations with known contaminants. In each case, a right skewness indicated higher proportions of bass with unusually high CV in these locations. Aneuploid-like patterns were detected in the DNA histograms of five fish, all from locations with histories of contamination. The percentage of cells distributed among phases of the cell cycle (G{sub 0}/G{sub 1}, S, and G{sub 2}M) varied significantly among locations, but there was no apparent relationship to contaminant distribution. Differences in CV and frequency of aneuploids among sites with and without histories of pollution were generally small, but increased variation in DNA content may be associated with contaminant exposure at some locations.

  13. Nuclear DNA Content Estimates in Green Algal Lineages: Chlorophyta and Streptophyta

    PubMed Central

    Kapraun, Donald F.

    2007-01-01

    Background and Aims Consensus higher-level molecular phylogenies present a compelling case that an ancient divergence separates eukaryotic green algae into two major monophyletic lineages, Chlorophyta and Streptophyta, and a residuum of green algae, which have been referred to prasinophytes or micromonadophytes. Nuclear DNA content estimates have been published for less than 1% of the described green algal members of Chlorophyta, which includes multicellular green marine algae and freshwater flagellates (e.g. Chlamydomonas and Volvox). The present investigation summarizes the state of our knowledge and adds substantially to our database of C-values, especially for the streptophyte charophycean lineage which is the sister group of the land plants. A recent list of 2C nuclear DNA contents for isolates and species of green algae is expanded by 72 to 157. Methods The DNA-localizing fluorochrome DAPI (4′,6-diamidino-2-phenylindole) and red blood cell (chicken erythrocytes) standard were used to estimate 2C values with static microspectrophotometry. Key Results In Chlorophyta, including Chlorophyceae, Prasinophyceae, Trebouxiophyceae and Ulvophyceae, 2C DNA estimates range from 0·01 to 5·8 pg. Nuclear DNA content variation trends are noted and discussed for specific problematic taxon pairs, including Ulotrichales–Ulvales, and Cladophorales–Siphonocladales. For Streptophyta, 2C nuclear DNA contents range from 0·2 to 6·4 pg, excluding the highly polyploid Charales and Desmidiales, which have genome sizes of up to 14·8 and 46·8 pg, respectively. Nuclear DNA content data for Streptophyta superimposed on a contemporary molecular phylogeny indicate that early diverging lineages, including some members of Chlorokybales, Coleochaetales and Klebsormidiales, have genomes as small as 0·1–0·5 pg. It is proposed that the streptophyte ancestral nuclear genome common to both the charophyte and the embryophyte lineages can be characterized as 1C = 0·2 pg and 1n = 6

  14. Gibberellic-acid-induced cell elongation in pea epicotyls: Effect on polyploidy and DNA content.

    PubMed

    Boeken, G; Van Oostveldt, P

    1977-01-01

    In gibberellic-acid(GA3)-treated epicotyls of dwarf peas (Pisum sativum L.) grown in the light, DNA (per cell and per epicotyl) is followed. Histofluorometric DNA determinations show that GA3-promoted cell elongation is not accompanied by increased endomitosis, but chemical estimations show an increased DNA content per epicotyl. This difference must therefore be the result of increased mitotic activity in the GA3-treated tissue. Epicotyls of seedlings grown with or without cotyledons under continuous light with GA3 are tetraploid, as are those of ecotylized embryos grown in darkness. These epicotyls reach no more than half the length of octaploid epicotyls of seedlings grown in darkness. This result provides evidence for a relationship between polyploidy and final possible cell length. PMID:24419898

  15. Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages.

    PubMed

    Goldfain, Aaron M; Garmann, Rees F; Jin, Yan; Lahini, Yoav; Manoharan, Vinothan N

    2016-07-01

    A complete understanding of the cellular pathways involved in viral infections will ultimately require a diverse arsenal of experimental techniques, including methods for tracking individual viruses and their interactions with the host. Here we demonstrate the use of holographic microscopy to track the position, orientation, and DNA content of unlabeled bacteriophages (phages) in solution near a planar, functionalized glass surface. We simultaneously track over 100 individual λ phages at a rate of 100 Hz across a 33 μm × 33 μm portion of the surface. The technique determines the in-plane motion of the phage to nanometer precision, and the height of the phage above the surface to 100 nm precision. Additionally, we track the DNA content of individual phages as they eject their genome following the addition of detergent-solubilized LamB receptor. The technique determines the fraction of DNA remaining in the phage to within 10% of the total 48.5 kilobase pairs. Analysis of the data reveals that under certain conditions, λ phages move along the surface with their heads down and intermittently stick to the surface by their tails, causing them to stand up. Furthermore, we find that in buffer containing high concentrations of both monovalent and divalent salts, λ phages eject their entire DNA in about 7 s. Taken together, these measurements highlight the potential of holographic microscopy to resolve the fast kinetics of the early stages of phage infection.

  16. Relevance of GC content to the conservation of DNA polymerase III/mismatch repair system in Gram-positive bacteria

    PubMed Central

    Akashi, Motohiro; Yoshikawa, Hirofumi

    2013-01-01

    The mechanism of DNA replication is one of the driving forces of genome evolution. Bacterial DNA polymerase III, the primary complex of DNA replication, consists of PolC and DnaE. PolC is conserved in Gram-positive bacteria, especially in the Firmicutes with low GC content, whereas DnaE is widely conserved in most Gram-negative and Gram-positive bacteria. PolC contains two domains, the 3′-5′exonuclease domain and the polymerase domain, while DnaE only possesses the polymerase domain. Accordingly, DnaE does not have the proofreading function; in Escherichia coli, another enzyme DnaQ performs this function. In most bacteria, the fidelity of DNA replication is maintained by 3′-5′ exonuclease and a mismatch repair (MMR) system. However, we found that most Actinobacteria (a group of Gram-positive bacteria with high GC content) appear to have lost the MMR system and chromosomes may be replicated by DnaE-type DNA polymerase III with DnaQ-like 3′-5′ exonuclease. We tested the mutation bias of Bacillus subtilis, which belongs to the Firmicutes and found that the wild type strain is AT-biased while the mutS-deletant strain is remarkably GC-biased. If we presume that DnaE tends to make mistakes that increase GC content, these results can be explained by the mutS deletion (i.e., deletion of the MMR system). Thus, we propose that GC content is regulated by DNA polymerase and MMR system, and the absence of polC genes, which participate in the MMR system, may be the reason for the increase of GC content in Gram-positive bacteria such as Actinobacteria. PMID:24062730

  17. Diet Assessment Based on Rumen Contents: A Comparison between DNA Metabarcoding and Macroscopy

    PubMed Central

    Nichols, Ruth V.; Åkesson, Mikael; Kjellander, Petter

    2016-01-01

    Dietary choices are central to our understanding of ecology and evolution. Still, many aspects of food choice have been hampered by time consuming procedures and methodological problems. Faster and cheaper methods, such as DNA metabarcoding, have therefore been widely adopted. However, there is still very little empirical support that this new method is better and more accurate compared to the classic methods. Here, we compare DNA metabarcoding to macroscopic identifications of rumen contents in two species of wild free-ranging ungulates: roe deer and fallow deer. We found that the methods were comparable, but they did not completely overlap. Sometimes the DNA method failed to identify food items that were found macroscopically, and the opposite was also true. However, the total number of taxa identified increased using DNA compared to the macroscopic analysis. Moreover, the taxonomic precision of metabarcoding was substantially higher, with on average 90% of DNA-sequences being identified to genus or species level compared to 75% of plant fragments using macroscopy. In niche overlap analyses, presence/absence data showed that both methods came to very similar conclusions. When using the sequence count data and macroscopic weight, niche overlap was lower than when using presence-absence data yet tended to increase when using DNA compared to macroscopy. Nevertheless, the significant positive correlation between macroscopic quantity and number of DNA sequences counted from the same plant group give support for the use of metabarcoding to quantify plants in the rumen. This study thus shows that there is much to be gained by using metabarcoding to quantitatively assess diet composition compared to macroscopic analysis, including higher taxonomic precision, sensitivity and cost efficiency. PMID:27322387

  18. Diet Assessment Based on Rumen Contents: A Comparison between DNA Metabarcoding and Macroscopy.

    PubMed

    Nichols, Ruth V; Åkesson, Mikael; Kjellander, Petter

    2016-01-01

    Dietary choices are central to our understanding of ecology and evolution. Still, many aspects of food choice have been hampered by time consuming procedures and methodological problems. Faster and cheaper methods, such as DNA metabarcoding, have therefore been widely adopted. However, there is still very little empirical support that this new method is better and more accurate compared to the classic methods. Here, we compare DNA metabarcoding to macroscopic identifications of rumen contents in two species of wild free-ranging ungulates: roe deer and fallow deer. We found that the methods were comparable, but they did not completely overlap. Sometimes the DNA method failed to identify food items that were found macroscopically, and the opposite was also true. However, the total number of taxa identified increased using DNA compared to the macroscopic analysis. Moreover, the taxonomic precision of metabarcoding was substantially higher, with on average 90% of DNA-sequences being identified to genus or species level compared to 75% of plant fragments using macroscopy. In niche overlap analyses, presence/absence data showed that both methods came to very similar conclusions. When using the sequence count data and macroscopic weight, niche overlap was lower than when using presence-absence data yet tended to increase when using DNA compared to macroscopy. Nevertheless, the significant positive correlation between macroscopic quantity and number of DNA sequences counted from the same plant group give support for the use of metabarcoding to quantify plants in the rumen. This study thus shows that there is much to be gained by using metabarcoding to quantitatively assess diet composition compared to macroscopic analysis, including higher taxonomic precision, sensitivity and cost efficiency. PMID:27322387

  19. DNA content alterations in Tetrahymena pyriformis macronucleus after exposure to food preservatives sodium nitrate and sodium benzoate.

    PubMed

    Loutsidou, Ariadni C; Hatzi, Vasiliki I; Chasapis, C T; Terzoudi, Georgia I; Spiliopoulou, Chara A; Stefanidou, Maria E

    2012-12-01

    The toxicity, in terms of changes in the DNA content, of two food preservatives, sodium nitrate and sodium benzoate was studied on the protozoan Tetrahymena pyriformis using DNA image analysis technology. For this purpose, selected doses of both food additives were administered for 2 h to protozoa cultures and DNA image analysis of T. pyriformis nuclei was performed. The analysis was based on the measurement of the Mean Optical Density which represents the cellular DNA content. The results have shown that after exposure of the protozoan cultures to doses equivalent to ADI, a statistically significant increase in the macronuclear DNA content compared to the unexposed control samples was observed. The observed increase in the macronuclear DNA content is indicative of the stimulation of the mitotic process and the observed increase in MOD, accompanied by a stimulation of the protozoan proliferation activity is in consistence with this assumption. Since alterations at the DNA level such as DNA content and uncontrolled mitogenic stimulation have been linked with chemical carcinogenesis, the results of the present study add information on the toxicogenomic profile of the selected chemicals and may potentially lead to reconsideration of the excessive use of nitrates aiming to protect public health.

  20. The relationships among IGF-1, DNA content, and protein accumulation during skeletal muscle hypertrophy

    NASA Technical Reports Server (NTRS)

    Adams, G. R.; Haddad, F.

    1996-01-01

    Insulin-like growth factor-1 (IGF-1) is known to have anabolic effects on skeletal muscle cells. This study examined the time course of muscle hypertrophy and associated IGF-1 peptide and mRNA expression. Data were collected at 3, 7, 14, and 28 days after surgical removal of synergistic muscles of both normal and hypophysectomized (HX) animals. Overloading increased the plantaris (Plant) mass, myofiber size, and protein-to-body weight ratio in both groups (normal and HX; P < 0.05). Muscle IGF-1 peptide levels peaked at 3 (normal) and 7 (HX) days of overloading with maximum 4.1-fold (normal) and 6.2-fold (HX) increases. Increases in muscle IGF-1 preceded the hypertrophic response. Total DNA content of the overloaded Plant increased in both groups. There was a strong positive relationship between IGF-1 peptide and DNA content in the overloaded Plant from both groups. These results indicate that 1) the muscles from rats with both normal and severely depressed systemic levels of IGF-1 respond to functional overload with an increase in local IGF-1 expression and 2) this elevated IGF-1 may be contributing to the hypertrophy response, possibly via the mobilization of satellite cells to provide increases in muscle DNA.

  1. Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents.

    PubMed

    Paula, Débora P; Linard, Benjamin; Crampton-Platt, Alex; Srivathsan, Amrita; Timmermans, Martijn J T N; Sujii, Edison R; Pires, Carmen S S; Souza, Lucas M; Andow, David A; Vogler, Alfried P

    2016-01-01

    Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks. PMID:27622637

  2. Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents

    PubMed Central

    Paula, Débora P.; Linard, Benjamin; Crampton-Platt, Alex; Srivathsan, Amrita; Timmermans, Martijn J. T. N.; Sujii, Edison R.; Pires, Carmen S. S.; Souza, Lucas M.; Andow, David A.; Vogler, Alfried P.

    2016-01-01

    Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks. PMID:27622637

  3. DNA content in reactive hyperplasia, precancerosis, and carcinomas of the oral cavity. A cytophotometric study.

    PubMed

    Doseva, D; Christov, K; Kristeva, K

    1984-01-01

    Cytophotometry has been used to study DNA content in oral epithelial cells of Feulgen-stained specimens from a total of 43 patients: 3 with erythema exudativum multiforme (EEM), 5 with pemphigus, 3 with stomatitis aphtosa, 5 with lichen ruber planus, 8 with leukoplakia, and 19 with carcinomas. In contrast to reactive hyperplasia (EEM, pemphigus, stomatitis aphthosa) leukoplakia has histograms closest to those of carcinoma, with a high percentage of cells in the polyploid regions. This emphasizes the significance of cytophotometry for diagnosis of preneoplastic and neoplastic lesions of the oral cavity.

  4. Direct interrogation of DNA content distribution in nanoparticles by a novel microfluidics-based single-particle analysis.

    PubMed

    Beh, Cyrus W; Pan, Deng; Lee, Jason; Jiang, Xuan; Liu, Kelvin J; Mao, Hai-Quan; Wang, Tza-Huei

    2014-08-13

    Nonviral gene delivery holds great promise not just as a safer alternative to viral vectors in traditional gene therapy applications, but also for regenerative medicine, induction of pluripotency in somatic cells, and RNA interference for gene silencing. Although it continues to be an active area of research, there remain many challenges to the rational design of vectors. Among these, the inability to characterize the composition of nanoparticles and its distribution has made it difficult to probe the mechanism of gene transfection process, since differences in the nanoparticle-mediated transfection exist even when the same vector is used. There is a lack of sensitive methods that allow for full characterization of DNA content in single nanoparticles and its distribution among particles in the same preparation. Here we report a novel spectroscopic approach that is capable of interrogating nanoparticles on a particle-by-particle basis. Using PEI/DNA and PEI-g-PEG/DNA nanoparticles as examples, we have shown that the distribution of DNA content among these nanoparticles was relatively narrow, with the average numbers of DNA of 4.8 and 6.7 per particle, respectively, in PEI/DNA and PEI-g-PEG/DNA nanoparticles. This analysis enables a more accurate description of DNA content in polycation/DNA nanoparticles. It paves the way toward comparative assessments of various types of gene carriers and provides insights into bridging the efficiency gap between viral and nonviral vehicles.

  5. SYBR Green-activated sorting of Arabidopsis pollen nuclei based on different DNA/RNA content.

    PubMed

    Schoft, Vera K; Chumak, Nina; Bindics, János; Slusarz, Lucyna; Twell, David; Köhler, Claudia; Tamaru, Hisashi

    2015-03-01

    Key message: Purification of pollen nuclei. Germ cell epigenetics is a critical topic in plants and animals. The male gametophyte (pollen) of flowering plants is an attractive model to study genetic and epigenetic reprogramming during sexual reproduction, being composed of only two sperm cells contained within, its companion, vegetative cell. Here, we describe a simple and efficient method to purify SYBR Green-stained sperm and vegetative cell nuclei of Arabidopsis thaliana pollen using fluorescence-activated cell sorting to analyze chromatin and RNA profiles. The method obviates generating transgenic lines expressing cell-type-specific fluorescence reporters and facilitates functional genomic analysis of various mutant lines and accessions. We evaluate the purity and quality of the sorted pollen nuclei and analyze the technique's molecular basis. Our results show that both DNA and RNA contents contribute to SYBR Green-activated nucleus sorting and RNA content differences impact on the separation of sperm and vegetative cell nuclei. We demonstrate the power of the approach by sorting wild-type and polyploid mutant sperm and vegetative cell nuclei from mitotic and meiotic mutants, which is not feasible using cell-type-specific transgenic reporters. Our approach should be applicable to pollen nuclei of crop plants and possibly to cell/nucleus types and cell cycle phases of different species containing substantially different amounts of DNA and/or RNA.

  6. Condylomata acuminata of the urinary bladder. Natural history, viral typing, and DNA content.

    PubMed

    Del Mistro, A; Koss, L G; Braunstein, J; Bennett, B; Saccomano, G; Simons, K M

    1988-03-01

    Three patients with condylomata acuminata of the urinary bladder are reported. Two of the patients were immunosuppressed, and one had longstanding extensive condylomata acuminata of the external genitalia and adjacent areas. All lesions recurred at least once and were difficult to treat. The diagnosis was confirmed by in situ hybridization on archival material with human papillomavirus (HPV) DNA probes under stringent conditions. In two of the patients, probes for HPV types 6 and 11 were positive; HPV 11 only was identified in one patient. Probes for HPV types 16 and 18 and pBR322 vector controls were negative. In one patient with a strong hybridization signal, the lesion was also positive for common papillomavirus antigen. DNA content measured by cytophotometry of Feulgen-stained whole nuclei isolated from lesions in two patients revealed a markedly aneuploid DNA pattern. Whether this is a factor in the behavior of the lesions is not known at this time. Although rare, HPV infection of the urinary bladder may result in widespread condylomatosis and may mimic giant condylomas of Buschke-Löwenstein or even verrucous carcinomas, sometimes necessitating radical treatment. Nevertheless, until there is proof to the contrary, the lesions must be considered benign and should not be confused with squamous cancer of the bladder.

  7. Mitochondrial DNA and STR analyses for human DNA from maggots crop contents: a forensic entomology case from central-southern China.

    PubMed

    Li, X; Cai, J F; Guo, Y D; Xiong, F; Zhang, L; Feng, H; Meng, F M; Fu, Y; Li, J B; Chen, Y Q

    2011-08-01

    Insect larvae and adult insects found on human corpses can provide important forensic evidence however it is useful to be able to prove evidence of association. Without this, it could be claimed that the insect evidence was a contaminant or had been planted on the body. This paper describes how mitochondrial DNA (mtDNA) and STR analysis of the crop contents of larvae of the blowfly Aldrichina grahami collected from separated body parts was used to provide evidence of association.

  8. Association of 5-methylcytosine and 5-hydroxymethylcytosine with mitochondrial DNA content and clinical and biochemical parameters in hepatocellular carcinoma.

    PubMed

    Shen, Fan; Huang, Wei; Qi, Jia-Hui; Yuan, Bi-Feng; Huang, Jing-Tao; Zhou, Xin; Feng, Yu-Qi; Liu, Ying-Juan; Liu, Song-Mei

    2013-01-01

    Increasing epidemiological evidence has indicated that inherited variations of mitochondrial DNA (mtDNA) copy number affect the genetic susceptibility of many malignancies in a tumour-specific manner and that DNA methylation also plays an important role in controlling gene expression during the differentiation and development of hepatocellular carcinoma (HCC). Our previous study demonstrated that HCC tissues showed a lower 5-hydroxymethylcytosine (5-hmC) content when compared to tumour-adjacent tissues, but the relationship among 5-hmC, 5-methylcytosine (5-mC) and mtDNA content in HCC patients is still unknown. This study aimed to clarify the correlation among mtDNA content, 5-mC and 5-hmC by quantitative real-time PCR and liquid chromatography tandem mass spectrometry analysis. We demonstrated that 5-hmC correlated with tumour size [odds ratio (OR) 0.847, 95% confidence interval (CI) 0.746-0.962, P = 0.011], and HCC patients with a tumour size ≥ 5.0 cm showed a lower 5-hmC content and higher levels of fasting plasma aspartate aminotransferase, the ratio of alanine aminotransferase to aspartate aminotransferase, γ-glutamyltransferase, alpha-fetoprotein than those with a tumour size <5 cm (all P<0.05). We further revealed that the mtDNA content of HCC tumour tissues was 225.97(105.42, 430.54) [median (25th Percentile, 75th Percentile)] and was negatively correlated with 5-mC content (P = 0.035), but not 5-hmC content, in genomic DNA from HCC tumour tissues. PMID:24143196

  9. Independent effects of leaf growth and light on the development of the plastid and its DNA content in Zea species.

    PubMed

    Zheng, Qi; Oldenburg, Delene J; Bendich, Arnold J

    2011-05-01

    In maize (Zea mays L.), chloroplast development progresses from the basal meristem to the mature leaf tip, and light is required for maturation to photosynthetic competence. During chloroplast greening, it was found that chloroplast DNA (cpDNA) is extensively degraded, falling to undetectable levels in many individual chloroplasts for three maize cultivars, as well as Zea mexicana (the ancestor of cultivated maize) and the perennial species Zea diploperennis. In dark-grown maize seedlings, the proplastid-to-etioplast transition is characterized by plastid enlargement, cpDNA replication, and the retention of high levels of cpDNA. When dark-grown seedlings are transferred to white light, the DNA content per plastid increases slightly during the first 4 h of illumination and then declines rapidly to a minimum at 24 h during the etioplast-to-chloroplast transition. Plastid autofluorescence (from chlorophyll) continues to increase as cpDNA declines, whereas plastid size remains constant. It is concluded that the increase in cpDNA that accompanies plastid enlargement is a consequence of cell and leaf growth, rather than illumination, whereas light stimulates photosynthetic capacity and cpDNA instability. When cpDNA from total tissue was monitored by blot hybridization and real-time quantitative PCR, no decline following transfer from dark to light was observed. The lack of agreement between DNA per plastid and cpDNA per cell may be attributed to nupts (nuclear sequences of plastid origin).

  10. Diosgenin contents and DNA fingerprint screening of various yam (Dioscorea sp.) genotypes.

    PubMed

    Vendl, Oliver; Wawrosch, Christoph; Noe, Christian; Molina, Carlos; Kahl, Günter; Kopp, Brigitte

    2006-01-01

    In addition to the importance of many Dioscorea species (yams) as starchy staple food, some representatives are known and still used as a source for the steroidal sapogenin diosgenin, which, besides phytosterols derived from tall-oil, is an important precursor for partial synthesis of steroids for pharmaceutical research and applications. While in edible yams the diosgenin content should be as low as possible, a high yield of the compound is preferable for cultivars which are grown for the extraction of sterols. In the past, miscalculations and insufficiently precise techniques for quantification of diosgenin prevailed. Therefore we set out to re-evaluate the steroid content of a world collection of Dioscorea species, using leaves as sample material. We optimized diosgenin quantification techniques and fingerprinted the whole collection with the DNA amplification fingerprinting (DAF) technique. Total diosgenin contents ranged from 0.04 to 0.93% of dry weight within the collection. Several Dioscorea cultivars can be characterized via their DAF fingerprint patterns.

  11. Nuclear DNA content affects the productivity of conifer forests by altering hydraulic architecture

    NASA Astrophysics Data System (ADS)

    Alday, Josu; Resco de Dios, Víctor

    2014-05-01

    Predictions of future global climate rely on feedbacks between terrestrial vegetation and the global carbon cycle, but the exact mechanisms underlying this relationship are still being discussed. One of the key knowledge gaps lies on the scaling of cellular processes to the ecosystem level. Here we examine whether an under-explored plant trait, inter-specific variation in the bulk amount of DNA in unreplicated somatic cells (2C DNA content), can explain inter-specific variation in the maximum productivity of conifer forests. We expected 2C DNA content to be negatively related to conifer productivity because: 1) it is positively correlated with cell volume (which, in turn, potentially affects structural features such as leaf mass area, a strong predictor of photosynthetic capacity); 2) it is positively correlated with stomatal size (with larger stomata leading to lower overall stomatal conductance and, by extension, lower CO2 uptake); and 3) larger genome sizes may reduce P availability in RNA (which has been hypothesized to slow growth). We present the results of regression and independent contrasts in different monospecific forests encompassing a 52º latitudinal gradient, each being dominated by 1 of 35 different conifer species. Contrary to expectations, we observed a positive correlation between genome size and maximum Gross Primary Productivity (R2 = 0.47) and also between genome size maximum tree height (R2 = 0.27). This correlation was apparently driven by the effects of genome size on stem hydraulics, since 2C DNA was positively correlated with wood density (R2 = 0.40) and also with resistance to cavitation (P50, R2 = 0.28). That is, increased genome sizes have a positive effect on the productivity of conifer forests by affecting the vascular tissues to increase their capacity for water transport. Our results shed a new light on the evolution of the vascular system of conifer forests and how they affect ecosystem productivity, and indicate the potential to

  12. The prognostic significance of determining DNA content in breast cancer by DNA image cytometry: the role of high grade aneuploidy in node negative breast cancer

    PubMed Central

    Yildirim‐Assaf, Selma; Coumbos, Alexandra; Hopfenmüller, Werner; Foss, Hans‐Dieter; Stein, Harald; Kühn, Wolfgang

    2007-01-01

    Aim To investigate the role of DNA aneuploidy, particularly in patients with node negative breast cancer, in order to identify the different risk profiles within the pool of heterogeneous breast cancers. Methods Imprint smears from 370 breast carcinomas were Feulgen‐stained and measured by DNA image analysis. DNA aneuploidy was graded by the amount of aneuploid cells (DNA content >5c) and highly aneuploid cells (DNA content >9c) in a breast tumour population. These results were correlated to the clinical long‐term follow‐up. A statistical cut‐off value of >10 aneuploid cells (>5c) and of >1 highly aneuploid cell (>9c) was evaluated as significant for disease‐free survival (DFS) and overall survival (OS). Results Subgroups among patients with breast cancer with aneuploid cells below the cut‐off value showed a significantly longer DFS and OS than those with aneuploid cells above this value. Patients with node negative breast cancer with >10 aneuploid cells (>5c) and >1 highly aneuploid cell (>9c) showed an unfavourable prognosis similar to patients with node positive breast cancer with <10 aneuploid cells (>5c) and <1 highly aneuploid tumour cell (>9c) in DFS and OS. Conclusion Nuclear DNA content, as an objective marker of tumour aggressiveness, provides prognostic information in patients with both node negative and node positive breast cancer. Based on DNA aneuploidy, the clinically inhomogeneous group of patients with node negative breast cancer can be stratified into low‐risk and high‐risk subgroups. Therefore, DNA ploidy analysis may identify high‐risk patients with lymph node negative breast cancer who might benefit from additional adjuvant therapy. PMID:17557867

  13. Karyological Features of Achyrocline (Asteraceae, Gnaphalieae): stable karyotypes, low DNA content variation and linkage of rRNA genes.

    PubMed

    Mazzella, C; Rodríguez, M; Vaio, M; Gaiero, P; López-Carro, B; Santiñaque, F F; Folle, G A; Guerra, M

    2010-01-01

    Many Achyrocline (Asteraceae, tribe Gnaphalieae) species are widely used in Argentina, Brazil and Uruguay as popular medicinal and aromatic plants. Achyrocline flaccida, A. satureioides, A. alata, and A. crassiuscula are distributed in Uruguay and popularly known as 'marcelas'. In order to characterize them, we performed chromosome counts, compared the karyotypes, mapped the 5S and 45S rDNA sites by fluorescent in situ hybridization, and estimated their DNA content. All species were diploid with 2n = 28 chromosomes, this being the first report for A. flaccida and A. crassiuscula. All species showed symmetrical karyotypes composed exclusively of biarmed chromosomes. DNA content estimated by flow cytometry revealed 2C values ranging from 5.73 to 6.03 pg, the amounts for A. alata and A. crassiuscula being higher than those for the other species. Cytogenetic mapping of 5S and 45S rDNA sequences in three species, A. flaccida, A. satureioides and A. alata, showed that in these species both sites co-localized in the pericentromeric region of chromosome 10. This site corresponds to the only DAPI(-) and CMA(+) band of their genomes. Southern blot hybridization of 5S and 45S rDNA on BamHI digested genomic DNA confirmed the tight linkage of these rDNA families into a single unit. Cytological data indicate that Achyrocline species are karyologically poorly differentiated, whereas the uncommon distribution of 5S and 45S rDNA suggests a close relationship with other genera of the Anthemidae tribe.

  14. Analysis of nuclear DNA content in Capsicum (Solanaceae) by flow cytometry and Feulgen densitometry.

    PubMed

    Moscone, Eduardo A; Baranyi, Monika; Ebert, Irma; Greilhuber, Johann; Ehrendorfer, Friedrich; Hunziker, Armando T

    2003-07-01

    Flow cytometric measurements of nuclear DNA content were performed using ethidium bromide as the DNA stain (internal standard, Hordeum vulgare 'Ditta', 1C = 5.063 pg) in 25 samples belonging to nine diploid species and four varieties of Capsicum: C. chacoense, C. parvifolium, C. frutescens, C. chinense, C. annuum var. annuum, C. baccatum var. baccatum, C. baccatum var. pendulum, C. baccatum var. umbilicatum, C. eximium and C. pubescens, all with 2n = 24, and C. campylopodium with 2n = 26. In addition, one sample each of C. annuum var. annuum and C. pubescens were also analysed using Feulgen densitometry (standard, Allium cepa 'Stuttgarter Riesen', 1C = 16.75 pg). Both staining methods resulted in very similar relative values. Genome size displays significant variation between but not within species (except in C. campylopodium), and contributes to their taxonomic grouping. 1C-values range from 3.34-3.43 pg (3273-3361 Mbp) in C. chacoense and the C. annuum complex to 4.53-5.77 pg (4439-5655 Mbp) in C. campylopodium and C. parvifolium. The data obtained support conclusions on phylogenetic relationships in the genus derived from karyotype analyses using chromosome banding approaches. In Capsicum, constitutive heterochromatin amount is correlated with genome size, except in C. parvifolium, and is regarded as an additive genomic component.

  15. Prenatal Ambient Air Pollution, Placental Mitochondrial DNA Content, and Birth Weight in the INMA (Spain) and ENVIRONAGE (Belgium) Birth Cohorts

    PubMed Central

    Clemente, Diana B.P.; Casas, Maribel; Vilahur, Nadia; Begiristain, Haizea; Bustamante, Mariona; Carsin, Anne-Elie; Fernández, Mariana F.; Fierens, Frans; Gyselaers, Wilfried; Iñiguez, Carmen; Janssen, Bram G.; Lefebvre, Wouter; Llop, Sabrina; Olea, Nicolás; Pedersen, Marie; Pieters, Nicky; Santa Marina, Loreto; Souto, Ana; Tardón, Adonina; Vanpoucke, Charlotte; Vrijheid, Martine; Sunyer, Jordi; Nawrot, Tim S.

    2015-01-01

    Background: Mitochondria are sensitive to environmental toxicants due to their lack of repair capacity. Changes in mitochondrial DNA (mtDNA) content may represent a biologically relevant intermediate outcome in mechanisms linking air pollution and fetal growth restriction. Objective: We investigated whether placental mtDNA content is a possible mediator of the association between prenatal nitrogen dioxide (NO2) exposure and birth weight. Methods: We used data from two independent European cohorts: INMA (n = 376; Spain) and ENVIRONAGE (n = 550; Belgium). Relative placental mtDNA content was determined as the ratio of two mitochondrial genes (MT-ND1 and MTF3212/R3319) to two control genes (RPLP0 and ACTB). Effect estimates for individual cohorts and the pooled data set were calculated using multiple linear regression and mixed models. We also performed a mediation analysis. Results: Pooled estimates indicated that a 10-μg/m3 increment in average NO2 exposure during pregnancy was associated with a 4.9% decrease in placental mtDNA content (95% CI: –9.3, –0.3%) and a 48-g decrease (95% CI: –87, –9 g) in birth weight. However, the association with birth weight was significant for INMA (–66 g; 95% CI: –111, –23 g) but not for ENVIRONAGE (–20 g; 95% CI: –101, 62 g). Placental mtDNA content was associated with significantly higher mean birth weight (pooled analysis, interquartile range increase: 140 g; 95% CI: 43, 237 g). Mediation analysis estimates, which were derived for the INMA cohort only, suggested that 10% (95% CI: 6.6, 13.0 g) of the association between prenatal NO2 and birth weight was mediated by changes in placental mtDNA content. Conclusion: Our results suggest that mtDNA content can be one of the potential mediators of the association between prenatal air pollution exposure and birth weight. Citation: Clemente DB, Casas M, Vilahur N, Begiristain H, Bustamante M, Carsin AE, Fernández MF, Fierens F, Gyselaers W, Iñiguez C, Janssen BG

  16. Assessment of heavy metal content and DNA damage in Hypsiboas faber (anuran amphibian) in coal open-casting mine.

    PubMed

    Zocche, Jairo José; Damiani, Adriani Paganini; Hainzenreder, Giana; Mendonça, Rodrigo Ávila; Peres, Poliana Bernardo; Santos, Carla Eliete Iochims Dos; Debastiani, Rafaela; Dias, Johnny Ferraz; Andrade, Vanessa Moraes de

    2013-07-01

    The aims of the study were to determine the heavy metal content in the tissues of Hypsiboas faber from a coal mining area and to compare the DNA damage in the blood cells of these animals with that of animals living in an unpolluted area. The heavy metal content was detected according to the technique of Particle-Induced X-ray Emission (PIXE) and the DNA damage was assessed by the Comet assay. Our results reveal that the specimens of H. faber collected from the coal mining area exhibited elements of order Fe>Cu>Al>Zn>Rb>Mn>Br, independently of the organ. The values of Comet assay parameters (DNA damage index and DNA damage frequency) were significantly higher in specimens collected from the coal mining area than in the reference animals. Our study concludes that the coal mining residues are genotoxic to amphibians and may have adverse effects on soil, water, vegetation and wild animals.

  17. Correlations of geographic distribution and temperature of embryonic development with the nuclear DNA content in the Salamandridae (Urodela, Amphibia).

    PubMed

    Litvinchuk, Spartak N; Rosanov, Jury M; Borkin, Leo J

    2007-04-01

    We used flow cytometry to measure the nuclear DNA content in erythrocytes of 27 salamandrid species. Across these species, diploid genome size varied more than 2 fold (51.3-104.4 pg). According to genome size and geographic distribution, 3 groups of newt species were recognized: West Palearctics with smaller amounts of nuclear DNA; Nearctic, with intermediate values; and East Asiatic, with higher genome sizes. Viviparous West Palearctic salamanders differed from most of the oviparous West Palearctic newts in possessing larger genome sizes. The nuclear DNA content strongly correlates with species range limits. At the same temperature, embryos of salamandrid species with larger genome sizes have a markedly longer developmental time than those with smaller genomes. We present an analysis of the relationships between the amount of nuclear DNA and water temperature at the breeding sites.

  18. Improved DNA content histograms from formalin-fixed, paraffin-embedded liver tissue by proteinase K digestion.

    PubMed

    Albro, J; Bauer, K D; Hitchcock, C L; Wittwer, C T

    1993-01-01

    An improved method for the enzymatic digestion of formalin-fixed, paraffin-embedded liver tissue for DNA content analysis by flow cytometry is presented. Forty samples of histologically normal liver were alternately digested by the traditional pepsin method or a new method utilizing proteinase K and heat. Sixteen (40%) of the pepsin-digested samples had apparent DNA aneuploid peaks by flow cytometry. False DNA aneuploid peaks were not present in any of the histograms obtained after proteinase K digestion. Microscopy showed that the pepsin-digested samples had residual cytoplasmic remnants which contained fluorescent material. Samples digested with proteinase K had few cytoplasmic remnants. The average G0/G1 coefficient of variation after proteinase K treatment was lower (41%) and the fluorescent intensity higher (128%) than the pepsin-treated samples. The apparent mean S-phase (a combination of S-phase cells and underlying debris) after proteinase K digestion was 35% of the pepsin-treated samples. Primary and secondary tumors of the liver that were DNA aneuploid after pepsin treatment were also DNA aneuploid after proteinase K treatment. A modified digestion protocol utilizing proteinase K and heat can provide superior results for DNA content analysis of formalin-fixed, paraffin-embedded liver tissue.

  19. The relationship between nuclear DNA content in salivary gland tumors and prognosis. Comparison of mucoepidermoid tumors and acinic cell tumors.

    PubMed

    Hamper, K; Caselitz, J; Arps, H; Askensten, U; Auer, G; Seifert, G

    1989-01-01

    Differences in prognosis between salivary gland mucoepidermoid tumors and acinic cell tumors were compared by means of conventional histopathological grading and nuclear DNA content which was assessed cytochemically by a scanning cytophotometric procedure. The mucoepidermoid tumors were found to show a stronger correlation between histopathological grading and prognosis than did the acinic cell tumors. By using DNA quantification, valuable additional information could be obtained for predicting the behavior of the mucoepidermoid tumors, whereas there was no correlation between DNA content and prognosis for the acinic cell tumors. Regarding the relatively "benign" clinical course of most mucoepidermoid tumors, the term "tumor"--as proposed by the World Health Organization's classification--seems appropriate. In contrast, the more severe clinical courses of the acinic cell tumors justify the use of the term "carcinoma" instead.

  20. DNA content and differentiation of root apical cells of Brassica rapa plants grown in microgravity.

    PubMed

    Kordyum, E L; Martin, G I; Zaslavsky, V A; Jiao, S; Hilaire, E; Guikema, J A

    1999-07-01

    Root cap is proposed to be a graviperceptive tissue in the plant root, and it is composed of several cell types. One such cell type, the columella cells, are thought to initiate the gravity-induced signal transduction cascade, and these cells arise from the activity of the meristematic zone of the root cap. There is, in fact, a continuum of cells in the central column of the root cap representing the meristematic cells, developing columella cells, mature cells, and those that will soon be sloughed off into the soil. In order to study the functional roles of the root cap cells in gravity-sensing, we compared the ultrastructural organization, differentiation, and DNA content in the meristematic, elongating, and differentiating cells of root tips in Brassica rapa plants grown in space microgravity and at 1g. The experiments were also designed to determine the reactions of root cap cells in both main roots (in which the original root cap was present in an embryonic form within the seed) and lateral roots (in which the root cap formed completely in space after seed germination on orbit) to the space microgravity. This study (ROOTS) was performed in collaboration with the B-PAC experiment on the Space shuttle "Columbia" mission STS-87 (Collaborative US/Ukrainian Experiment (CUE) during November 19-December 5, 1997.

  1. Effect of section thickness on quality of flow cytometric DNA content determinations in paraffin-embedded tissues.

    PubMed

    Stephenson, R A; Gay, H; Fair, W R; Melamed, M R

    1986-01-01

    DNA content determinations were carried out by flow cytometry on nuclear suspensions prepared from the same paraffin-embedded tissue block for each of eight surgically resected human carcinomas at section thicknesses of 5,10,20,30,40,50, and 100 millimicrons. Flow cytometric DNA determinations were also obtained on fresh tissue specimens in four of the eight carcinomas. As section thickness decreased below 50 millimicrons, there was a progressive increase in the histogram baseline noise at low DNA values and a decrease in the relative peak height of aneuploid DNA. The former was attributed to an increase of nuclear fragments in thinner sections, and the latter to the greater probability of transection of the larger aneuploid cells within a specimen. Both artifacts were minimized at section thickness of 50 millimicrons or greater.

  2. Stable isotope probing with 15N achieved by disentangling the effects of genome G+C content and isotope enrichment on DNA density.

    PubMed

    Buckley, Daniel H; Huangyutitham, Varisa; Hsu, Shi-Fang; Nelson, Tyrrell A

    2007-05-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool that can identify the functional capabilities of noncultivated microorganisms as they occur in microbial communities. While it has been suggested previously that nucleic acid SIP can be performed with 15N, nearly all applications of this technique to date have used 13C. Successful application of SIP using 15N-DNA (15N-DNA-SIP) has been limited, because the maximum shift in buoyant density that can be achieved in CsCl gradients is approximately 0.016 g ml-1 for 15N-labeled DNA, relative to 0.036 g ml-1 for 13C-labeled DNA. In contrast, variation in genome G+C content between microorganisms can result in DNA samples that vary in buoyant density by as much as 0.05 g ml-1. Thus, natural variation in genome G+C content in complex communities prevents the effective separation of 15N-labeled DNA from unlabeled DNA. We describe a method which disentangles the effects of isotope incorporation and genome G+C content on DNA buoyant density and makes it possible to isolate 15N-labeled DNA from heterogeneous mixtures of DNA. This method relies on recovery of "heavy" DNA from primary CsCl density gradients followed by purification of 15N-labeled DNA from unlabeled high-G+C-content DNA in secondary CsCl density gradients containing bis-benzimide. This technique, by providing a means to enhance separation of isotopically labeled DNA from unlabeled DNA, makes it possible to use 15N-labeled compounds effectively in DNA-SIP experiments and also will be effective for removing unlabeled DNA from isotopically labeled DNA in 13C-DNA-SIP applications.

  3. Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density▿ †

    PubMed Central

    Buckley, Daniel H.; Huangyutitham, Varisa; Hsu, Shi-Fang; Nelson, Tyrrell A.

    2007-01-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool that can identify the functional capabilities of noncultivated microorganisms as they occur in microbial communities. While it has been suggested previously that nucleic acid SIP can be performed with 15N, nearly all applications of this technique to date have used 13C. Successful application of SIP using 15N-DNA (15N-DNA-SIP) has been limited, because the maximum shift in buoyant density that can be achieved in CsCl gradients is approximately 0.016 g ml−1 for 15N-labeled DNA, relative to 0.036 g ml−1 for 13C-labeled DNA. In contrast, variation in genome G+C content between microorganisms can result in DNA samples that vary in buoyant density by as much as 0.05 g ml−1. Thus, natural variation in genome G+C content in complex communities prevents the effective separation of 15N-labeled DNA from unlabeled DNA. We describe a method which disentangles the effects of isotope incorporation and genome G+C content on DNA buoyant density and makes it possible to isolate 15N-labeled DNA from heterogeneous mixtures of DNA. This method relies on recovery of “heavy” DNA from primary CsCl density gradients followed by purification of 15N-labeled DNA from unlabeled high-G+C-content DNA in secondary CsCl density gradients containing bis-benzimide. This technique, by providing a means to enhance separation of isotopically labeled DNA from unlabeled DNA, makes it possible to use 15N-labeled compounds effectively in DNA-SIP experiments and also will be effective for removing unlabeled DNA from isotopically labeled DNA in 13C-DNA-SIP applications. PMID:17369331

  4. Adsorption of DNA on colloidal Ag nanoparticles: effects of nanoparticle surface charge, base content and length of DNA.

    PubMed

    Abbasian, Sara; Moshaii, Ahmad; Nikkhah, Maryam; Farkhari, Nahid

    2014-04-01

    The adsorption of single and double stranded DNA on colloidal silver nanoparticles has been studied to investigate the effects of surface charge of the nanoparticles, the composition of the oligonucleotide and its length on the adsorption characteristics. The results explain that the nanoparticle surface charge is a key parameter determining the propensity of oligonucleotides to adsorb on nanoparticles. The adsorption also depends on the length and composition of oligonucleotide. The protective effects of both single and double stranded DNA against salt-induced aggregation dramatically increase as the DNA length increases. In contrast to other available reports, we observed that long oligonucleotides (single-stranded and double stranded) can well be adsorbed on the nanoparticles as the short ones leading to almost complete protection of nanoparticles against salt induced aggregation and hence are not suitable for the sensing applications. Finally, the light scattering from the Ag nanoparticles has been simulated and the results compared with the experiments. Our understanding should improve development of colorimetric assays for DNA detection based on aggregation of unmodified metallic nanoparticles.

  5. Detection of genetically modified maize DNA fragments in the intestinal contents of pigs fed StarLink CBH351.

    PubMed

    Chowdhury, E H; Mikami, O; Nakajima, Y; Hino, A; Kuribara, H; Suga, K; Hanazumi, M; Yomemochi, C

    2003-03-01

    We tried to detect DNA fragments derived from maize in the intestinal contents of pigs fed genetically modified (GM) StarLink CBH351 maize (SL) or non-GM maize. Intestinal contents of 8 SL and 8 non-GM maize-fed pigs were collected at slaughter, and the genes of the recombinant cry9C and the maize intrinsic zein (Zel) were assayed by polymerase chain reaction (PCR) 3 times with a total of 4 primer pairs of different expected lengths. The cry9C gene (either 103 or 170 bp) was detected in the rectal contents (with a frequency of 25-37.5%) and in the cecal contents (25-50%) of the pigs fed SL. In a similar fashion, the zein (Zel) gene (either 242 or 329 bp) was detected in the rectal contents (with a frequency of 31.3%) and in the cecal contents (25-37.5%) of pigs fed on SL non-GM maize. These results suggested that ingested DNA was not totally degraded, but is present in a form detectable by PCR.

  6. Accurate measurement of circulating mitochondrial DNA content from human blood samples using real-time quantitative PCR.

    PubMed

    Ajaz, Saima; Czajka, Anna; Malik, Afshan

    2015-01-01

    We describe a protocol to accurately measure the amount of human mitochondrial DNA (MtDNA) in peripheral blood samples which can be modified to quantify MtDNA from other body fluids, human cells, and tissues. This protocol is based on the use of real-time quantitative PCR (qPCR) to quantify the amount of MtDNA relative to nuclear DNA (designated the Mt/N ratio). In the last decade, there have been increasing numbers of studies describing altered MtDNA or Mt/N in circulation in common nongenetic diseases where mitochondrial dysfunction may play a role (for review see Malik and Czajka, Mitochondrion 13:481-492, 2013). These studies are distinct from those looking at genetic mitochondrial disease and are attempting to identify acquired changes in circulating MtDNA content as an indicator of mitochondrial function. However, the methodology being used is not always specific and reproducible. As more than 95 % of the human mitochondrial genome is duplicated in the human nuclear genome, it is important to avoid co-amplification of nuclear pseudogenes. Furthermore, template preparation protocols can also affect the results because of the size and structural differences between the mitochondrial and nuclear genomes. Here we describe how to (1) prepare DNA from blood samples; (2) pretreat the DNA to prevent dilution bias; (3) prepare dilution standards for absolute quantification using the unique primers human mitochondrial genome forward primer (hMitoF3) and human mitochondrial genome reverse primer(hMitoR3) for the mitochondrial genome, and human nuclear genome forward primer (hB2MF1) and human nuclear genome reverse primer (hB2MR1) primers for the human nuclear genome; (4) carry out qPCR for either relative or absolute quantification from test samples; (5) analyze qPCR data; and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high-throughput use.

  7. Using flow cytometry to estimate pollen DNA content: improved methodology and applications

    PubMed Central

    Kron, Paul; Husband, Brian C.

    2012-01-01

    Background and Aims Flow cytometry has been used to measure nuclear DNA content in pollen, mostly to understand pollen development and detect unreduced gametes. Published data have not always met the high-quality standards required for some applications, in part due to difficulties inherent in the extraction of nuclei. Here we describe a simple and relatively novel method for extracting pollen nuclei, involving the bursting of pollen through a nylon mesh, compare it with other methods and demonstrate its broad applicability and utility. Methods The method was tested across 80 species, 64 genera and 33 families, and the data were evaluated using established criteria for estimating genome size and analysing cell cycle. Filter bursting was directly compared with chopping in five species, yields were compared with published values for sonicated samples, and the method was applied by comparing genome size estimates for leaf and pollen nuclei in six species. Key Results Data quality met generally applied standards for estimating genome size in 81 % of species and the higher best practice standards for cell cycle analysis in 51 %. In 41 % of species we met the most stringent criterion of screening 10 000 pollen grains per sample. In direct comparison with two chopping techniques, our method produced better quality histograms with consistently higher nuclei yields, and yields were higher than previously published results for sonication. In three binucleate and three trinucleate species we found that pollen-based genome size estimates differed from leaf tissue estimates by 1·5 % or less when 1C pollen nuclei were used, while estimates from 2C generative nuclei differed from leaf estimates by up to 2·5 %. Conclusions The high success rate, ease of use and wide applicability of the filter bursting method show that this method can facilitate the use of pollen for estimating genome size and dramatically improve unreduced pollen production estimation with flow cytometry. PMID

  8. Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield.

    PubMed

    Li, Li; Paulo, Maria-João; Strahwald, Josef; Lübeck, Jens; Hofferbert, Hans-Reinhard; Tacke, Eckhart; Junghans, Holger; Wunder, Jörg; Draffehn, Astrid; van Eeuwijk, Fred; Gebhardt, Christiane

    2008-05-01

    Complex characters of plants such as starch and sugar content of seeds, fruits, tubers and roots are controlled by multiple genetic and environmental factors. Understanding their molecular basis will facilitate diagnosis and combination of superior alleles in crop improvement programs ("precision breeding"). Association genetics based on candidate genes is one approach toward this goal. Tetraploid potato varieties and breeding clones related by descent were evaluated for 2 years for chip quality before and after cold storage, tuber starch content, yield and starch yield. Chip quality is inversely correlated with tuber sugar content. A total of 36 loci on 11 potato chromosomes were evaluated for natural DNA variation in 243 individuals. These loci included microsatellites and genes coding for enzymes that function in carbohydrate metabolism or transport (candidate loci). The markers were used to analyze population structure and were tested for association with the tuber quality traits. Highly significant and robust associations of markers with 1-4 traits were identified. Most frequent were associations with chip quality and tuber starch content. Alleles increasing tuber starch content improved chip quality and vice versa. With two exceptions, the most significant and robust associations (q < 0.01) were observed with DNA variants in genes encoding enzymes that function in starch and sugar metabolism or transport. Comparing linkage and linkage disequilibrium between loci provided evidence for the existence of large haplotype blocks in the breeding materials analyzed.

  9. The relationships between the /sup 67/Ga uptake and nuclear DNA Feulgen content in thyroid tumors: concise communication

    SciTech Connect

    Higashi, T.; Watanabe, Y.; Yamaguchi, M.; Hisada, T.; Mimura, T.; Ito, K.; Allison, J.R.

    1982-11-01

    It has been reported that /sup 67/Ga uptake by malignant tumors differs somewhat according to the histologic type. Previously, we reported that uptake of /sup 67/Ga is predictably low in well-differentiated adenocarcinoma of the thyroid gland but high in anaplastic carcinoma and malignant lymphoma. We studied the relationship between /sup 67/Ga uptake and nuclear DNA content in four papillary adenocarcinomas, three follicular adenocarcinomas, three anaplastic carcinomas, and five malignant lymphomas of the thyroid gland. In anaplastic carcinoma and malignant lymphoma, the nuclear DNA content and proliferative index were significantly higher than in well-differentiated adenocarcinoma. These results suggest that there is close correlation between /sup 67/Ga uptake and degree of malignancy of thyroid tumor cells.

  10. The relationships between the Ga-67 uptake and nuclear DNA feulgen content in thyroid tumors: concise communication

    SciTech Connect

    Higashi, T.; Watanabe, Y.; Yamaguchi, M.; Hisada, T.; Mimura, T.; Ito, K.; Allison, J.R.

    1982-11-01

    It has been reported that Ga-67 uptake by malignant tumors differs somewhat according to the histologic type. Previously, we reported that uptake of Ga-67 is predictably low in well-differentiated adenocarcinoma of the thyroid gland but high in anaplastic carcinoma and malignant lymphoma. We studied the relationship between Ga-67 uptake and nuclear DNA content in four papillary adenocarcinomas, three follicular adenocarcinomas, three anaplastic carcinomas, and five malignant lymphomas of the thyroid gland. In anaplastic carcinoma and malignant lymphoma, the nuclear DNA content and proliferative index were significantly higher than in well-differentiated adenocarcinoma. These results suggest that there is close correlation between Ga-67 uptake and degree of malignancy of thyroid tumor cells.

  11. Equine sperm nuclei with different ploidy levels: relationship between the nuclear DNA content and the nuclear area.

    PubMed

    Spirito, S; Campi, S; Boquet, M; Fernández, H; Ferrari, M

    2011-08-01

    The aims of this study were to estimate the ability of the Feulgen reaction to identify equine sperm nuclei with different ploidy levels, to determine the frequency of haploid, diploid and polyploid sperm nuclei in the semen of fertile equines and to evaluate the relationship between the nuclear DNA content and the nuclear area. Determination of the ploidy level of Feulgen-stained spermatozoa using a scanning microspectrophotometer was very similar to the subjective estimations made with a light microscope. This indicates that the Feulgen reaction is a simple, inexpensive and reliable technique to recognise the ploidy level of equine spermatozoa. The incidence of diploid and polyploid spermatozoa, determined with a light microscope in 11 fertile equines, was 0.17 ± 0.08% and 0.027 ± 0.027% respectively. DNA content values obtained by microspectrophotometry in the only equine that presented polyploid spermatozoa allowed us to discriminate between haploid, diploid and polyploid subpopulations. Measurement of the nuclear area discriminated only two subpopulations: one including the haploid and diploid subpopulations and the other including the polyploid one. The similarity between the area of the haploid and diploid sperm nuclei suggests that the increase in DNA content is anisotropic, with a privileged direction of growth perpendicular to the nuclear flattening plane.

  12. Thermodynamic Post-Processing versus GC-Content Pre-Processing for DNA Codes Satisfying the Hamming Distance and Reverse-Complement Constraints.

    PubMed

    Tulpan, Dan; Smith, Derek H; Montemanni, Roberto

    2014-01-01

    Stochastic, meta-heuristic and linear construction algorithms for the design of DNA strands satisfying Hamming distance and reverse-complement constraints often use a GC-content constraint to pre-process the DNA strands. Since GC-content is a poor predictor of DNA strand hybridization strength the strands can be filtered by post-processing using thermodynamic calculations. An alternative approach is considered here, where the algorithms are modified to remove consideration of GC-content and rely on post-processing alone to obtain large sets of DNA strands with satisfactory melting temperatures. The two approaches (pre-processing GC-content and post-processing melting temperatures) are compared and are shown to be complementary when large DNA sets are desired. In particular, the second approach can give significant improvements when linear constructions are used.

  13. [The double DNA content is detected in hemocytes of snail Lymnaea stagnalis from a population with high radiation load].

    PubMed

    Koneva, O Iu

    2014-01-01

    The research of hemocytes of laboratory cultivated pond snails Lymnaea stagnalis originating from two areas near Chernobyl with different radiation load has been carried out by means of comet assay. Significant interpopulation distinctions in parameters of DNA-comets have been revealed by means of the software analysis of hemocyte DNA-comet images: hemocytes of mollusks from radiationally unfavourable "Perstok" population have contained a twice DNA quantity in comparison with "Pripyat" population, and also have been statistically more resistant to the influence of strontium. Strontium reduces the amount of DNA in hemocytes, at that strontium dose of 0.5 MPC is already substantial (i.e., causes a negative impact).for snail Lymnaea stagnalis. According to a RAPD-analysis previously conducted, the snails of two populations are characterized by high genetic similarity, on the basis of which a hypothesis is suggested that the observed differences in the DNA content of hemocytes and resistance to strontium are inherited as prolonged adaptive modification (epigenetic change) in response to the intensive damaging impact of environment. Comet assay can be its indicator while carrying out the environmental monitoring.

  14. [The double DNA content is detected in hemocytes of snail Lymnaea stagnalis from a population with high radiation load].

    PubMed

    Koneva, O Iu

    2014-01-01

    The research of hemocytes of laboratory cultivated pond snails Lymnaea stagnalis originating from two areas near Chernobyl with different radiation load has been carried out by means of comet assay. Significant interpopulation distinctions in parameters of DNA-comets have been revealed by means of the software analysis of hemocyte DNA-comet images: hemocytes of mollusks from radiationally unfavourable "Perstok" population have contained a twice DNA quantity in comparison with "Pripyat" population, and also have been statistically more resistant to the influence of strontium. Strontium reduces the amount of DNA in hemocytes, at that strontium dose of 0.5 MPC is already substantial (i.e., causes a negative impact).for snail Lymnaea stagnalis. According to a RAPD-analysis previously conducted, the snails of two populations are characterized by high genetic similarity, on the basis of which a hypothesis is suggested that the observed differences in the DNA content of hemocytes and resistance to strontium are inherited as prolonged adaptive modification (epigenetic change) in response to the intensive damaging impact of environment. Comet assay can be its indicator while carrying out the environmental monitoring. PMID:25782279

  15. Ploidy Level and DNA Content of Erianthus arundinaceus as Determined by Flow Cytometry and the Association with Biological Characteristics

    PubMed Central

    Sun, Kaiyan; Chang, Dan; Bai, Shiqie; Shen, Yixin; Huang, Linkai; Zhang, Jin; Zhang, Yu; Dong, Yanhai

    2016-01-01

    Erianthus arundinaceus is not only an important germplasm resource for sugarcane breeding but also a potential bioenergy plant. Making clear the distribution of the chromosome ploidy of wild E. arundinaceus in china is the premise of the research and utilization of this species. Therefore, the objectives of this study were to determine the ploidy level and DNA content of the 55 E. arundinaceus accessions using flow cytometry and to identify the correlation between ploidy and phenotypic traits. Among the 55 accessions, four tetraploids and 51 hexaploids were identified. The four tetraploids originated from Mengma Yunnan, Shuangjiang Yunnan, Gaozhou Guangdong and Chengle Sichuan. The mean DNA content was 4.82 pg/2C for the tetraploid and 7.30 pg/2C for the hexaploid plants. The ploidy was negatively correlated with cellulose content and positively correlated (P<0.05) with plant height, stem diameter, leaf width, dry weight per plant, fresh weight per plant and hemicellulose content. However, ploidy was not correlated with leaf length, tiller number and the ratio of dry weight and fresh weight. This study will be useful for revealing the distribution of the ploidy of wild E. arundinaceus in Chin, traits markers analysis, and utilization of this species, such as cultivar improvement and sugarcane breeding in the future. PMID:27010798

  16. Ploidy Level and DNA Content of Erianthus arundinaceus as Determined by Flow Cytometry and the Association with Biological Characteristics.

    PubMed

    Yan, Jiajun; Zhang, Jianbo; Sun, Kaiyan; Chang, Dan; Bai, Shiqie; Shen, Yixin; Huang, Linkai; Zhang, Jin; Zhang, Yu; Dong, Yanhai

    2016-01-01

    Erianthus arundinaceus is not only an important germplasm resource for sugarcane breeding but also a potential bioenergy plant. Making clear the distribution of the chromosome ploidy of wild E. arundinaceus in china is the premise of the research and utilization of this species. Therefore, the objectives of this study were to determine the ploidy level and DNA content of the 55 E. arundinaceus accessions using flow cytometry and to identify the correlation between ploidy and phenotypic traits. Among the 55 accessions, four tetraploids and 51 hexaploids were identified. The four tetraploids originated from Mengma Yunnan, Shuangjiang Yunnan, Gaozhou Guangdong and Chengle Sichuan. The mean DNA content was 4.82 pg/2C for the tetraploid and 7.30 pg/2C for the hexaploid plants. The ploidy was negatively correlated with cellulose content and positively correlated (P<0.05) with plant height, stem diameter, leaf width, dry weight per plant, fresh weight per plant and hemicellulose content. However, ploidy was not correlated with leaf length, tiller number and the ratio of dry weight and fresh weight. This study will be useful for revealing the distribution of the ploidy of wild E. arundinaceus in Chin, traits markers analysis, and utilization of this species, such as cultivar improvement and sugarcane breeding in the future. PMID:27010798

  17. Bacterial DNA Content in the Intestinal Wall from Infants with Necrotizing Enterocolitis

    PubMed Central

    Bucher, Brian T.; McDuffie, Lucas A.; Shaikh, Nurmohammad; Tarr, Phillip I.; Warner, Barbara B.; Hamvas, Aaron; White, Francis V.; Erwin, Christopher R.; Warner, Brad W.

    2011-01-01

    PURPOSE The objectives of our study were to quantify mucosal bacterial DNA within specimens from neonates undergoing small bowel resection for necrotizing enterocolitis (NEC). METHODS We obtained clinical information and pathologic specimens from all infants diagnosed with NEC who underwent surgical treatment at our institution from 1999–2008. Bacterial and human DNA were isolated from paraffin-embedded surgical specimens and real-time PCR was used to amplify bacterial and human genes. Linear regression was used to quantify the amount of human and bacterial DNA in our specimens. RESULTS From a cohort of fifty infants, we identified twenty-three infants who underwent both surgical resection and subsequent intestinal reanastomosis. Thirteen (59%) of the neonates had Bell's Stage III NEC, and nine (41%) had Stage II. There was significantly more bacterial DNA in the resection specimens than in the reanastomosis specimens. This corresponds to a median (IQR) increase of 1.81 (1.11–4.69) fold bacterial DNA in the resection specimen compared to the reanastomosis specimen (p<0.05). CONCLUSION There is more bacterial DNA in infants with acute NEC compared with the same infants after the NEC had clinically resolved. These findings underscore the potential relevance of adherent or invasive bacteria across the bowel wall in the pathogenesis of NEC. PMID:21683193

  18. Decreased Mitochondrial DNA Content in Association with Exposure to Polycyclic Aromatic Hydrocarbons in House Dust during Wintertime: From a Population Enquiry to Cell Culture

    PubMed Central

    Pieters, Nicky; Koppen, Gudrun; Smeets, Karen; Napierska, Dorota; Plusquin, Michelle; De Prins, Sofie; Van De Weghe, Hendrik; Nelen, Vera; Cox, Bianca; Cuypers, Ann; Hoet, Peter; Schoeters, Greet; Nawrot, Tim S.

    2013-01-01

    Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental pollutants that are formed in combustion processes. At the cellular level, exposure to PAHs causes oxidative stress and/or some of it congeners bind to DNA, which may interact with mitochondrial function. However, the influence of these pollutants on mitochondrial DNA (mtDNA) content remains largely unknown. We determined whether indoor exposure to PAHs is associated with mitochondrial damage as represented by blood mtDNA content. Blood mtDNA content (ratio mitochondrial/nuclear DNA copy number) was determined by real-time qPCR in 46 persons, both in winter and summer. Indoor PAH exposure was estimated by measuring PAHs in sedimented house dust, including 6 volatile PAHs and 8 non-volatile PAHs. Biomarkers of oxidative stress at the level of DNA and lipid peroxidation were measured. In addition to the epidemiologic enquiry, we exposed human TK6 cells during 24 h at various concentrations (range: 0 to 500 µM) of benzo(a)pyrene and determined mtDNA content. Mean blood mtDNA content averaged (±SD) 0.95±0.185. The median PAH content amounted 554.1 ng/g dust (25th–75th percentile: 390.7–767.3) and 1385ng/g dust (25th–75th percentile: 1000–1980) in winter for volatile and non-volatile PAHs respectively. Independent for gender, age, BMI and the consumption of grilled meat or fish, blood mtDNA content decreased by 9.85% (95% CI: −15.16 to −4.2; p = 0.002) for each doubling of non-volatile PAH content in the house dust in winter. The corresponding estimate for volatile PAHs was −7.3% (95% CI: −13.71 to −0.42; p = 0.04). Measurements of oxidative stress were not correlated with PAH exposure. During summer months no association was found between mtDNA content and PAH concentration. The ability of benzo(a)pyrene (range 0 µM to 500 µM) to lower mtDNA content was confirmed in vitro in human TK6 cells. Based on these findings, mtDNA content can be a target of PAH toxicity in humans

  19. DNA cell cycle distribution and glutathione (GSH) content according to circadian stage in bone marrow of cancer patients.

    PubMed Central

    Smaaland, R.; Abrahamsen, J. F.; Svardal, A. M.; Lote, K.; Ueland, P. M.

    1992-01-01

    DNA cell cycle distribution and glutathione (GSH) content in bone marrow were measured both at daytime and midnight over single 24 h periods in 15 cancer patients. Between patients the S-phase demonstrated a difference from lowest to highest value of 700%, whereas the corresponding difference for the G2/M-phase was nearly 900%. The mean GSH content measured in the bone marrow at the two timepoints was 2.24 +/- 0.21 nmol mg-1 protein, range 0.91-4.19 nmol mg-1 protein. A statistically significant higher fraction of cells in S-phase and G2/M-phase was found at daytime as compared to midnight when excluding the four patients with an abnormal circadian variation in cortisol. No significant temporal variation in total bone marrow GSH content was found, although a weak correlation between S-phase and GSH content was demonstrated (r = 0.42; P less than 0.05). This correlation was strengthened when not including the six patients with an abnormal cortisol pattern (4) and bone marrow infiltration (2) (r = 0.66; P = 0.005). Cells in S-phase demonstrated a positive correlation with cells in G2/M-phase (r = 0.64; P less than 0.0001). A negative correlation was found between GSH content and age (r = 0.53; P less than 0.005). Finally, a statistically significant positive correlation was demonstrated between cortisol and both S-phase and G2/M-phase (r = 0.57; P less than 0.001 and r = 0.38; P less than 0.05, respectively). The present study suggests a possibility of optimising cancer therapy and use of hematopoietic growth factors by determining individual average values and circadian stage dependent variation in bone marrow DNA cell cycle distribution. Furthermore, GSH content in bone marrow may predict this tissue's sensitivity to cytotoxic agents. PMID:1637674

  20. Influence of cell size and DNA content on growth rate and photosystem II function in cryptic species of Ditylum brightwellii.

    PubMed

    Sharpe, Susan C; Koester, Julie A; Loebl, Martina; Cockshutt, Amanda M; Campbell, Douglas A; Irwin, Andrew J; Finkel, Zoe V

    2012-01-01

    DNA content and cell volume have both been hypothesized as controls on metabolic rate and other physiological traits. We use cultures of two cryptic species of Ditylum brightwellii (West) Grunow with an approximately two-fold difference in genome size and a small and large culture of each clone obtained by isolating small and large cells to compare the physiological consequences of size changes due to differences in DNA content and reduction in cell size following many generations of asexual reproduction. We quantified the growth rate, the functional absorption cross-section of photosystem II (PSII), susceptibility of PSII to photoinactivation, PSII repair capacity, and PSII reaction center proteins D1 (PsbA) and D2 (PsbD) for each culture at a range of irradiances. The species with the smaller genome has a higher growth rate and, when acclimated to growth-limiting irradiance, has higher PSII repair rate capacity, PSII functional optical absorption cross-section, and PsbA per unit protein, relative to the species with the larger genome. By contrast, cell division rates vary little within clonal cultures of the same species despite significant differences in average cell volume. Given the similarity in cell division rates within species, larger cells within species have a higher demand for biosynthetic reductant. As a consequence, larger cells within species have higher numbers of PSII per unit protein (PsbA), since PSII photochemically generates the reductant to support biosynthesis. These results suggest that DNA content, as opposed to cell volume, has a key role in setting the differences in maximum growth rate across diatom species of different size while PSII content and related photophysiological traits are influenced by both growth rate and cell size.

  1. Influence of Cell Size and DNA Content on Growth Rate and Photosystem II Function in Cryptic Species of Ditylum brightwellii

    PubMed Central

    Sharpe, Susan C.; Koester, Julie A.; Loebl, Martina; Cockshutt, Amanda M.; Campbell, Douglas A.; Irwin, Andrew J.; Finkel, Zoe V.

    2012-01-01

    DNA content and cell volume have both been hypothesized as controls on metabolic rate and other physiological traits. We use cultures of two cryptic species of Ditylum brightwellii (West) Grunow with an approximately two-fold difference in genome size and a small and large culture of each clone obtained by isolating small and large cells to compare the physiological consequences of size changes due to differences in DNA content and reduction in cell size following many generations of asexual reproduction. We quantified the growth rate, the functional absorption cross-section of photosystem II (PSII), susceptibility of PSII to photoinactivation, PSII repair capacity, and PSII reaction center proteins D1 (PsbA) and D2 (PsbD) for each culture at a range of irradiances. The species with the smaller genome has a higher growth rate and, when acclimated to growth-limiting irradiance, has higher PSII repair rate capacity, PSII functional optical absorption cross-section, and PsbA per unit protein, relative to the species with the larger genome. By contrast, cell division rates vary little within clonal cultures of the same species despite significant differences in average cell volume. Given the similarity in cell division rates within species, larger cells within species have a higher demand for biosynthetic reductant. As a consequence, larger cells within species have higher numbers of PSII per unit protein (PsbA), since PSII photochemically generates the reductant to support biosynthesis. These results suggest that DNA content, as opposed to cell volume, has a key role in setting the differences in maximum growth rate across diatom species of different size while PSII content and related photophysiological traits are influenced by both growth rate and cell size. PMID:23300819

  2. Influence of cell size and DNA content on growth rate and photosystem II function in cryptic species of Ditylum brightwellii.

    PubMed

    Sharpe, Susan C; Koester, Julie A; Loebl, Martina; Cockshutt, Amanda M; Campbell, Douglas A; Irwin, Andrew J; Finkel, Zoe V

    2012-01-01

    DNA content and cell volume have both been hypothesized as controls on metabolic rate and other physiological traits. We use cultures of two cryptic species of Ditylum brightwellii (West) Grunow with an approximately two-fold difference in genome size and a small and large culture of each clone obtained by isolating small and large cells to compare the physiological consequences of size changes due to differences in DNA content and reduction in cell size following many generations of asexual reproduction. We quantified the growth rate, the functional absorption cross-section of photosystem II (PSII), susceptibility of PSII to photoinactivation, PSII repair capacity, and PSII reaction center proteins D1 (PsbA) and D2 (PsbD) for each culture at a range of irradiances. The species with the smaller genome has a higher growth rate and, when acclimated to growth-limiting irradiance, has higher PSII repair rate capacity, PSII functional optical absorption cross-section, and PsbA per unit protein, relative to the species with the larger genome. By contrast, cell division rates vary little within clonal cultures of the same species despite significant differences in average cell volume. Given the similarity in cell division rates within species, larger cells within species have a higher demand for biosynthetic reductant. As a consequence, larger cells within species have higher numbers of PSII per unit protein (PsbA), since PSII photochemically generates the reductant to support biosynthesis. These results suggest that DNA content, as opposed to cell volume, has a key role in setting the differences in maximum growth rate across diatom species of different size while PSII content and related photophysiological traits are influenced by both growth rate and cell size. PMID:23300819

  3. Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

    PubMed Central

    Zagoskin, Maxim V.; Lazareva, Valentina I.; Grishanin, Andrey K.; Mukha, Dmitry V.

    2014-01-01

    The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals. PMID:25215300

  4. Variation of karyotype and nuclear DNA content among four species of Plectranthus L' Héritier, 1788 (Lamiaceae) from Brazil.

    PubMed

    Nani, Thaís Furtado; Mesquita, Amanda Teixeira; Bustamante, Fernanda de Oliveira; Barbosa, Sandro; Barbosa, João Vítor Calvelli; Davide, Lisete Chamma

    2015-01-01

    Plectranthus is a genus which includes species of ornamental and medicinal potential. It faces taxonomic problems due to aggregating species previously belonging to the genus Coleus, a fact that has contributed to the existence of various synonymies. The species Plectranthus amboinicus, Plectranthus barbatus, Plectranthus grandis and Plectranthus neochilus are included in this context. Some authors consider Plectranthus barbatus and Plectranthus grandis as synonyms. The present work was carried out with the aim of comparing plants of the above-mentioned species, originating from different localities in Brazil, with regards to chromosome number and karyotypic morphology, correlated to the nuclear DNA content. There was no variation in chromosome number among plants of the same species. Plectranthus amboinicus was the only species to exhibit 2n=34, whereas the others had 2n=30. No karyotypic differences were found among the plants of each species, except for Plectranthus barbatus. The plants of the Plectranthus species revealed little coincidence between chromosome pairs. The nuclear DNA content allowed grouping Plectranthus amboinicus and Plectranthus neochilus, with the highest mean values, and Plectranthus grandis and Plectranthus barbatus with the lowest ones. Differences in DNA amount among the plants were identified only for Plectranthus barbatus. These results allow the inference that the populations of Plectranthus amboinicus and Plectranthus neochilus present coincident karyotypes among their plants, and Plectranthus grandis is probably a synonym of Plectranthus barbatus. PMID:26753074

  5. Variation of karyotype and nuclear DNA content among four species of Plectranthus L’ Héritier, 1788 (Lamiaceae) from Brazil

    PubMed Central

    Nani, Thaís Furtado; Mesquita, Amanda Teixeira; Bustamante, Fernanda de Oliveira; Barbosa, Sandro; Barbosa, João Vítor Calvelli; Davide, Lisete Chamma

    2015-01-01

    Abstract Plectranthus is a genus which includes species of ornamental and medicinal potential. It faces taxonomic problems due to aggregating species previously belonging to the genus Coleus, a fact that has contributed to the existence of various synonymies. The species Plectranthus amboinicus, Plectranthus barbatus, Plectranthus grandis and Plectranthus neochilus are included in this context. Some authors consider Plectranthus barbatus and Plectranthus grandis as synonyms. The present work was carried out with the aim of comparing plants of the above-mentioned species, originating from different localities in Brazil, with regards to chromosome number and karyotypic morphology, correlated to the nuclear DNA content. There was no variation in chromosome number among plants of the same species. Plectranthus amboinicus was the only species to exhibit 2n=34, whereas the others had 2n=30. No karyotypic differences were found among the plants of each species, except for Plectranthus barbatus. The plants of the Plectranthus species revealed little coincidence between chromosome pairs. The nuclear DNA content allowed grouping Plectranthus amboinicus and Plectranthus neochilus, with the highest mean values, and Plectranthus grandis and Plectranthus barbatus with the lowest ones. Differences in DNA amount among the plants were identified only for Plectranthus barbatus. These results allow the inference that the populations of Plectranthus amboinicus and Plectranthus neochilus present coincident karyotypes among their plants, and Plectranthus grandis is probably a synonym of Plectranthus barbatus. PMID:26753074

  6. Synthesis of bicyclo[4.n.1]alkanones.

    PubMed

    Montalt, Joaquin; Linker, Frédéric; Ratel, Frédéric; Miesch, Michel

    2004-10-01

    Cyclic beta-keto ester monoanions react with 1,4-dihalobutenes to give C-alkylated products which subsequently undergo a stereoselective SN2' O-alkylation reaction to yield functionalized enol ethers. When the starting material was ethyl cyclopentanone carboxylate, the C-alkylated product, treated with a base, directly afforded the functionalized bicyclo[4.2.1]nonanone. The enol ethers were submitted to a flash vacuum thermolysis (FVT) reaction to readily afford functionalized bicyclo[4.n.1]alkanones (n = 3, 4). This reaction sequence was applied to the synthesis of a functionalized tricyclo[7.4.1.0(1,5)]tetradecanone, which represents an analogue to the tricyclic core of ingenol. PMID:15387595

  7. TOTO and YOYO: New very bright fluorochromes for DNA content analyses by flow cytometry

    SciTech Connect

    Hirons, G.T.; Fawcett, J.J.; Crissman, H.A. )

    1994-02-01

    Flow cytometric (FCM) studies were performed on nuclei, ethanol-fixed CHO cells, and isolated human GM130 chromosomes stained with two new cyanine dyes, TOTO and YOYO. These fluorochromes, which are dimers of thiazole orange and oxazole yellow, respectively, have high quantum efficiencies and exhibit specificities for both DNA and RNA. Bound to dsDNA in solution, TOTO and YOYO emit at 530 and 510 nm, respectively, when excited at 488 nm and 457 nm, wavelengths available from most lasers employed in FCM. RNase-treated CHO nuclei, stained with either TOTO or YOYO, provided DNA histograms, with low coefficients of variation, that were as good as or better than those obtained with nuclei stained with propidium iodide (PI) or mithramycin (MI). In addition, by comparison on an equimolar basis, nuclei stained with YOYO fluoresced over 1,000 times more intensely than nuclei stained with MI. Fluorescence ratio analyses of nuclei stained with both YOYO and Hoechst 33258 showed that the ratio of YOYO to Hoechst fluorescence remained relatively constant for G[sub 1] and S phase cells, but decreased significantly for cells in G[sub 2]/M. These results indicate that the cyanine dyes may be useful in examining specific changes in chromatin structure during G[sub 2]/M phases of the cell cycle. Ethanol-fixed CHO cells stained with TOTO or YOYO did not yield reproducible DNA histograms of good quality, presumably because of the poor accessibility of DNA to these large fluorochromes. However, bivariate analyses of human GM130 chromosomes stained with TOTO or YOYO alone and excited sequentially with uv and visible wavelengths showed resolution of many individual chromosome peaks similar to results obtained for chromosomes stained with HO and chromomycin A[sub 3]. Collectively, these studies show potential advantages for the use of these new cyanine dyes in FCM studies that require the sensitive detection of DNA. 20 refs., 5 figs., 2 tabs.

  8. Effect of serotonin on the expression of antigens and DNA levels in Yersinia pestis cells with different plasmid content

    NASA Astrophysics Data System (ADS)

    Klueva, Svetlana N.; Korsukov, Vladimir N.; Schukovskaya, Tatyana N.; Kravtsov, Alexander L.

    2004-08-01

    Using flow cytometry (FCM) the influence of exogenous serotonin on culture growth, DNA content and fluorescence intensity of cells binding FITC-labelled plague polyclonal immunoglobulins was studied in Yersinia pestis EV (pFra+, pCad+, pPst+), Yersinia pestis KM218 (pFra-, pCad-, pPst-), Yersinia pestis KM 216 (pFra-, pCad-, pPst+). The results have been obtained by FCM showed serotonin accelerated Yersinia pestis EV (pFra+, pCad+, pPst+), Yersinia pestis KM218 (pFra-, pCad-, pPst-) culture growth during cultivation in Hottinger broth pH 7.2 at 28°C at concentration of 10-5 M. The presence of 10-5 M serotonin in nutrient broth could modulate DNA content in 37°C growing population of plague microbe independently of their plasmid content. Serotonin have been an impact on the distribution pattern of the cells according to their phenotypical characteristics, which was reflected in the levels of population heterogeneity in the intensity of specific immunofluorescence determined by FMC.

  9. Folate supplementation differently affects uracil content in DNA in the mouse colon and liver

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High folate intake may increase the risk of cancer, especially in the elderly. The present study examined the effects of ageing and dietary folate on uracil misincorporation into DNA, which has a mutagenic effect, in the mouse colon and liver. Old (18 months; n 42) and young (4 months; n 42) male C5...

  10. The content of mutant EGFR DNA correlates with response to EGFR-TKIs in lung adenocarcinoma patients with common EGFR mutations

    PubMed Central

    Hung, Ming-Szu; Lung, Jr-Hau; Lin, Yu-Ching; Fang, Yu-Hung; Hsieh, Meng-Jer; Tsai, Ying-Huang

    2016-01-01

    Abstract This study aimed to elucidate the association of the content of mutant epidermal growth factor receptor (EGFR) deoxyribonucleic acid (DNA) with the treatment response to EGFR-tyrosine kinase inhibitor (TKI) and survival in patients with lung cancer. This retrospective cohort study included 77 lung adenocarcinoma patients with common EGFR mutations from December 2012 to February 2015. The content of mutant EGFR DNA in lung cancer tissues was determined using an Amplification Refractory Mutation System. The association of the amount of mutant EGFR DNA with treatment response, the clinical variables, and the progression-free survival (PFS) after EGFR-TKI therapy were evaluated. Using the amount of mutant EGR DNA above 4.77% as the cut-off value, the sensitivity to predict EGFR-TKI responder is 82.0% and the specificity is 75.0% (area under the curve [AUC]: 0.734, P = 0.003). The high content of mutant EGFR DNA is an independent factor associated with the response to EGFR-TKIs (odds ratio: 13.07, 95% confidence interval [CI]: 3.23–52.11, P = 0.0003). A significantly longer PFS was observed in the group with the high content of mutant EGFR DNA (26.3 months, 95% CI: 12.2–26.3) compared with the low content of mutant EGFR DNA groups (12.3 months, 95% CI: 5.7–14.8, P = 0.0155). A better predictive value of the content of mutant EGFR DNA was noted in patients with exon 19 deletions (AUC: 0.892, P < 0.0001) than exon 21 L858R mutations (AUC: 0.675, P = 0.0856). Our results show that the content of mutant EGFR DNA is associated with the clinical response to EGFR-TKIs, especially in patients with exon 19 deletions mutation. PMID:27368002

  11. The content of mutant EGFR DNA correlates with response to EGFR-TKIs in lung adenocarcinoma patients with common EGFR mutations.

    PubMed

    Hung, Ming-Szu; Lung, Jr-Hau; Lin, Yu-Ching; Fang, Yu-Hung; Hsieh, Meng-Jer; Tsai, Ying-Huang

    2016-06-01

    This study aimed to elucidate the association of the content of mutant epidermal growth factor receptor (EGFR) deoxyribonucleic acid (DNA) with the treatment response to EGFR-tyrosine kinase inhibitor (TKI) and survival in patients with lung cancer.This retrospective cohort study included 77 lung adenocarcinoma patients with common EGFR mutations from December 2012 to February 2015. The content of mutant EGFR DNA in lung cancer tissues was determined using an Amplification Refractory Mutation System. The association of the amount of mutant EGFR DNA with treatment response, the clinical variables, and the progression-free survival (PFS) after EGFR-TKI therapy were evaluated.Using the amount of mutant EGR DNA above 4.77% as the cut-off value, the sensitivity to predict EGFR-TKI responder is 82.0% and the specificity is 75.0% (area under the curve [AUC]: 0.734, P = 0.003). The high content of mutant EGFR DNA is an independent factor associated with the response to EGFR-TKIs (odds ratio: 13.07, 95% confidence interval [CI]: 3.23-52.11, P = 0.0003). A significantly longer PFS was observed in the group with the high content of mutant EGFR DNA (26.3 months, 95% CI: 12.2-26.3) compared with the low content of mutant EGFR DNA groups (12.3 months, 95% CI: 5.7-14.8, P = 0.0155). A better predictive value of the content of mutant EGFR DNA was noted in patients with exon 19 deletions (AUC: 0.892, P < 0.0001) than exon 21 L858R mutations (AUC: 0.675, P = 0.0856).Our results show that the content of mutant EGFR DNA is associated with the clinical response to EGFR-TKIs, especially in patients with exon 19 deletions mutation. PMID:27368002

  12. Free energy and information contents of conformons in proteins and DNA.

    PubMed

    Ji, S

    2000-01-01

    Sequence-specific conformational strains (SSCS) of biopolymers that carry free energy and genetic information have been called conformons, a term coined independently by two groups over two and a half decades ago [Green, D.E., Ji, S., 1972. The electromechanochemical model of mitochondrial structure and function. In: Schultz, J., Cameron, B.F. (Eds.), Molecular Basis of Electron Transport. Academic Press, New York, pp. 1-44; Volkenstein, M.V., 1972. The Conformon. J. Theor. Biol. 34, 193-195]. Conformons provide the molecular mechanisms necessary and sufficient to account for all biological processes in the living cell on the molecular level in principle--including the origin of life, enzymic catalysis, control of gene expression, oxidative phosphorylation, active transport, and muscle contraction. A clear example of SSCS is provided by SIDD (strain-induced duplex destabilization) in DNA recently reported by Benham [Benham, C.J., 1996a. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425-434; Benham, C.J., 1996b. Computation of DNA structural variability--a new predictor of DNA regulatory regions. CABIOS 12(5), 375-381]. Experimental as well as theoretical evidence indicates that conformons in proteins carry 8-16 kcal/mol of free energy and 40-200 bits of information, while those in DNA contain 500-2500 kcal/mol of free energy and 200-600 bits of information. The similarities and differences between conformons and solitons have been analyzed on the basis of the generalized Franck-Condon principle [Ji, S., 1974a. A general theory of ATP synthesis and utilization. Ann. N.Y. Acad. Sci. 227, 211-226; Ji, S., 1974b. Energy and negentropy in enzymic catalysis. Ann. N.Y. Acad. Sci. 227, 419-437]. To illustrate a practical application, the conformon theory was applied to the molecular-clamp model of DNA gyrase proposed by Berger and Wang [Berger, J.M., Wang, J.C., 1996. Recent developments

  13. Radiation effects on DNA content of cervical cancer cells: A rapid evaluation of radiation sensitivity by laser scanning cytometry

    PubMed Central

    FUJIYOSHI, NAOKI; USHIJIMA, KIMIO; KAWANO, KOUICHIRO; FUJIYOSHI, KEIZO; YAMAGUCHI, TOMOHIKO; ARAKI, YUKO; KAKUMA, TATSUYUKI; WATANABE, SUMIKO; KAKU, TSUNEHISA; NISHIDA, TAKASHI; KAMURA, TOSHIHARU

    2015-01-01

    Since uterine cervical cancer is regarded as a radiosensive tumor, ionizing radiation is the most frequently used treatment modality against the disease. Although the crucial end-point is radiation-induced cell death, the tumors are not equally sensitive to radiation. Determining the criteria that may be used to predict tumor radiosensitivity is of importance; however, little success has been achieved thus far. In radioresistant cases the therapeutic strategy should be changed, thereby avoiding ineffective or unnecessary treatment. Furthermore, identification of the underlying molecular processes leading to radioresistance may lead to novel radiosensitising strategies. Cervical smears were obtained from seven patients with locally advanced cervical cancer following each radiotherapy, and the radiation-induced damage of cancer tissue was examined by routine cytology. Since the formation of DNA double-strand breaks is considered critical for the cytocidal effect of radiation therapy, the molecular changes of the neoplastic cells were also assessed by laser scanning cytometry (LSC). Radiation-induced morphological changes of cancer cells were evident at a dose of 7.2 Gy, whereas increased DNA content (or DNA index) was observed prior to the onset of morphological changes. Molecular change was detected earlier than the morphological change of the irradiated cancer cells, indicating the feasibility of LSC in predicting the radiosensitivity of cervical cancer tissue. PMID:25469269

  14. Ötzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps

    PubMed Central

    Rollo, Franco; Ubaldi, Massimo; Ermini, Luca; Marota, Isolina

    2002-01-01

    Samples of the intestinal content were collected from the ileum and colon of the Neolithic glacier mummy popularly known as the Tyrolean Iceman, or Ötzi. DNA was extracted from the samples and PCR amplified, using a variety of primer pairs designed to bind to different genes (mammal mitochondrial 12S ribosomal RNA gene, plant/fungal nuclear 18S ribosomal RNA gene, plant chloroplast ribulose bisphosphate carboxylase large subunit gene). This made it possible to distinguish between animal and plant food residues (macroremains) and pollen (microremains). According to the DNA reconstruction, the man's last meal was composed of red deer (Cervus elaphus) meat, and, possibly, cereals; this meal had been preceded by another one based on ibex (Capra ibex), different species of dicots, and cereals. The DNA spectrum corresponding to pollen residues in the colon, on the other hand, fits with the hypothesis that the last journey of the Neolithic hunter/warrior was made through a subalpine coniferous forest to the site at over 3,200 m above sea level, where his mummified body was to be discovered 5,000 years later. PMID:12244211

  15. Otzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps.

    PubMed

    Rollo, Franco; Ubaldi, Massimo; Ermini, Luca; Marota, Isolina

    2002-10-01

    Samples of the intestinal content were collected from the ileum and colon of the Neolithic glacier mummy popularly known as the Tyrolean Iceman, or Otzi. DNA was extracted from the samples and PCR amplified, using a variety of primer pairs designed to bind to different genes (mammal mitochondrial 12S ribosomal RNA gene, plant/fungal nuclear 18S ribosomal RNA gene, plant chloroplast ribulose bisphosphate carboxylase large subunit gene). This made it possible to distinguish between animal and plant food residues (macroremains) and pollen (microremains). According to the DNA reconstruction, the man's last meal was composed of red deer (Cervus elaphus) meat, and, possibly, cereals; this meal had been preceded by another one based on ibex (Capra ibex), different species of dicots, and cereals. The DNA spectrum corresponding to pollen residues in the colon, on the other hand, fits with the hypothesis that the last journey of the Neolithic hunter/warrior was made through a subalpine coniferous forest to the site at over 3,200 m above sea level, where his mummified body was to be discovered 5,000 years later.

  16. DNA content determination of micronucleated polychromatic erythrocytes induced by clastogens and spindle poisons in mouse bone marrow and peripheral blood

    SciTech Connect

    Grawe, J.; Amneus, H. Uppsala Univ. ); Zetterberg, G. )

    1993-01-01

    The frequencies and DNA distributions of micronuclei in polychromatic erythrocytes from the bone marrow and peripheral blood of mice after four different treatments were determined by flow cytometry. Polychromatic erthrocytes were detected using the fluorescent RNA stain thiazole orange, while micronuclei were detected with the DNA stain Hoechst 33342. The treatments were X-irradiation (1 Gy), cyclophosphamide (30 mg/kg), vincristine sulfphate (0.08 mg/kg), and cochicine (1 mg/kg). All treatments showed increased frequencies of micronucleated polychromatic erythrocytes at 30h after treatment in the bone marrow (colchicine 50h) and at 50h in the peripheral blood. The clostogenic agents X-irradiation and cyclophosphamide and the spindle poisons vincristine sulphate and cochicine could be grouped according to the fluorescent characteristics of the induced micronuclei as well as the relative frequency of small (0.5-2% if the diploid G1 DNA content) and large (2-10%) micronuclei. In the peripheral blood the relative frequency of large micronuclei was lower than in the bone marrow, indicating that they were partly eliminated before entrance into the peripheral circulation. The nature of presumed micronuclei was verified by sorting. The potential of this approach to give information on the mechanism of induction of micronuclei is discussed.

  17. The mutational spectrum of non-CpG DNA varies with CpG content.

    PubMed

    Walser, Jean-Claude; Furano, Anthony V

    2010-07-01

    The accumulation of base substitutions (mutations) not subject to natural selection is the neutral mutation rate. Because this rate reflects the in vivo processes involved in maintaining the integrity of genetic information, the factors that affect the neutral mutation rate are of considerable interest. Mammals exhibit two dramatically different neutral mutation rates: the CpG mutation rate, wherein the C of most CpGs (i.e., methyl-CpG) mutate at 10-50 times that of C in any other context or of any other base. The latter mutations constitute the non-CpG rate. The high CpG rate results from the spontaneous deamination of methyl-C to T and incomplete restoration of the ensuing T:G mismatches to C:Gs. Here, we determined the neutral non-CpG mutation rate as a function of CpG content by comparing sequence divergence of thousands of pairs of neutrally evolving chimpanzee and human orthologs that differ primarily in CpG content. Both the mutation rate and the mutational spectrum (transition/transversion ratio) of non-CpG residues change in parallel as sigmoidal (logistic) functions of CpG content. As different mechanisms generate transitions and transversions, these results indicate that both mutation rate and mutational processes are contingent on the local CpG content. We consider several possible mechanisms that might explain how CpG exerts these effects. PMID:20498119

  18. Removing external DNA decontamination from arthropod predators destined for molecular gut-content analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  19. Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  20. Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores

    PubMed Central

    Zahid, Osama K.; Zhao, Boxuan Simen; He, Chuan; Hall, Adam R.

    2016-01-01

    5-hydroxymethylcytosine (5 hmC), the oxidized form of 5-methylcytosine (5 mC), is a base modification with emerging importance in biology and disease. However, like most epigenetic elements, it is transparent to many conventional genetic techniques and is thus challenging to probe. Here, we report a rapid solid-state nanopore assay that is capable of resolving 5 hmC with high specificity and sensitivity and demonstrate its utility in assessing global modification abundance in genomic DNA. PMID:27383905

  1. Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores.

    PubMed

    Zahid, Osama K; Zhao, Boxuan Simen; He, Chuan; Hall, Adam R

    2016-01-01

    5-hydroxymethylcytosine (5 hmC), the oxidized form of 5-methylcytosine (5 mC), is a base modification with emerging importance in biology and disease. However, like most epigenetic elements, it is transparent to many conventional genetic techniques and is thus challenging to probe. Here, we report a rapid solid-state nanopore assay that is capable of resolving 5 hmC with high specificity and sensitivity and demonstrate its utility in assessing global modification abundance in genomic DNA. PMID:27383905

  2. Flow cytometric analysis of DNA content and Ki-67-positive fractions in the diagnosis of salivary gland tumors.

    PubMed

    Horii, A; Yoshida, J; Sakai, M; Okamoto, S; Kubo, T

    1998-01-01

    To explore the utility of flow cytometry (FCM) for the diagnosis of histopathology of salivary gland tumors, fresh materials taken at surgery from 23 Warthin's tumors, 57 pleomorphic adenomas, and 14 malignant tumors were analyzed for DNA ploidy and proliferative cell activities, including S-phase fraction (SPF), G2- plus M-phase fraction (G2M), and Ki-67-positive fraction. To facilitate this study, glands were taken from all major salivary sites and minor glands in the head and neck. DNA aneuploidy was not detected in the benign tumors. Nine of 14 malignant tumors showed DNA aneuploidy. The percentage of SPF or G2M of the malignant tumors was significantly higher than those of the benign tumors. The percentage of Ki-67-positive fraction of pleomorphic adenomas was comparable to that of malignant tumors and was significantly higher than that of Warthin's tumors. Ki-67 of 20% as a cut-off had a sensitivity of 88%, specificity of 100%, and accuracy of 91% for differentiating pleomorphic adenomas from Warthin's tumors. In analyzing DNA content and proliferative activities by FCM, we could distinguish among the three major histopathologies of salivary gland tumors. Warthin's tumors showed low SPF + G2M with low Ki-67, pleomorphic adenomas had low SPF + G2M with high Ki-67, and malignant tumor showed high SPF + G2M with high Ki-67. The high percentage of the Ki-67-positive fraction seen in pleomorphic adenomas may reflect their potential biological aggressiveness manifested as tumor recurrence or malignant transformation.

  3. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  4. Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents.

    PubMed

    Inaba, Satomi; Fukada, Harumi; Oda, Masayuki

    2016-01-01

    The conformational and thermal stabilities of the minimum functional unit for c-Myb DNA-binding domain, tandem repeat 2 and 3 (R2R3), were analyzed under different pH conditions, ranging from 4.0 to 7.5, using circular dichroism and differential scanning calorimetry. Secondary structure analysis showed that the solution pH largely affects the conformational stability of the protein domain. Of all conditions analyzed, the α-helical content was maximal at pH 6.5, and the thermal stability was highest at pH 5.0. Thermodynamic parameters for thermal unfolding of R2R3 were determined using differential scanning calorimetry, and the origin of folding thermodynamics at the different pHs and its correlation with the α-helical content were further analyzed. It should be noted that the α-helical content correlates well with the enthalpy change in the pH range from 4.5 to 7.5, suggesting that the strength of hydrogen bonds and salt bridges needed for maintenance of helical structure is related to enthalpy in the native state. Under physiological pH conditions, c-Myb R2R3 exists in the enthalpically unstable but entropically stable state. Due to loss of rigid structure and high stability, the protein can now obtain structural flexibility, befitting its function.

  5. New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes for radiation molecular cytogenetics

    PubMed Central

    Repin, Mikhail V; Golubev, Pavel I; Repina, Ludmila A

    2009-01-01

    Background The objective of this work is to obtain the correct relative DNA contents of chromosomes in the normal male and female human diploid genomes for the use at FISH analysis of radiation-induced chromosome aberrations. Results The relative DNA contents of chromosomes in the male and female human diploid genomes have been calculated from the publicly available international Human Genome Project data. New sequence-based data on the relative DNA contents of human chromosomes were compared with the data recommended by the International Atomic Energy Agency in 2001. The differences in the values of the relative DNA contents of chromosomes obtained by using different approaches for 15 human chromosomes, mainly for large chromosomes, were below 2%. For the chromosomes 13, 17, 20 and 22 the differences were above 5%. Conclusion New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes were obtained. This approach, based on the genome sequence, can be recommended for the use in radiation molecular cytogenetics. PMID:19500331

  6. Probabilities of radiation-induced inter- and intrachromosomal exchanges and their dependence on the DNA content of the chromosome

    NASA Technical Reports Server (NTRS)

    Wu, H.; Yang, T. C. (Principal Investigator)

    2001-01-01

    A biophysical model has been developed that is based on the assumptions that an interphase chromosome occupies a spherical territory and that chromosome exchanges are formed by the misrejoining of two DNA double-strand breaks induced within a defined interaction distance. The model is used to explain the relative frequencies of inter- and intrachromosomal exchanges and the relationship between radiation-induced aberrations in individual chromosomes and the DNA content of the chromosome. Although this simple model predicts a higher ratio of inter- to intrachromosomal exchanges for low-LET radiation than for high-LET radiation, as has been suggested by others, we argue that the comparison of the prediction of the model with experimental results is not straightforward. With the model, we also show that the probability of the formation of interchromosomal exchanges is proportional to the "surface area" of the chromosome domain plus a correction term. The correction term is small if the interaction distance is less than 1 microm for both low- and high-LET radiations.

  7. Evaluation of two new fluorochromes, TOTO and YOYO, for DNA content analysis in cells and chromosomes by flow cytometry

    SciTech Connect

    Hirons, G.T.; Crissman, H.A. )

    1993-01-01

    The fluorochromes TOTO and YOYO were evaluated for their effectiveness in staining for DNA content analysis by flow cytometry (FCM). The dyes are dimers of thiazole orange (TO) and yellow oxazole (YO), respectively (Molecular Probes, Eugene, OR), and both have a very high quantum efficiency. Spectrofluorometric analysis showed that TOTO and YOYO had little fluorescence until bound to DNA or RNA. YOYO, the brighter of the two dyes, had an emission peak at [approximately]510 nm and TOTO at [approximately]530 nm. Analysis by flow cytometry indicated that cells stained with either dye at a concentration of [approximately]4.0 [mu]M could be preferentially excited at either 457 or 488 nm. Unfixed nuclei and fixed cells both treated with RNase, stained with either TOTO or YOYO, and analyzed by FCM yielded coefficients of variation (CV) comparable to CVs obtained for the same samples stained with mithramycin (MI) when excited at 457 nm and propidium iodide (PI) when excited at 488 nm. Both TOTO and YOYO are also being evaluated for their effectiveness in staining Chinese hamster embryo chromosomes; these results are being compared with results obtained with PI stained chromosomes.

  8. Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa.

    PubMed

    Zaitlin, David; Pierce, Andrew J

    2010-12-01

    The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet (Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea, Saintpaulia, and Streptocarpus, all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia, a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%-26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine-cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon (Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ~633 × 10⁶ base pairs, which is approximately 40% of the previously published estimate. PMID:21164539

  9. Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa.

    PubMed

    Zaitlin, David; Pierce, Andrew J

    2010-12-01

    The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet (Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea, Saintpaulia, and Streptocarpus, all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia, a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%-26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine-cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon (Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ~633 × 10⁶ base pairs, which is approximately 40% of the previously published estimate.

  10. Utilizing stomach content and faecal DNA analysis techniques to assess the feeding behaviour of largemouth bass Micropterus salmoides and bluegill Lepomis macrochirus.

    PubMed

    Taguchi, T; Miura, Y; Krueger, D; Sugiura, S

    2014-05-01

    In this study, the feeding behaviour of the non-native invasive predatory fishes largemouth bass Micropterus salmoides and bluegill Lepomis macrochirus was studied in the Ezura River, a northern tributary of Lake Biwa, Japan. Prey composition was estimated based on visual examination of stomach contents and faecal DNA analysis to determine feeding habits of these predatory fishes. Stomach content analysis showed that native fishes (e.g. ayu Plecoglossus altivelis and gobies Rhinogobius spp.) and shrimps (e.g. Palaemon paucidens) were the major prey items for M. salmoides, while snails, larval Chironomidae and submerged macrophytes were the dominant prey items of L. macrochirus. Micropterus salmoides tended to select larger fish in the case of crucian carp Carassius spp., but smaller fishes in the case of P. altivelis and Rhinogobius spp. Faecal DNA analyses revealed prey compositions similar to those identified in predator stomach contents, and identified additional prey species not detected in stomach content inspection. This study demonstrated that both stomach content inspection and DNA-based analysis bear several inherent shortcomings and advantages. The former method is straightforward, although identification of species can be inaccurate or impossible, whereas the latter method allows for accurate species identification, but cannot distinguish prey size or stage. Hence, integration of morphology-based and DNA-based methods can provide more reliable estimates of foraging habits of predatory fishes. PMID:24661110

  11. Utilizing stomach content and faecal DNA analysis techniques to assess the feeding behaviour of largemouth bass Micropterus salmoides and bluegill Lepomis macrochirus.

    PubMed

    Taguchi, T; Miura, Y; Krueger, D; Sugiura, S

    2014-05-01

    In this study, the feeding behaviour of the non-native invasive predatory fishes largemouth bass Micropterus salmoides and bluegill Lepomis macrochirus was studied in the Ezura River, a northern tributary of Lake Biwa, Japan. Prey composition was estimated based on visual examination of stomach contents and faecal DNA analysis to determine feeding habits of these predatory fishes. Stomach content analysis showed that native fishes (e.g. ayu Plecoglossus altivelis and gobies Rhinogobius spp.) and shrimps (e.g. Palaemon paucidens) were the major prey items for M. salmoides, while snails, larval Chironomidae and submerged macrophytes were the dominant prey items of L. macrochirus. Micropterus salmoides tended to select larger fish in the case of crucian carp Carassius spp., but smaller fishes in the case of P. altivelis and Rhinogobius spp. Faecal DNA analyses revealed prey compositions similar to those identified in predator stomach contents, and identified additional prey species not detected in stomach content inspection. This study demonstrated that both stomach content inspection and DNA-based analysis bear several inherent shortcomings and advantages. The former method is straightforward, although identification of species can be inaccurate or impossible, whereas the latter method allows for accurate species identification, but cannot distinguish prey size or stage. Hence, integration of morphology-based and DNA-based methods can provide more reliable estimates of foraging habits of predatory fishes.

  12. DNA

    ERIC Educational Resources Information Center

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  13. Genome exclusion and gametic DAPI-DNA content in the hybridogenetic Bacillus rossius-grandii benazzii complex (Insecta Phasmatodea).

    PubMed

    Tinti, F; Scali, V

    1992-11-01

    Among Sicilian stick insects, two hybridogenetic complexes have been discovered: Bacillus rossius-grandii benazzii and B. rossius-grandii grandii, which also produce androgenetic offspring. The egg maturation of the former is analyzed here through DAPI fluorometry, which, besides the assessment of the meiotic stages, also allows their DNA measurements and the analysis of sperm-head evolution into male pronuclei in these polyspermic eggs. Hybridogenetic eggs undergo an extrasynthesis of chromosomes, because two groups of n autobivalents (4C each) are segregated at metaphase 1st; the two groups must correspond to the pure parental species haplosets. Then the grandii chromosomes degenerate (1st polar body), while the rossius chromosomes divide further to produce two groups of n autodiads (2C each); one of them degenerates (2nd polar body), and the other is ready to perform syngamy (female pronucleus). Meanwhile, several B. grandii sperm evolve into male pronuclei by doubling their DNA (from 1C to 2C content) and assuming an interphase nucleus appearance. If regular mixis occurs, the F1 hybrid constitution is restored but, if it fails, a fusion between two sperms may occur, originating fully paternal descendants (natural androgenesis). The genome exclusion mechanism of stick-insect hybridogens appears to be more primitive than those observed in the already known hybridogenetic complexes of Poeciliopsis and Rana esculenta. Unfertilized eggs of hybridogens are capable of self-activation, but the cytology of the related clonally reproducing B. whitei indicates that its parthenogenetic mechanism stems from the hybridization event (hybrid theory) rather than from tychoparthenogenetic potentialities (spontaneous theory).

  14. Performance of intermittent aeration reactor on NH4-N removal from groundwater resources.

    PubMed

    Khanitchaidecha, W; Nakamura, T; Sumino, T; Kazama, F

    2010-01-01

    To study the effect of intermittent aeration period on ammonium-nitrogen (NH4-N) removal from groundwater resources, synthetic groundwater was prepared and three reactors were operated under different conditions--"reactor A" under continuous aeration, "reactor B" under 6 h intermittent aeration, and "reactor C" under 2 h intermittent aeration. To facilitate denitrification simultaneously with nitrification, "acetate" was added as an external carbon source with step-wise increase from 0.5 to 1.5 C/N ratio, where C stands for total carbon content in the system, and N for NH4-N concentration in the synthetic groundwater. Results show that complete NH4-N removal was obtained in "reactor B" and "reactor C" at 1.3 and 1.5 C/N ratio respectively; and partial NH4-N removal in "reactor A". These results suggest that intermittent aeration at longer interval could enhance the reactor performance on NH4-N removal in terms of efficiency and low external carbon requirement. Because of consumption of internal carbon by the process, less amount of external carbon is required. Further increase in carbon in a form of acetate (1.5 to 2.5 C/N ratios) increases removal rate (represented by reaction rate coefficient (k) of kinetic equation) as well as occurrence of free cells. It suggests that the operating condition at reactor B with 1.3 C/N ratio is more appropriate for long-term operation at a pilot-scale.

  15. Genetic characterization of avian influenza subtype H4N6 and H4N9 from live bird market, Thailand

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A one year active surveillance program for influenza A viruses among avian species in a live-bird market (LBM) in Bangkok, Thailand was conducted in 2009. Out of 970 samples collected, influenza A virus subtypes H4N6 (n=2) and H4N9 (n=1), were isolated from healthy Muscovy ducks. All three viruses w...

  16. [Macronuclear DNA and total protein contents of mating types I and II of Paramecium primaurelia, during the phase of maturity and the transition to senescence. Preliminary observations].

    PubMed

    Delmonte Corrado, M U; Crippa Franceschi, T

    1992-01-01

    Concerning the studies on mating type differentiation and life cycle development in Paramecium primaurelia stock 90, both macronuclear DNA and total protein contents have been measured cytofluorometrically in mating type I and mating type II isogenic cell lines growing in logarithmic phase, throughout their maturity period and transition to senescence. The target was to investigate whether the two mating types undergo clonal decline in different times, as the previous studies suggested. The results indicate that, throughout the maturity period, macronuclear DNA and total protein contents vary both in mating type I and mating type II cell lines; moreover, aged phenotypes as the dramatic decrease of both contents, firstly occur in mating type II which, therefore, appears to be submitted to clonal decline before mating type I. PMID:1294201

  17. p53 and Cell Cycle Effects After DNA Damage

    PubMed Central

    Senturk, Emir; Manfredi, James J.

    2016-01-01

    Flow cytometry, a valuable technique that employs the principles of light scattering, light excitation, and emission of fluorochrome molecules, can be used to assess the cell cycle position of individual cells based on DNA content. After the permeabilization of cells, the DNA can be stained with a fluorescent dye. Cells which have a 2N amount of DNA can be distinguished from cells with a 4N amount of DNA, making flow cytometry a very useful tool for the analysis of cell cycle checkpoints following DNA damage. A critical feature of the cellular response to DNA damage is the ability to pause and repair the damage so that consequential mutations are not passed along to daughter generations of cells. If cells arrest prior to DNA replication, they will contain a 2N amount of DNA, whereas arrest after replication but before mitosis will result in a 4N amount of DNA. Using this technique, the role that p53 plays in cell cycle checkpoints following DNA damage can be evaluated based on changes in the profile of the G1, S, and G2/M phases of the cell cycle. PMID:23150436

  18. Comparison of performance of genetics 4N6 FLOQSwabs™ with or without surfactant to rayon swabs.

    PubMed

    Frippiat, Christophe; Noel, Fabrice

    2016-08-01

    The collection of traces is the first step in the process of forensic genetics analysis. Currently, several different techniques are used (eg. gauze). Nevertheless, swabbing appears to be the most common of these. In a second step, the sampling devices should allow the use of preliminary tests in combination with an immunological confirmatory test (e.g. Hexagon Obti or Hemdirect). Our previous study shows that sampling with Genetics 4N6FLOQswabs™ coated with surfactant reduces by a factor of at least 100 the detection threshold of blood using two immunological tests. The aim of this work was to compare the ability to recover blood trace and the compatibility with immunological confirmatory test of various Genetics 4N6FLOQswabs™ nylon flocked swabs with or without surfactant. The results obtain in this study show that Genetics 4N6FLOQswabs™ not coated with surfactant and Human DNA free FLOQswabs™ were suitable for the used in combination with immunological blood detection tests. Nevertheless, the Genetics 4N6FLOQswabs™ not surfactant coated give a better blood trace recovery. PMID:27314974

  19. Comparison of performance of genetics 4N6 FLOQSwabs™ with or without surfactant to rayon swabs.

    PubMed

    Frippiat, Christophe; Noel, Fabrice

    2016-08-01

    The collection of traces is the first step in the process of forensic genetics analysis. Currently, several different techniques are used (eg. gauze). Nevertheless, swabbing appears to be the most common of these. In a second step, the sampling devices should allow the use of preliminary tests in combination with an immunological confirmatory test (e.g. Hexagon Obti or Hemdirect). Our previous study shows that sampling with Genetics 4N6FLOQswabs™ coated with surfactant reduces by a factor of at least 100 the detection threshold of blood using two immunological tests. The aim of this work was to compare the ability to recover blood trace and the compatibility with immunological confirmatory test of various Genetics 4N6FLOQswabs™ nylon flocked swabs with or without surfactant. The results obtain in this study show that Genetics 4N6FLOQswabs™ not coated with surfactant and Human DNA free FLOQswabs™ were suitable for the used in combination with immunological blood detection tests. Nevertheless, the Genetics 4N6FLOQswabs™ not surfactant coated give a better blood trace recovery.

  20. Gram-positive bacteria with a high DNA G+C content are characterized by a common insertion within their 23S rRNA genes.

    PubMed

    Roller, C; Ludwig, W; Schleifer, K H

    1992-06-01

    An insertion of about 100 bases within the central part of the 23S rRNA genes was found to be a phylogenetic marker for the bacterial line of descent of Gram-positive bacteria with a high DNA G + C content. The insertion was present in 23S rRNA genes of 64 strains representing the major phylogenetic groups of Gram-positive bacteria with a high DNA G+C content, whereas it was not found in 23S rRNA genes of 55 (eu)bacteria representing Gram-positive bacteria with a low DNA G + C content and all other known (eu)bacterial phyla. The presence of the insertion could be easily demonstrated by comparative gel electrophoretic analysis of in vitro-amplified 23S rDNA fragments, which contained the insertion. The nucleotide sequences of the amplified fragments were determined and sequence similarities of at least 44% were found. The overall similarity values are lower than those of 16S and 23S rRNA sequences of the particular organism. Northern hybridization experiments indicated the presence of the insertion within the mature 23S rRNA of Corynebacterium glutamicum.

  1. Evaluation of the impacts of different nuclear DNA content in the hull, endosperm, and embryo of rice seeds on GM rice quantification.

    PubMed

    Liu, Donger; Shen, Jie; Yang, Litao; Zhang, Dabing

    2010-04-28

    Rice (Oryza sativa) is a main staple food in the world, and several genetically modified (GM) rice events have been approved for commercialization. To accurately quantify GM contents in rice derived products, we have evaluated the variation of seed DNA density and nuclear DNA content in the hull, endosperm, and embryo of rice seeds from 19 cultivars, as well as their impacts on GM rice quantification. Rice endosperm DNA accounts for 73.71% of total seed DNA, whereas the hull and embryo DNAs account for 3.98% and 22.31%, respectively. Two formulas were established to describe the relationship between GM content on the basis of weight ratio (GM(wt)%) and that on the basis of haploid genome copy number ratio (GM(hg)%) for the samples containing heterozygous GM rice seeds. These two equations were well confirmed in quantification of the heterozygous GM rice TT51-1 seeds containing the GM allele from a female parent or that from a male parent. This work is useful for accurate quantification of GM rice using reference materials containing the heterozygous GM rice seed powder.

  2. Effect of treated-sewage contamination upon bacterial energy charge, adenine nucleotides, and DNA content in a sandy aquifer on cape cod

    USGS Publications Warehouse

    Metge, D.W.; Brooks, M.H.; Smith, R.L.; Harvey, R.W.

    1993-01-01

    Changes in adenylate energy charge (EC(A)) and in total adenine nucleotides (A(T)) and DNA content (both normalized to the abundance of free- living, groundwater bacteria) in response to carbon loading were determined for a laboratory-grown culture and for a contaminated aquifer. The latter study involved a 3-km-long transect through a contaminant plume resulting from continued on-land discharge of secondary sewage to a shallow, sandy aquifer on Cape Cod, Mass. With the exception of the most contaminated groundwater immediately downgradient from the contaminant source, DNA and adenylate levels correlated strongly with bacterial abundance and decreased exponentially with increasing distance downgradient. EC(A)s (0.53 to 0.60) and the ratios of ATP to DNA (0.001 to 0.003) were consistently low, suggesting that the unattached bacteria in this groundwater study are metabolically stressed, despite any eutrophication that might have occurred. Elevated EC(A)s (up to 0.74) were observed in glucose-amended groundwater, confirming that the metabolic state of this microbial community could be altered. In general, per-bacterium DNA and ATP contents were approximately twofold higher in the plume than in surrounding groundwater, although EC(A) and per-bacterium levels of A(T) differed little in the plume and the surrounding uncontaminated groundwater. However, per-bacterium levels of DNA and A(T) varied six- and threefold, respectively, during a 6-h period of decreasing growth rate for an unidentified pseudomonad isolated from contaminated groundwater and grown in batch culture. These data suggest that the DNA content of groundwater bacteria may be more sensitive than their A(T) to the degree of carbon loading, which may have significant ramifications in the use of nucleic acids and adenine nucleotides for estimating the metabolic status of bacterial communities within more highly contaminated aquifers.

  3. The human DNA content in artifacts deposited by the blowfly Lucilia cuprina fed human blood, semen and saliva.

    PubMed

    Durdle, Annalisa; Mitchell, Robert John; van Oorschot, Roland A H

    2013-12-10

    Adult flies of some species are known to be attracted to crime scenes where they feed on the proteinaceous decomposition products of dead bodies. The flies leave deposits through excretion and regurgitation, and these artifacts often appear morphologically similar to bloodstains. To date, little consideration has been given to the possibility of the fly artifacts containing forensically useful levels of human DNA, or of flies as vectors of human DNA. In the present study, groups of artifacts collected after the adult blowfly Lucilia cuprina fed on biological fluids were examined and found to contain human DNA sufficient for profiling. Random samples from each group of artifacts were then subjected to human DNA profiling. Of the samples analysed, full or partial human DNA profiles were found in 57% of samples deposited by flies after blood meals, 92% after semen meals, 46% after saliva meals, 93% after blood/semen meals, 58% after blood/saliva meals and 95% after semen/saliva meals. DNA from artifacts deposited after flies were fed blood, semen, saliva, blood/semen, blood/saliva or semen/saliva was extracted at various time points up to 750 days, and the human DNA component quantified. The human DNA extracted from blood- and semen-based fly artifacts demonstrated a clear trend in which the amount of DNA extracted increased over the first 400 days, and full human DNA profiles were still obtained 750 days after artifact deposition. Saliva- and blood/saliva-based samples were tested at intervals up to 60 days and generated partial profiles at this final time. Blood/semen- and semen/saliva-based samples generated full profiles at 250 days. The presence of human DNA in fly artifacts has considerable forensic significance. Fly artifacts could potentially compromise crime reconstruction, and/or contaminate DNA evidence, up to at least two years after their deposition. Alternatively, fly artifacts may be a useful source of DNA if an offender has attempted to clean up a

  4. New use for an old reagent: Cell cycle analysis of DNA content using flow cytometry in formamide treated cells.

    PubMed

    Carbonari, Maurizio

    2016-05-01

    Formamide has long been one of the most widely used reagents in the study of nucleic acids. However, the use of formamide for treating cells to be analyzed by flow cytometry is a recent development and is restricted to measuring telomere lengths by flow-FISH. In this field, we have published several papers in order to observe the effects of formamide treatment on cells at room temperature. We therefore discovered that, with suitable modifications, a short and simple incubation in this ionizing solvent facilitates cell cycle analysis by flow cytometry, equivalent or superior to that obtained with treatments in alcohol, acetone or detergent in hypotonic solution. Even using a bulky and problematic stain (low quantum efficiency and G-C base preference), such as 7-aminoactinomycin D (7-AAD) which, on the other hand, has the advantage of being excited at 488 nm and does not bind to the RNA, it is possible to obtain excellent coefficients of variation and (G2-M) mode/(G0-G1) mode ratios. These parameters, especially if stained cells are washed before acquisition, arrive at optimal values. It is noteworthy that the ability to wash the cells stained for DNA content analysis without affecting the stoichiometry of the staining has not been described elsewhere in the literature. With formamide treatment the doublets are practically absent, sample recovery is efficient, as well as the preservation of physical parameters, and the stained cells can be stored for at least 10 days at room temperature before acquisition. © 2016 International Society for Advancement of Cytometry. PMID:26866418

  5. Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G + C content.

    PubMed

    Meier, H; Amann, R; Ludwig, W; Schleifer, K H

    1999-05-01

    Almost one thousand 16S rRNA sequences of Gram-positive bacteria with a low DNA G + C content from public databases were analyzed using the ARB software package. A signature region was identified between positions 354 and 371 (E. coli numbering) for the Bacillus sub-branch of the Gram-positive bacteria with a low DNA G + C content, the former orders Bacillales and Lactobacillales. Three oligonucleotide probes, namely LGC354A, LGC354B, and LGC354C, were designed to target this diagnostic site. Their fluorescent derivatives were suitable for whole cell detection by fluorescence in situ hybridization (FISH). Hybridization conditions were adjusted for differentiation of target and related non-target reference species. When applying FISH to whole bacterial cells in a sample of activated sludge from a communal wastewater treatment plant, members of the Bacillus sub-branch were detected at levels from 0.01% of cells in samples fixed with paraformaldehyde to over 8 percent in the same samples fixed with ethanol and treated with lysozyme. The problems of quantitative in situ analysis of Gram-positive bacteria with a low DNA G + C content in biofilm flocs are discussed and recommendations made. Members of the Bacillus sub-branch were detected in different abundances in activated sludge samples from different wastewater plants.

  6. The human DNA content in artifacts deposited by the blowfly Lucilia cuprina fed human blood, semen and saliva.

    PubMed

    Durdle, Annalisa; Mitchell, Robert John; van Oorschot, Roland A H

    2013-12-10

    Adult flies of some species are known to be attracted to crime scenes where they feed on the proteinaceous decomposition products of dead bodies. The flies leave deposits through excretion and regurgitation, and these artifacts often appear morphologically similar to bloodstains. To date, little consideration has been given to the possibility of the fly artifacts containing forensically useful levels of human DNA, or of flies as vectors of human DNA. In the present study, groups of artifacts collected after the adult blowfly Lucilia cuprina fed on biological fluids were examined and found to contain human DNA sufficient for profiling. Random samples from each group of artifacts were then subjected to human DNA profiling. Of the samples analysed, full or partial human DNA profiles were found in 57% of samples deposited by flies after blood meals, 92% after semen meals, 46% after saliva meals, 93% after blood/semen meals, 58% after blood/saliva meals and 95% after semen/saliva meals. DNA from artifacts deposited after flies were fed blood, semen, saliva, blood/semen, blood/saliva or semen/saliva was extracted at various time points up to 750 days, and the human DNA component quantified. The human DNA extracted from blood- and semen-based fly artifacts demonstrated a clear trend in which the amount of DNA extracted increased over the first 400 days, and full human DNA profiles were still obtained 750 days after artifact deposition. Saliva- and blood/saliva-based samples were tested at intervals up to 60 days and generated partial profiles at this final time. Blood/semen- and semen/saliva-based samples generated full profiles at 250 days. The presence of human DNA in fly artifacts has considerable forensic significance. Fly artifacts could potentially compromise crime reconstruction, and/or contaminate DNA evidence, up to at least two years after their deposition. Alternatively, fly artifacts may be a useful source of DNA if an offender has attempted to clean up a

  7. AQ4N: an alkylaminoanthraquinone N-oxide showing bioreductive potential and positive interaction with radiation in vivo.

    PubMed Central

    McKeown, S. R.; Hejmadi, M. V.; McIntyre, I. A.; McAleer, J. J.; Patterson, L. H.

    1995-01-01

    AQ4N (1,4-bis([2-(dimethylamino-N-oxide)ethyl]amino)5,8-dihydroxy- anthracene-9,10-dione) is a novel alkylaminoanthraquinone N-oxide which, on reduction, forms a stable DNA affinic cytotoxic compound AQ4. The in vivo anti-tumour efficacy of AQ4N was investigated in B6D2F1 mice bearing the T50/80 mammary carcinoma. The effect of the drug was evaluated in combination with hypobaric hypoxia and with radiation (single and multiple fractions). Systemic toxicity was assessed by weight loss post treatment. This was low for AQ4N and was less than that obtained with the bioreductive drugs, RSU 1069 (1-[3-aziridinyl-2-hydroxypropyl]-2-nitroimidazole) and SR 4233 (Tirapazamine, 3-amino-1,2,4-benzotriazine-1,4-dioxide). The anti-tumour effect of AQ4N was potentiated in vivo by combination with hypobaric hypoxia with a dose enhancement ratio of 5.1. This is consistent with the proposal that AQ4N was reduced in vivo to AQ4, resulting in enhanced anti-tumour toxicity. When AQ4N (200 mg kg-1) was combined with single dose radiation (12 Gy) the drug was shown to have an additive interaction with radiation. This was obtained even if the drug was administered from 4 days before to 6 h after radiation treatment. Equivalent anti-tumour activity was also shown when both AQ4N (200 mg kg-1) and radiation (5 x 3 Gy) were administered in fractionated schedules. In conclusion, AQ4N shows significant potential as a bioreductive drug for combination with fractionated radiotherapy. PMID:7599069

  8. Effect of treated-sewage contamination upon bacterial energy charge, adenine nucleotides, and DNA content in a sandy aquifer on Cape Cod.

    PubMed

    Metge, D W; Brooks, M H; Smith, R L; Harvey, R W

    1993-07-01

    Changes in adenylate energy charge (ECA) and in total adenine nucleotides (A(T) and DNA content (both normalized to the abundance of free-living, groundwater bacteria) in response to carbon loading were determined for a laboratory-grown culture and for a contaminated aquifer. The latter study involved a 3-km-long transect through a contaminant plume resulting from continued on-land discharge of secondary sewage to a shallow, sandy aquifer on Cape Cod, Mass. With the exception of the most contaminated groundwater immediately downgradient from the contaminant source, DNA and adenylate levels correlated strongly with bacterial abundance and decreased exponentially with increasing distance downgradient. ECAS (0.53 to 0.60) and the ratios of ATP to DNA (0.001 to 0.003) were consistently low, suggesting that the unattached bacteria in this groundwater study are metabolically stressed, despite any eutrophication that might have occurred. Elevated ECAS (up to 0.74) were observed in glucose-amended groundwater, confirming that the metabolic state of this microbial community could be altered. In general, per-bacterium DNA and ATP contents were approximately twofold higher in the plume than in surrounding groundwater, although ECA and per-bacterium levels of A(T) differed little in the plume and the surrounding uncontaminated groundwater. However, per-bacterium levels of DNA and A(T) varied six- and threefold, respectively, during a 6-h period of decreasing growth rate for an unidentified pseudomonad isolated from contaminated groundwater and grown in batch culture.(ABSTRACT TRUNCATED AT 250 WORDS)

  9. [Mechanism of NH(4+)-N removal in drinking water biofilter].

    PubMed

    Liu, Bing; Fan, Hui; Yu, Guo-Zhong; Yu, Xin; Zhao, Cheng-Mei; Li, Qing-Fei; Zhang, Shu-Ting; Wei, Bo

    2012-07-01

    In order to explore the mechanism of NH(4+)-N removal in drinking water biofilter, water quality parameters, such as NH(4+)-N, NO(2-)-N, NO(3-)-N, total phosphorus, permanganate index, nitrogen gas, temperature and dissolved oxygen etc, were determined in the inflow and outflow of biofilter. Samples of granular activated carbon (GAC) at different height (0, 10, 20, 40, 60 cm) of the biofiter media were collected and analyzed for the bacterial community with molecular biology techniques. The bacterial diversity in the activated carbon biofilm sample was studied based on the phylogenetic analysis of sequences. The results showed that there were three stages according to the NH(4+)-N concentration in the influent. The "nitrogen loss" phenomenon (total inorganic nitrogen in the effluent was less than that in the influent) occurred at the first, second and third stages and the amount of nitrogen loss were 0.94, 0.32 and 0.15 mg x L(-1), respectively. The amount of nitrogen loss had a good positive correlation with the NH(4+)-N concentration in the influent, but not a linear relationship with the concentration of the permanganate index in the influent. The average concentrations of N2 increased gradually with the height of media in the biofilter, with values of 14.04 and 14.67 mg x L(-1) in the influent and the effluent, respectively. Based on the sequencing results, the ammonia-oxidizing bacteria (AOB) in the activated carbon biofilm were classified into three common genera: Nitrosococcus, Nitrosomonas and Nitrosospira. When the NH(4+)-N concentration in the influent was relatively high, the "nitrogen loss" phenomenon in biofilter was caused by the AOB.

  10. Potential for 4-n-nonylphenol biodegradation in stream sediments

    USGS Publications Warehouse

    Bradley, P.M.; Barber, L.B.; Kolpin, D.W.; McMahon, P.B.; Chapelle, F.H.

    2008-01-01

    The potential for in situ biodegradation of 4-nonylphenol (4-NP) was investigated in three hydrologically distinct streams impacted by wastewater treatment plants (WWTPs) in the United States. Microcosms were prepared with sediments from each site and amended with [U-ring-14C]4-n-nonylphenol (4-n-NP) as a model test substrate. Microcosms prepared with sediment collected upstream of the WWTP outfalls and incubated under oxic conditions showed rapid and complete mineralization of [U-ring-14C]4- n-NP to 14CO2 in all three systems. In contrast, no mineralization of [U-ring-14C]4-n-NP was observed in these sediments under anoxic (methanogenic) conditions. The initial linear rate of [U-ring-14C]4-n-NP mineralization in sediments from upstream and downstream of the respective WWTP outfalls was inversely correlated with the biochemical oxygen demand (BOD) of the streambed sediments. These results suggest that the net supply of dissolved oxygen to streambed sediments is a key determinant of the rate and extent of 4-NP biodegradation in stream systems. In the stream systems considered by the present study, dissolved oxygen concentrations in the overlying water column (8–10 mg/L) and in the bed sediment pore water (1–3 mg/L at a depth of 10 cm below the sediment–water interface) were consistent with active in situ 4-NP biodegradation. These results suggest WWTP procedures that maximize the delivery of dissolved oxygen while minimizing the release of BOD to stream receptors favor efficient biodegradation of 4-NP contaminants in wastewater-impacted stream environments.

  11. DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

    PubMed Central

    Rawlence, Nicolas J.; Wood, Jamie R.; Armstrong, Kyle N.; Cooper, Alan

    2009-01-01

    Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains. PMID:19570784

  12. Degradation of 4-n-nonylphenol under nitrate reducing conditions

    PubMed Central

    Viñas, Marc; Grotenhuis, Tim; Rijnaarts, Huub H. M.; Langenhoff, Alette A. M.

    2010-01-01

    Nonylphenol (NP) is an endocrine disruptor present as a pollutant in river sediment. Biodegradation of NP can reduce its toxicological risk. As sediments are mainly anaerobic, degradation of linear (4-n-NP) and branched nonylphenol (tNP) was studied under methanogenic, sulphate reducing and denitrifying conditions in NP polluted river sediment. Anaerobic bioconversion was observed only for linear NP under denitrifying conditions. The microbial population involved herein was further studied by enrichment and molecular characterization. The largest change in diversity was observed between the enrichments of the third and fourth generation, and further enrichment did not affect the diversity. This implies that different microorganisms are involved in the degradation of 4-n-NP in the sediment. The major degrading bacteria were most closely related to denitrifying hexadecane degraders and linear alkyl benzene sulphonate (LAS) degraders. The molecular structures of alkanes and LAS are similar to the linear chain of 4-n-NP, this might indicate that the biodegradation of linear NP under denitrifying conditions starts at the nonyl chain. Initiation of anaerobic NP degradation was further tested using phenol as a structure analogue. Phenol was chosen instead of an aliphatic analogue, because phenol is the common structure present in all NP isomers while the structure of the aliphatic chain differs per isomer. Phenol was degraded in all cases, but did not affect the linear NP degradation under denitrifying conditions and did not initiate the degradation of tNP and linear NP under the other tested conditions. PMID:20640878

  13. Isolation of the human anionic glutathione S-transferase cDNA and the relation of its gene expression to estrogen-receptor content in primary breast cancer.

    PubMed Central

    Moscow, J A; Townsend, A J; Goldsmith, M E; Whang-Peng, J; Vickers, P J; Poisson, R; Legault-Poisson, S; Myers, C E; Cowan, K H

    1988-01-01

    The development of multidrug resistance in MCF7 human breast cancer cells is associated with overexpression of P-glycoprotein, changes in activities of several detoxication enzymes, and loss of hormone sensitivity and estrogen receptors (ERs). We have cloned the cDNA for one of the drug-detoxifying enzymes overexpressed in multidrug-resistant MCF7 cells (AdrR MCF7), the anionic isozyme of glutathione S-transferase (GST pi). Hybridization with this GST pi cDNA, GST pi-1, demonstrated that increased GST pi activity in AdrR MCF7 cells is associated with overexpression but not with amplification of the gene. We mapped the GST pi gene to human chromosome 11q13 by in situ hybridization. Since multidrug resistance and GST pi overexpression are associated with the loss of ERs in AdrR MCF7 cells, we examined several other breast cancer cell lines that were not selected for drug resistance. In each of these cell lines we found an inverse association between GST pi expression and ER content. We also examined RNA from 21 primary breast cancers and found a similar association between GST pi expression and ER content in vivo. GST pi mRNA content in 11 ER-positive tumors (less than or equal to 10 fmol/mg of protein) was significantly different from the GST pi content of 10 ER-negative tumors (P = 0.002; Mann-Whitney Wilcoxon test for two independent samples). The finding of similar patterns of expression of a drug-detoxifying enzyme and of ERs in vitro as well as in vivo suggests that ER-negative breast cancer cells may have greater protection against antineoplastic agents conferred by GST pi than ER-positive tumors. Images PMID:2842775

  14. Fat Content and Nitrite-Curing Influence the Formation of Oxidation Products and NOC-Specific DNA Adducts during In Vitro Digestion of Meat

    PubMed Central

    Van Hecke, Thomas; Vossen, Els; Vanden Bussche, Julie; Raes, Katleen; Vanhaecke, Lynn; De Smet, Stefaan

    2014-01-01

    The effects of fat content and nitrite-curing of pork were investigated on the formation of cytotoxic and genotoxic lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal, volatile simple aldehydes), protein oxidation products (protein carbonyl compounds) and NOC-specific DNA adducts (O6-carboxy-methylguanine) during in vitro digestion. The formation of these products during digestion is suggested to be responsible for the association between red meat and processed meat consumption and colorectal cancer risk. Digestion of uncured pork to which fat was added (total fat content 5 or 20%), resulted in significantly higher lipid and protein oxidation in the mimicked duodenal and colonic fluids, compared to digestion of pork without added fat (1% fat). A higher fat content also significantly favored the formation of O6-carboxy-methylguanine in the colon. Nitrite-curing of meat resulted in significantly lower lipid and protein oxidation before and after digestion, while an inconsistent effect on the formation of O6-carboxy-methylguanine was observed. The presented results demonstrate that haem-Fe is not solely responsible for oxidation and nitrosation reactions throughout an in vitro digestion approach but its effect is promoted by a higher fat content in meat. PMID:24978825

  15. Fat content and nitrite-curing influence the formation of oxidation products and NOC-specific DNA adducts during in vitro digestion of meat.

    PubMed

    Van Hecke, Thomas; Vossen, Els; Vanden Bussche, Julie; Raes, Katleen; Vanhaecke, Lynn; De Smet, Stefaan

    2014-01-01

    The effects of fat content and nitrite-curing of pork were investigated on the formation of cytotoxic and genotoxic lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal, volatile simple aldehydes), protein oxidation products (protein carbonyl compounds) and NOC-specific DNA adducts (O6-carboxy-methylguanine) during in vitro digestion. The formation of these products during digestion is suggested to be responsible for the association between red meat and processed meat consumption and colorectal cancer risk. Digestion of uncured pork to which fat was added (total fat content 5 or 20%), resulted in significantly higher lipid and protein oxidation in the mimicked duodenal and colonic fluids, compared to digestion of pork without added fat (1% fat). A higher fat content also significantly favored the formation of O6-carboxy-methylguanine in the colon. Nitrite-curing of meat resulted in significantly lower lipid and protein oxidation before and after digestion, while an inconsistent effect on the formation of O6-carboxy-methylguanine was observed. The presented results demonstrate that haem-Fe is not solely responsible for oxidation and nitrosation reactions throughout an in vitro digestion approach but its effect is promoted by a higher fat content in meat.

  16. The Effect of Leonurus sibiricus Plant Extracts on Stimulating Repair and Protective Activity against Oxidative DNA Damage in CHO Cells and Content of Phenolic Compounds

    PubMed Central

    Sitarek, Przemysław; Skała, Ewa; Wysokińska, Halina; Wielanek, Marzena; Szemraj, Janusz; Toma, Monika; Śliwiński, Tomasz

    2016-01-01

    Leonurus sibiricus L. has been used as a traditional and medicinal herb for many years in Asia and Europe. This species is known to have antibacterial, anti-inflammatory, and antioxidant activity and has demonstrated a reduction of intracellular reactive oxygen species. All tested extracts of L. sibiricus showed protective and DNA repair stimulating effects in Chinese hamster ovary (CHO) cells exposed to H2O2. Preincubation of the CHO cells with 0.5 mg/mL of plant extracts showed increased expression level of antioxidant genes (SOD2, CAT, and GPx). LC-MS/MS and HPLC analyses revealed the presence of nine phenolic compounds in L. sibiricus plant extracts: catechin, verbascoside, two flavonoids (quercetin and rutin), and five phenolic acids (4-hydroxybenzoic acid, chlorogenic acid, caffeic acid, p-coumaric acid, and ferulic acid). The roots and aerial parts of in vitro L. sibiricus plant extracts, which had the strongest antioxidant properties, may be responsible for stimulating CHO cells to repair oxidatively induced DNA damage, as well as protecting DNA via enhanced activation of the antioxidant genes (SOD2, CAT, and GPx) regulating intracellular antioxidant capacity. The content of phenolic compounds in in vitro raised plants was greater than the levels found in plants propagated from seeds. PMID:26788249

  17. The Effect of Leonurus sibiricus Plant Extracts on Stimulating Repair and Protective Activity against Oxidative DNA Damage in CHO Cells and Content of Phenolic Compounds.

    PubMed

    Sitarek, Przemysław; Skała, Ewa; Wysokińska, Halina; Wielanek, Marzena; Szemraj, Janusz; Toma, Monika; Śliwiński, Tomasz

    2016-01-01

    Leonurus sibiricus L. has been used as a traditional and medicinal herb for many years in Asia and Europe. This species is known to have antibacterial, anti-inflammatory, and antioxidant activity and has demonstrated a reduction of intracellular reactive oxygen species. All tested extracts of L. sibiricus showed protective and DNA repair stimulating effects in Chinese hamster ovary (CHO) cells exposed to H2O2. Preincubation of the CHO cells with 0.5 mg/mL of plant extracts showed increased expression level of antioxidant genes (SOD2, CAT, and GPx). LC-MS/MS and HPLC analyses revealed the presence of nine phenolic compounds in L. sibiricus plant extracts: catechin, verbascoside, two flavonoids (quercetin and rutin), and five phenolic acids (4-hydroxybenzoic acid, chlorogenic acid, caffeic acid, p-coumaric acid, and ferulic acid). The roots and aerial parts of in vitro L. sibiricus plant extracts, which had the strongest antioxidant properties, may be responsible for stimulating CHO cells to repair oxidatively induced DNA damage, as well as protecting DNA via enhanced activation of the antioxidant genes (SOD2, CAT, and GPx) regulating intracellular antioxidant capacity. The content of phenolic compounds in in vitro raised plants was greater than the levels found in plants propagated from seeds.

  18. Detection of TP53 mutation, loss of heterozygosity and DNA content in fine-needle aspirates of breast carcinoma.

    PubMed Central

    Lavarino, C.; Corletto, V.; Mezzelani, A.; Della Torre, G.; Bartoli, C.; Riva, C.; Pierotti, M. A.; Rilke, F.; Pilotti, S.

    1998-01-01

    Recent preclinical and clinical data suggest that TP53 status and TP53 mutations may be important in determining tumour aggressiveness and therapy response. In this study we investigate the feasibility of a structural and quantitative analysis of TP53 on fine-needle aspiration (FNA) material obtained from 31 consecutive female patients with breast carcinoma, enrolled in a primary chemotherapy protocol. Tumours were screened for p53 protein overexpression and TP53 mutations (exons 5-8) using immunocytochemistry, polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing analyses, and finally using fluorescence in situ hybridization (FISH) analysis. Positive nuclear staining was identified in six cases whereas mutations were detected in nine. Although the immunoreactive pattern fitted fully with the characterized TP53 mutation type, the considerable number of null p53 mutations (i.e. four) coupled with the lack of information regarding the localization of TP53 mutations make immunocytochemistry an inadequate indicator of TP53 function deregulation. Combining molecular and FISH analyses, we detected three cases with TP53 deletion and one case with deletion and mutation. Finally, DNA static-image analysis performed on 29 cases showed aneuploidy in 26 cases, which included all TP53-mutated cases. The present results show that FNA may assist clinical decisions by allowing the evaluation of a variety of biological parameters relevant for prognosis and treatment planning. Images Figure 1 PMID:9459157

  19. Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis

    SciTech Connect

    Georgescu, Walter; Osseiran, Alma; Rojec, Maria; Liu, Yueyong; Bombrun, Maxime; Tang, Jonathan; Costes, Sylvain V.; Huen, Michael Shing-Yan

    2015-06-24

    Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too

  20. Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis

    DOE PAGES

    Georgescu, Walter; Osseiran, Alma; Rojec, Maria; Liu, Yueyong; Bombrun, Maxime; Tang, Jonathan; Costes, Sylvain V.; Huen, Michael Shing-Yan

    2015-06-24

    Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were ablemore » to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too many

  1. UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions.

    PubMed

    Robasky, Kimberly; Bulyk, Martha L

    2011-01-01

    The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.

  2. Real-time quantitative polymerase chain reaction methods for four genetically modified maize varieties and maize DNA content in food.

    PubMed

    Brodmann, Peter D; Ilg, Evelyn C; Berthoud, Hélène; Herrmann, Andre

    2002-01-01

    Quantitative detection methods are needed for enforcement of the recently introduced labeling threshold for genetically modified organisms (GMOs) in food ingredients. This labeling threshold, which is set to 1% in the European Union and Switzerland, must be applied to all approved GMOs. Four different varieties of maize are approved in the European Union: the insect-resistant Bt176 maize (Maximizer), Btl 1 maize, Mon810 (YieldGard) maize, and the herbicide-tolerant T25 (Liberty Link) maize. Because the labeling must be considered individually for each ingredient, a quantitation system for the endogenous maize content is needed in addition to the GMO-specific detection systems. Quantitative real-time polymerase chain reaction detection methods were developed for the 4 approved genetically modified maize varieties and for an endogenous maize (invertase) gene system.

  3. Computational chemical studies on thermochemistry and ring strains in cyclic [n]metaphenyleneacetylenes, butadiyne-bridged [4n]metacyclophynes, and butadiyne-bridged [4n]paracyclophynes.

    PubMed

    Ali, Mohamad Akbar; Krishnan, Mangala Sunder

    2010-09-01

    The thermochemical properties and ring strains in cyclic [n]metaphenyleneacetylenes ([n]CMPAs), butadiyne-bridged [4(n)]metacyclophynes (B-B[4(n)]MCs), and butadiyne-bridged [4(n)]paracyclophynes (B-B[4(n)]PCs) were studied using a homodesmotic reaction scheme coupled with density functional theory (B3LYP/6-31G*, mPW1PW91/6-31G*, and M06-2X/6-31+G**//B3LYP/6-31G*). Strain energies of [n]CMPAs and B-B[4(n)]MCs decrease first from very high values for small rings to become zero when n becomes 6, then increase with n, and finally decrease as n becomes larger than 8. In the case of B-B[4(n)]PCs, strain energies decrease with increasing n. Heats of formation of [n]CMPAs, B-B[4(n)]MCs, and B-B[4(n)]PCs increase steadily with increasing numbers of phenylacetylene and 1-(buta-1,3-diynyl)benzene to reach a near-constant value per unit monomer as n increases. The geometries and (vibrational and nuclear magnetic resonance) spectroscopic properties of [n]CMPAs, B-B[4(n)]MCs, and B-B[4(n)]PCs were also studied. Geometrical parameters, Raman frequencies, and (1)H NMR chemical shifts of [3]CMPA and [4]CMPA are found to be in good agreement with compounds for which there are experimentally available values at the B3LYP/6-31G* level of theory. In addition, electronic structure calculations were carried out for [n]CMPAs, B-B[4(n)]MCs, and B-B[4(n)]PCs. Ring diameters were also calculated for B-B[4(n)]PCs. PMID:20695635

  4. In situ probing of gram-positive bacteria with high DNA G + C content using 23S rRNA-targeted oligonucleotides.

    PubMed

    Roller, C; Wagner, M; Amann, R; Ludwig, W; Schleifer, K H

    1994-10-01

    23S-rRNA-targeted oligonucleotide probes were designed for the phylogenetic group 'Gram-positive bacteria with high G + C content of DNA' (GPBHGC). A sequence idiosyncrasy in two adjacent base pairs in the stem of helix 69 in domain IV of the 23S rRNA is present in all hitherto analysed strains of GPBHGC. An oligonucleotide probe targeted to this region hybridized only with strains of GPBHGC and was successfully used for in situ monitoring of these cells in activated sludge. Another unique feature of the 23S rRNA molecules of GPBHGC is a large insertion in domain III. Fluorescent oligonucleotides targeted to the highly variable regions of the rRNA within the insertions of Corynebacterium glutamicum DSM 20300, Aureobacterium testaceum DSM 20166 and Brevibacterium sp. DSM 20165 hybridized specifically to their target strains, whereas probing with oligonucleotides complementary to the rRNA-coding strand of the 23S rDNA and to the spacer between 16S and 23S rRNA of C. glutamicum did not result in detectable fluorescence. This confirmed that the large 23S insertions are indeed present in 23S rRNAs of GPBHGC and provide potential target sites for highly specific nucleic acid probes.

  5. On the way to identify microorganisms in drinking water distribution networks via DNA analysis of the gut content of freshwater isopods.

    PubMed

    Mayer, Michael; Keller, Adrian; Szewzyk, Ulrich; Warnecke, Hans-Joachim

    2015-05-10

    Pure drinking water is the basis for a healthy society. In Germany the drinking water regulations demand for analysis of water via detection of certain microbiological parameters by cultivation only. However, not all prokaryotes can be detected by these standard methods. How to gain more and better information about the bacteria present in drinking water and its distribution systems? The biofilms in drinking water distribution systems are built by bacteria and therefore represent a valuable source of information about the species present. Unfortunately, these biofilms are badly accessible. We thus exploited the circumstance that a lot of metazoans graze the biofilms, so that the content of their guts partly reflects the respective biofilm biocenosis. Therefore, we collected omnivorous isopods, prepared their guts and examined and characterized their contents based on 16S und 18S rDNA analysis. These molecularbiological investigations provide a profound basis for the characterization of the biocenosis and thereby biologically assess the drinking water ecosystems. Combined with a thorough identification of the species and the knowledge of their habitats, this approach can provide useful indications for the assessment of drinking-water quality and the early detection of problems in the distribution system.

  6. On the way to identify microorganisms in drinking water distribution networks via DNA analysis of the gut content of freshwater isopods.

    PubMed

    Mayer, Michael; Keller, Adrian; Szewzyk, Ulrich; Warnecke, Hans-Joachim

    2015-05-10

    Pure drinking water is the basis for a healthy society. In Germany the drinking water regulations demand for analysis of water via detection of certain microbiological parameters by cultivation only. However, not all prokaryotes can be detected by these standard methods. How to gain more and better information about the bacteria present in drinking water and its distribution systems? The biofilms in drinking water distribution systems are built by bacteria and therefore represent a valuable source of information about the species present. Unfortunately, these biofilms are badly accessible. We thus exploited the circumstance that a lot of metazoans graze the biofilms, so that the content of their guts partly reflects the respective biofilm biocenosis. Therefore, we collected omnivorous isopods, prepared their guts and examined and characterized their contents based on 16S und 18S rDNA analysis. These molecularbiological investigations provide a profound basis for the characterization of the biocenosis and thereby biologically assess the drinking water ecosystems. Combined with a thorough identification of the species and the knowledge of their habitats, this approach can provide useful indications for the assessment of drinking-water quality and the early detection of problems in the distribution system. PMID:25558805

  7. Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome

    NASA Astrophysics Data System (ADS)

    Li, Wentian; Holste, Dirk

    2005-04-01

    Spatial fluctuations of guanine and cytosine base content (GC%) are studied by spectral analysis for the complete set of human genomic DNA sequences. We find that (i) 1/fα decay is universally observed in the power spectra of all 24 chromosomes, and (ii) the exponent α≈1 extends to about 107 bases, one order of magnitude longer than has previously been observed. We further find that (iii) almost all human chromosomes exhibit a crossover from α1≈1 (1/fα1) at lower frequency to α2<1 (1/fα2) at higher frequency, typically occurring at around 30 000-100 000 bases, while (iv) the crossover in this frequency range is virtually absent in human chromosome 22. In addition to the universal 1/fα noise in power spectra, we find (v) several lines of evidence for chromosome-specific correlation structures, including a 500 000 base long oscillation in human chromosome 21. The universal 1/fα spectrum in the human genome is further substantiated by a resistance to reduction in variance of guanine and cytosine content when the window size is increased.

  8. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    SciTech Connect

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably

  9. [In vitro studies on the influence of volatile anaesthetics on cell number, cell volume, and cellular protein, DNA, and RNA content (author's transl)].

    PubMed

    Hack, G; Karzel, K; Panthong, A; Stein, P

    1981-03-01

    The aim of the present investigations was to see, if halothane (h), enflurane (e), isoflurane (i), and methoxyflurane (m) exert cytostatic or cytotoxic effects. The experiments were performed on suspension cultures of an established line of Ehrlich ascites tumor cells, which were gased by a mixture of N2 (78%), O2 (20%), and CO2 (2%) to which the volatile anaesthetics in 5 different concentrations were added by vaporizers. Under standardized conditions (incubation time: 24 or 48 hrs; initial cell density: 2 X 10(5) cells/ml culture medium) the following results were obtained: 1. All anaesthetics exerted dose dependent cytostatic effects, which were reversible up to concentrations of 2.0 vol% (m), 3.0 vol% (h), and 5.0 vol% (e, i). The cytostatic ID50 values (mmol/l) were found to be 0.50 (h), 1.00 (e), 0.72 (i), 1.25 (m). 2. In cell cultures, which were exposed to anaesthetics for 48 hrs cytotoxic effects were observed after doses of 2.0 vol% (m), 3.0 and 4.0 vol% (h), 4.0 and 5.0 vol% (e and i). 3. In contrast to colchicine, which was studied in comparison to the volatile anaesthetics, the mean cell volume of anaesthetic treated cultures showed only minimal deviations from control values. 4. With exception of m, which produced a significant decrease of the cellular protein content in the dose range 1.5-2.0 vol% and of the cellular DNA content in all concentrations applied the 3 other anaesthetics caused an increase of the cellular protein content and a somewhat smaller increase of the cellular nucleic acids content. The obtained results indicate that the effect of anaesthetic agents on dividing cells is not due to the same mode or site of action, but to an influence on different stage of the cell cycle, particularly the interphase. Colchicine-like c-mitosis were not obtained.

  10. Treatment of licorice seeds with colchicine: changes in seedling DNA levels and anthocyanin and glycyrrhizic acid contents of derived callus cultures.

    PubMed

    Bernard, Françoise; Moghbel, Nahid; Hassannejad, Sahar

    2012-11-01

    The use of colchicine to induce polyploids increases secondary metabolite production potential and has been used for many years for the production of valuable compounds in plants. This project took advantage of this method to increase the production of secondary metabolites in licorice. For this purpose, seeds of licorice, Glycyrrhiza glabra var. glandulifera, were treated with different concentrations of colchicine for 24 hours and then cultivated in vitro. After a month, the effect of colchicine on the cellular DNA level of cotyledons was analyzed by spectrophotometry and flow cytometry. For callus induction, root explants of one month old plantlets derived from colchicine treated seeds were transferred to MS medium containing growth regulators and the anthocyanin and glycyrrhizic acid levels of the callus tissues were measured after two months of growth. The total DNA content of plantlets derived from seeds treated with 0.05%, 0.08% and 0.1% of colchicine for 24 hours was increased significantly. Treated plants had increased numbers of larger stomata, significantly in those treated with 0.1% of colchicine for 24 hours. After colchicine treatment, the root, shoot and leaf thickness was found to be increased, while their length was decreased. Results of flow cytometry showed changes in ploidy level in plantlets obtained from treatment with 0.08% (mixoploids) and 0.1% (tetraploids) of colchicine. Anthocyanin level was significantly increased in callus obtained from plantlets treated with 0.08% of colchicine. The amount of glycyrrhizic acid in all treatments increased, especially in the 0.1 and 0.03% colchicine treatments and this seems to prove an increased production of metabolites in polyploid licorice tissues. PMID:23285806

  11. Modification of tumor cell exosome content by transfection with wt-p53 and microRNA-125b expressing plasmid DNA and its effect on macrophage polarization.

    PubMed

    Trivedi, M; Talekar, M; Shah, P; Ouyang, Q; Amiji, M

    2016-01-01

    Exosomes are responsible for intercellular communication between tumor cells and others in the tumor microenvironment. These microvesicles promote oncogensis and can support towards metastasis by promoting a pro-tumorogenic environment. Modifying the exosomal content and exosome delivery are emerging novel cancer therapies. However, the clinical translation is limited due to feasibility of isolating and delivery of treated exosomes as well as an associated immune response in patients. In this study, we provide proof-of-concept for a novel treatment approach for manipulating exosomal content by genetic transfection of tumor cells using dual-targeted hyaluronic acid-based nanoparticles. Following transfection with plasmid DNA encoding for wild-type p53 (wt-p53) and microRNA-125b (miR-125b), we evaluate the transgene expression in the SK-LU-1 cells and in the secreted exosomes. Furthermore, along with modulation of wt-p53 and miR-125b expression, we also show that the exosomes (i.e., wt-p53/exo, miR-125b/exo and combination/exo) have a reprogramed global miRNA profile. The miRNAs in the exosomes were mainly related to the activation of genes associated with apoptosis as well as p53 signaling. More importantly, these altered miRNA levels in the exosomes could mediate macrophage repolarization towards a more pro-inflammatory/antitumor M1 phenotype. However, further studies, especially in vivo studies, are warranted to assess the direct influence of such macrophage reprogramming on cancer cells and oncogenesis post-treatment. The current study provides a novel platform enabling the development of therapeutic strategies affecting not only the cancer cells but also the tumor microenvironment by utilizing the 'bystander effect' through genetic transfer with secreted exosomes. Such modification could also support antitumor environment leading to decreased oncogenesis. PMID:27500388

  12. Modification of tumor cell exosome content by transfection with wt-p53 and microRNA-125b expressing plasmid DNA and its effect on macrophage polarization

    PubMed Central

    Trivedi, M; Talekar, M; Shah, P; Ouyang, Q; Amiji, M

    2016-01-01

    Exosomes are responsible for intercellular communication between tumor cells and others in the tumor microenvironment. These microvesicles promote oncogensis and can support towards metastasis by promoting a pro-tumorogenic environment. Modifying the exosomal content and exosome delivery are emerging novel cancer therapies. However, the clinical translation is limited due to feasibility of isolating and delivery of treated exosomes as well as an associated immune response in patients. In this study, we provide proof-of-concept for a novel treatment approach for manipulating exosomal content by genetic transfection of tumor cells using dual-targeted hyaluronic acid-based nanoparticles. Following transfection with plasmid DNA encoding for wild-type p53 (wt-p53) and microRNA-125b (miR-125b), we evaluate the transgene expression in the SK-LU-1 cells and in the secreted exosomes. Furthermore, along with modulation of wt-p53 and miR-125b expression, we also show that the exosomes (i.e., wt-p53/exo, miR-125b/exo and combination/exo) have a reprogramed global miRNA profile. The miRNAs in the exosomes were mainly related to the activation of genes associated with apoptosis as well as p53 signaling. More importantly, these altered miRNA levels in the exosomes could mediate macrophage repolarization towards a more pro-inflammatory/antitumor M1 phenotype. However, further studies, especially in vivo studies, are warranted to assess the direct influence of such macrophage reprogramming on cancer cells and oncogenesis post-treatment. The current study provides a novel platform enabling the development of therapeutic strategies affecting not only the cancer cells but also the tumor microenvironment by utilizing the ‘bystander effect' through genetic transfer with secreted exosomes. Such modification could also support antitumor environment leading to decreased oncogenesis. PMID:27500388

  13. A novel cold-active xylanase gene from the environmental DNA of goat rumen contents: direct cloning, expression and enzyme characterization.

    PubMed

    Wang, Guozeng; Luo, Huiying; Wang, Yaru; Huang, Huoqing; Shi, Pengjun; Yang, Peilong; Meng, Kun; Bai, Yingguo; Yao, Bin

    2011-02-01

    A xylanase-coding gene, xynGR40, was cloned directly from the environmental DNA of goat rumen contents and expressed in Escherichia coli BL21 (DE3). The 1446-bp full-length gene encodes a 481-residue polypeptide (XynGR40) containing a catalytic domain belonging to glycosyl hydrolase (GH) family 10. Phylogenetic analysis indicated that XynGR40 was closely related with microbial xylanases of gastrointestinal source. Purified recombinant XynGR40 exhibited high activity at low temperatures, and remained active (∼10% of the activity) even at 0°C. The optimal temperature of XynGR40 was 30°C, much lower than other xylanases from rumen. Compared with mesophilic and thermophilic counterparts, XynGR40 had fewer hydrogen bonds and salt bridges, and lengthened loops in the catalytic domain. The enzyme also had relatively better stability at mesophilic temperatures and a higher catalytic efficiency than other known GH 10 cold active xylanases. These properties suggest that XynGR40 is a novel cold active xylanase and has great potential for basic research and industrial applications.

  14. Dynamic Heterogeneity of DNA Methylation and Hydroxymethylation in Embryonic Stem Cell Populations Captured by Single-Cell 3D High-Content Analysis

    PubMed Central

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    2015-01-01

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a ten-day differentiation course in vitro: by means of confocal and super-resolution imaging together with high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU per day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17:0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, DNA global methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC+/5mC−, 5hmC+/5mC+, and 5hmC−/5mC+ cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC+/5mC+ cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in remodeling. We

  15. DNA systematics. Volume II

    SciTech Connect

    Dutta, S.K.

    1986-01-01

    This book discusses the following topics: PLANTS: PLANT DNA: Contents and Systematics. Repeated DNA Sequences and Polyploidy in Cereal Crops. Homology of Nonrepeated DNA Sequences in Phylogeny of Fungal Species. Chloropast DNA and Phylogenetic Relationships. rDNA: Evolution Over a Billion Years. 23S rRNA-derived Small Ribosomal RNAs: Their Structure and Evolution with Reference to Plant Phylogeny. Molecular Analysis of Plant DNA Genomes: Conserved and Diverged DNA Sequences. A Critical Review of Some Terminologies Used for Additional DNA in Plant Chromosomes and Index.

  16. A novel quantitative assay of mitophagy: Combining high content fluorescence microscopy and mitochondrial DNA load to quantify mitophagy and identify novel pharmacological tools against pathogenic heteroplasmic mtDNA.

    PubMed

    Diot, Alan; Hinks-Roberts, Alex; Lodge, Tiffany; Liao, Chunyan; Dombi, Eszter; Morten, Karl; Brady, Stefen; Fratter, Carl; Carver, Janet; Muir, Rebecca; Davis, Ryan; Green, Charlotte J; Johnston, Iain; Hilton-Jones, David; Sue, Carolyn; Mortiboys, Heather; Poulton, Joanna

    2015-10-01

    Mitophagy is a cellular mechanism for the recycling of mitochondrial fragments. This process is able to improve mitochondrial DNA (mtDNA) quality in heteroplasmic mtDNA disease, in which mutant mtDNA co-exists with normal mtDNA. In disorders where the load of mutant mtDNA determines disease severity it is likely to be an important determinant of disease progression. Measuring mitophagy is technically demanding. We used pharmacological modulators of autophagy to validate two techniques for quantifying mitophagy. First we used the IN Cell 1000 analyzer to quantify mitochondrial co-localisation with LC3-II positive autophagosomes. Unlike conventional fluorescence and electron microscopy, this high-throughput system is sufficiently sensitive to detect transient low frequency autophagosomes. Secondly, because mitophagy preferentially removes pathogenic heteroplasmic mtDNA mutants, we developed a heteroplasmy assay based on loss of m.3243A>G mtDNA, during culture conditions requiring oxidative metabolism ("energetic stress"). The effects of the pharmacological modulators on these two measures were consistent, confirming that the high throughput imaging output (autophagosomes co-localising with mitochondria) reflects mitochondrial quality control. To further validate these methods, we performed a more detailed study using metformin, the most commonly prescribed antidiabetic drug that is still sometimes used in Maternally Inherited Diabetes and Deafness (MIDD). This confirmed our initial findings and revealed that metformin inhibits mitophagy at clinically relevant concentrations, suggesting that it may have novel therapeutic uses. PMID:26196248

  17. Mitochondrial DNA copy number is maintained during spermatogenesis and in the development of male larvae to sustain the doubly uniparental inheritance of mitochondrial DNA system in the blue mussel Mytilus galloprovincialis.

    PubMed

    Sano, Natsumi; Obata, Mayu; Ooie, Yosiyasu; Komaru, Akira

    2011-08-01

    Doubly uniparental inheritance (DUI) of mitochondrial (mt) DNA has been reported in the blue mussel Mytilus galloprovincialis. In DUI, males inherit both paternal (M type) and maternal (F type) mtDNA. Here we investigated changes in M type mtDNA copy numbers and mitochondrial mass in testicular cells by real-time polymerase chain reaction and flow cytometry. The ratios of M type mtDNA copy numbers to nuclear DNA content were not different between haploid (1n), diploid (2n) and tetraploid (4n) spermatogenic cells. The mitochondrial mass decreased gradually during spermatogenesis. These results suggest that mtDNA and mitochondrial mass are maintained during spermatogenesis. We then traced M type mtDNA in larvae after fertilization. M type mtDNA was maintained up to 24 h after fertilization in the male-biased crosses, but decreased significantly in female-biased crosses (predicted by Mito Tracker staining pattern). These results are strikingly different from those reported for mammals and fish, where it is well known that the mitochondria and mtDNA are reduced during spermatogenesis and that sperm mitochondria and mtDNA are eliminated soon after fertilization. Thus, the M type mtDNA copy number is maintained during spermatogenesis and in the development of male larvae to sustain the DUI system in the blue mussel.

  18. Constructing optimal entanglement witnesses. II. Witnessing entanglement in 4N×4N systems

    NASA Astrophysics Data System (ADS)

    Chruściński, Dariusz; Pytel, Justyna

    2010-11-01

    We provide a class of optimal nondecomposable entanglement witnesses for 4N×4N composite quantum systems or, equivalently, another construction of nondecomposable positive maps in the algebra of 4N×4N complex matrices. This construction provides natural generalization of the Robertson map. It is shown that their structural physical approximations give rise to entanglement breaking channels.

  19. Constructing optimal entanglement witnesses. II. Witnessing entanglement in 4Nx4N systems

    SciTech Connect

    Chruscinski, Dariusz; Pytel, Justyna

    2010-11-15

    We provide a class of optimal nondecomposable entanglement witnesses for 4Nx4N composite quantum systems or, equivalently, another construction of nondecomposable positive maps in the algebra of 4Nx4N complex matrices. This construction provides natural generalization of the Robertson map. It is shown that their structural physical approximations give rise to entanglement breaking channels.

  20. Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

    PubMed

    Lukoschek, V; Waycott, M; Keogh, J S

    2008-07-01

    Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

  1. [Effect of humic acids on migration and transformation of NH4(+) -N in saturated aquifer].

    PubMed

    Meng, Qing-Jun; Zhang, Yan; Feng, Qi-Yan; Zhang, Shuang-Sheng

    2011-11-01

    Isothermal adsorption experiment was used to study the adsorbing process of NH4(+) -N in quartz sands under the conditions with and without humic acid; the Langmuir and Freundlich equations were used to fit the absorption result and the maximum adsorption capacity of NH4(+) -N by quarts sands was calculated. Through the soil column experiments, the concentration of NH4(+) -N, NO3(-) -N and NO2(-) -N in effluent water in the tested soil column was investigated, and the effect of humic acid on migration and transformation of NH4(+) -N in saturated aquifer was analyzed, and Pseudo-second-order Kinetics Equation and Two-step Adsorption Kinetics Rate Equation were applied to fit the kinetic processes. The results showed that both Langmuir and Freundlich models can well describe the isothermal adsorption process of NH4(+) -N on the surface of quartz sands, which means that NH4(+) -N adsorbed by the quartz sand was mainly in the form of monolayer adsorption. The humic acid could increase the adsorption capacity of NH4(+) -N on quartz sand, and the saturated adsorption capacity was 0.354 mg x g(-1) under the condition with humic acid and 0.205 mg x g(-1) with the absence of humic acid. The experiment indicated that humic acid increased the adsorption capacity of NH4(+) -N on the surface of quartz sand by increasing adsorption space in the initial stage. After saturation, humic acid influenced the migration and transformation of NH4(+) -N to NO3(-) -N and NO2(-) -N probably through providing carbon source and energy for microorganisms such as nitrifying bacteria and then resulting in lower NH4(+) -N concentration in effluent water. Both Pseudo-second-order Kinetics Equation and Two-step Adsorption Kinetics Rate Equations can well describe the process of NH4(+) -N adsorption kinetics on quartz sand (R2 = 0.997 7 and R2 = 0.998 1 with humic acid; R2 = 0.992 3 and R2 = 0.994 4 without humic acid), indicating that this process was chemical adsorption. By comparing the

  2. Synthesis of two-dimensional titanium nitride Ti4N3 (MXene)

    NASA Astrophysics Data System (ADS)

    Urbankowski, Patrick; Anasori, Babak; Makaryan, Taron; Er, Dequan; Kota, Sankalp; Walsh, Patrick L.; Zhao, Mengqiang; Shenoy, Vivek B.; Barsoum, Michel W.; Gogotsi, Yury

    2016-06-01

    We report on the synthesis of the first two-dimensional transition metal nitride, Ti4N3-based MXene. In contrast to the previously reported MXene synthesis methods - in which selective etching of a MAX phase precursor occurred in aqueous acidic solutions - here a molten fluoride salt is used to etch Al from a Ti4AlN3 powder precursor at 550 °C under an argon atmosphere. We further delaminated the resulting MXene to produce few-layered nanosheets and monolayers of Ti4N3Tx, where T is a surface termination (F, O, or OH). Density functional theory calculations of bare, non-terminated Ti4N3 and terminated Ti4N3Tx were performed to determine the most energetically stable form of this MXene. Bare and functionalized Ti4N3 are predicted to be metallic. Bare Ti4N3 is expected to show magnetism, which is significantly reduced in the presence of functional groups.We report on the synthesis of the first two-dimensional transition metal nitride, Ti4N3-based MXene. In contrast to the previously reported MXene synthesis methods - in which selective etching of a MAX phase precursor occurred in aqueous acidic solutions - here a molten fluoride salt is used to etch Al from a Ti4AlN3 powder precursor at 550 °C under an argon atmosphere. We further delaminated the resulting MXene to produce few-layered nanosheets and monolayers of Ti4N3Tx, where T is a surface termination (F, O, or OH). Density functional theory calculations of bare, non-terminated Ti4N3 and terminated Ti4N3Tx were performed to determine the most energetically stable form of this MXene. Bare and functionalized Ti4N3 are predicted to be metallic. Bare Ti4N3 is expected to show magnetism, which is significantly reduced in the presence of functional groups. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02253g

  3. Search for 4n contributions in the reaction 14Be(CH2,X)10He

    NASA Astrophysics Data System (ADS)

    Jones, M. D.; Kohley, Z.; Baumann, T.; Christian, G.; DeYoung, P. A.; Finck, J. E.; Frank, N.; Haring-Kaye, R. A.; Kuchera, A. N.; Luther, B.; Mosby, S.; Smith, J. K.; Snyder, J.; Spyrou, A.; Stephenson, S. L.; Thoennessen, M.

    2016-03-01

    A previously published measurement of the ground state resonance of 10He, populated by a reaction of a 59 MeV/u 14Be beam on a deuterated polyethylene target, was further analyzed to search for 4n emission resulting from 2p removal. No evidence for 4n events was found. A lower limit of about 1 MeV was determined for a possible resonance in 12He.

  4. The Grapevine Root-Specific Aquaporin VvPIP2;4N Controls Root Hydraulic Conductance and Leaf Gas Exchange under Well-Watered Conditions But Not under Water Stress1[W

    PubMed Central

    Perrone, Irene; Gambino, Giorgio; Chitarra, Walter; Vitali, Marco; Pagliarani, Chiara; Riccomagno, Nadia; Balestrini, Raffaella; Kaldenhoff, Ralf; Uehlein, Norbert; Gribaudo, Ivana; Schubert, Andrea; Lovisolo, Claudio

    2012-01-01

    We functionally characterized the grape (Vitis vinifera) VvPIP2;4N (for Plasma membrane Intrinsic Protein) aquaporin gene. Expression of VvPIP2;4N in Xenopus laevis oocytes increased their swelling rate 54-fold. Northern blot and quantitative reverse transcription-polymerase chain reaction analyses showed that VvPIP2;4N is the most expressed PIP2 gene in root. In situ hybridization confirmed root localization in the cortical parenchyma and close to the endodermis. We then constitutively overexpressed VvPIP2;4N in grape ‘Brachetto’, and in the resulting transgenic plants we analyzed (1) the expression of endogenous and transgenic VvPIP2;4N and of four other aquaporins, (2) whole-plant, root, and leaf ecophysiological parameters, and (3) leaf abscisic acid content. Expression of transgenic VvPIP2;4N inhibited neither the expression of the endogenous gene nor that of other PIP aquaporins in both root and leaf. Under well-watered conditions, transgenic plants showed higher stomatal conductance, gas exchange, and shoot growth. The expression level of VvPIP2;4N (endogenous + transgene) was inversely correlated to root hydraulic resistance. The leaf component of total plant hydraulic resistance was low and unaffected by overexpression of VvPIP2;4N. Upon water stress, the overexpression of VvPIP2;4N induced a surge in leaf abscisic acid content and a decrease in stomatal conductance and leaf gas exchange. Our results show that aquaporin-mediated modifications of root hydraulics play a substantial role in the regulation of water flow in well-watered grapevine plants, while they have a minor role upon drought, probably because other signals, such as abscisic acid, take over the control of water flow. PMID:22923680

  5. Phase stability of graphitelike BC{sub 4}N up to 2100 K and 7 GPa

    SciTech Connect

    Solozhenko, V.L.; Turkevich, V.Z.; Sato, Tadao

    1997-12-01

    Thermal phase stability of graphitelike BC{sub 4}N (g-BC{sub 4}N) has been studied up to 7 GPa and 2,100 K using in-situ powder diffraction of synchrotron radiation. It has been shown that the process of g-BC{sub 4}N decomposition at ambient pressure starts at 2,050 K and occurs to form highly ordered hexagonal graphitelike boron nitride (hBN) and disordered graphite. As the pressure increases up to 6.6 GPa, the temperature of the decomposition onset decreases to 1,070 K. At this pressure in the 1,070--1,400 K temperature range (decomposition degree of < 0.1), the decomposition products remain the same, whereas at higher temperatures, the decomposition of g-BC{sub 4}N is accompanied by the formation of cubic boron nitride (cBN) and disordered graphite. Measurement of 298 K equation of state of g-BC{sub 4}N results in a zero-pressure bulk modulus of 18.1 {+-} 0.2 GPa and its pressure derivative of 6.6 {+-} 0.1. Thermodynamic analysis has shown that the g-BC{sub 4}N decomposition is a nonequilibrium process and the phase itself is metastable.

  6. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.

    PubMed

    Hume, Maxwell A; Barrera, Luis A; Gisselbrecht, Stephen S; Bulyk, Martha L

    2015-01-01

    The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org.

  7. HAG3, a Histone Acetyltransferase, Affects UV-B Responses by Negatively Regulating the Expression of DNA Repair Enzymes and Sunscreen Content in Arabidopsis thaliana.

    PubMed

    Fina, Julieta P; Casati, Paula

    2015-07-01

    Histone acetylation is regulated by histone acetyltransferases and deacetylases. In Arabidopsis, there are 12 histone acetyltransferases and 18 deacetylases. Histone acetyltransferases are organized in four families: the GNAT/HAG, the MYST, the p300/CBP and the TAFII250 families. Previously, we demonstrated that Arabidopsis mutants in the two members of the MYST acetyltransferase family show increased DNA damage after UV-B irradiation. To investigate further the role of other histone acetyltransferases in UV-B responses, a putative role for enzymes of the GNAT family, HAG1, HAG2 and HAG3, was analyzed. HAG transcripts are not UV-B regulated; however, hag3 RNA interference (RNAi) transgenic plants show a lower inhibition of leaf and root growth by UV-B, higher levels of UV-B-absorbing compounds and less UV-B-induced DNA damage than Wassilewskija (Ws) plants, while hag1 RNAi transgenic plants and hag2 mutants do not show significant differences from wild-type plants. Transcripts for UV-B-regulated genes are highly expressed under control conditions in the absence of UV-B in hag3 RNAi transgenic plants, suggesting that the higher UV-B tolerance may be due to increased levels of proteins that participate in UV-B responses. Together, our data provide evidence that HAG3, directly or indirectly, participates in UV-B-induced DNA damage repair and signaling.

  8. Immobilization of Mn and NH4 (+)-N from electrolytic manganese residue waste.

    PubMed

    Chen, Hongliang; Liu, Renlong; Liu, Zuohua; Shu, Jiancheng; Tao, Changyuan

    2016-06-01

    The objective of this work was the immobilization of soluble manganese (Mn) and ammonium nitrogen (NH4 (+)-N) leached from electrolytic manganese residue (EMR). Immobilization of Mn was investigated via carbonation using carbon dioxide (CO2) and alkaline additives. NH4 (+)-N immobilization was evaluated via struvite precipitation using magnesium and phosphate sources. Results indicated that the immobilization efficiency of Mn using CO2 and quicklime (CaO) was higher than using CO2 and sodium hydroxide (NaOH). This higher efficiency was likely due to the slower release of OH(-) during CaO hydrolysis. The immobilization efficiency of Mn was >99.99 % at the CaO:EMR mass ratio of 0.05:1 for 20-min reaction time. The struvite precipitation of NH4 (+)-N was conducted in the carbonated EMR slurry and the immobilization efficiency was 89 % using MgCl2 · 6H2O + Na3PO4 · 12H2O at the Mg:P:N molar ratio of 1.5:1.5:1 for 90-min reaction time. A leaching test showed that the concentrations of Mn and NH4 (+)-N in the filtrate of the treated EMR were 0.2 and 9 mg/L, respectively. The combined immobilization of Mn and NH4 (+)-N was an effective pretreatment method in the harmless treatment of the EMR.

  9. Perpendicular magnetic anisotropy of Mn4N films fabricated by reactive sputtering method

    NASA Astrophysics Data System (ADS)

    Kabara, Kazuki; Tsunoda, Masakiyo

    2015-05-01

    Manganese nitride films were fabricated on MgO substrates by changing N2 flow ratio into Ar gas ( P N2 ) during reactive sputtering deposition of the films, and their crystal structures and magnetic properties were investigated. Single phased ɛ-Mn4N films were obtained when P N2 was 5%-9%, and the tetragonal lattice distortion was identified in all the Mn4N films (the lattice constant ratio, c/a = 0.99). Perpendicular magnetic anisotropy was observed in all the specimens. The Mn4N film, fabricated with P N2 = 8%, has a low saturation magnetization (Ms = 110 emu/cc) and relatively high magnetic anisotropic energy (Ku = 8.8 × 105 erg/cc). Both Ms and Ku of the films drastically changed with mixing other phases (α-Mn, β-Mn, η-Mn3N2, and possibly γ-Mn) by varying P N2 .

  10. Spin Polarization Inversion at Benzene-Absorbed Fe4N Surface

    PubMed Central

    Zhang, Qian; Mi, Wenbo; Wang, Xiaocha; Wang, Xuhui

    2015-01-01

    We report a first-principle study on electronic structure and simulation of the spin-polarized scanning tunneling microscopy graphic of a benzene/Fe4N interface. Fe4N is a compound ferromagnet suitable for many spintronic applications. We found that, depending on the particular termination schemes and interface configurations, the spin polarization on the benzene surface shows a rich variety of properties ranging from cosine-type oscillation to polarization inversion. Spin-polarization inversion above benzene is resulting from the hybridizations between C pz and the out-of-plane d orbitals of Fe atom. PMID:26012892

  11. The Impact of Antiaromatic Subunits in [4n+2] π-Systems: Bispentalenes with [4n+2] π-Electron Perimeters and Antiaromatic Character.

    PubMed

    Cao, Jing; London, Gábor; Dumele, Oliver; von Wantoch Rekowski, Margarete; Trapp, Nils; Ruhlmann, Laurent; Boudon, Corinne; Stanger, Amnon; Diederich, François

    2015-06-10

    Three series of stable, neutral, π-extended bispentalene derivatives, with two pentalenes fused to a central benzene or naphthalene moiety, have been prepared through a modified double carbopalladation cascade reaction. While these chromophores feature skeletons with [4n+2] π-electron perimeters, the two 8 π-electron pentalene subunits strongly influence bonding and spectral properties. (1)H NMR spectra showed large upfield shifts of the protons in the pentalene moieties, comparable to antiaromatic monobenzopentalenes. Further investigations on magnetic ring currents through NICS-XY-scans suggest a global paratropic current and a local diatropic current at the central benzene ring in two of the series, while the third series, with a central naphthalene ring, showed more localized ring currents, with stronger paratropic ring currents on the pentalene moieties. X-ray diffraction analyses revealed planar bispentalene cores with large double- and single-bond alternation in the pentalene units, characteristic for antiaromaticity, and small alternation in the central aromatic rings. In agreement with TD-DFT calculations, both optical and electrochemical data showed much smaller HOMO-LUMO energy gaps compared to other neutral, acene-like hydrocarbons with the same number of fused rings. Both experimental and computational results suggest that the molecular properties of the presented bispentalenes are dominated by the antiaromatic pentalene-subunits despite the [4n+2] π-electron perimeter of the skeletons. PMID:25978774

  12. The Impact of Antiaromatic Subunits in [4n+2] π-Systems: Bispentalenes with [4n+2] π-Electron Perimeters and Antiaromatic Character.

    PubMed

    Cao, Jing; London, Gábor; Dumele, Oliver; von Wantoch Rekowski, Margarete; Trapp, Nils; Ruhlmann, Laurent; Boudon, Corinne; Stanger, Amnon; Diederich, François

    2015-06-10

    Three series of stable, neutral, π-extended bispentalene derivatives, with two pentalenes fused to a central benzene or naphthalene moiety, have been prepared through a modified double carbopalladation cascade reaction. While these chromophores feature skeletons with [4n+2] π-electron perimeters, the two 8 π-electron pentalene subunits strongly influence bonding and spectral properties. (1)H NMR spectra showed large upfield shifts of the protons in the pentalene moieties, comparable to antiaromatic monobenzopentalenes. Further investigations on magnetic ring currents through NICS-XY-scans suggest a global paratropic current and a local diatropic current at the central benzene ring in two of the series, while the third series, with a central naphthalene ring, showed more localized ring currents, with stronger paratropic ring currents on the pentalene moieties. X-ray diffraction analyses revealed planar bispentalene cores with large double- and single-bond alternation in the pentalene units, characteristic for antiaromaticity, and small alternation in the central aromatic rings. In agreement with TD-DFT calculations, both optical and electrochemical data showed much smaller HOMO-LUMO energy gaps compared to other neutral, acene-like hydrocarbons with the same number of fused rings. Both experimental and computational results suggest that the molecular properties of the presented bispentalenes are dominated by the antiaromatic pentalene-subunits despite the [4n+2] π-electron perimeter of the skeletons.

  13. Electrical detection of magnetic domain wall in Fe4N nanostrip by negative anisotropic magnetoresistance effect

    NASA Astrophysics Data System (ADS)

    Gushi, Toshiki; Ito, Keita; Higashikozono, Soma; Takata, Fumiya; Oosato, Hirotaka; Sugimoto, Yoshimasa; Toko, Kaoru; Honda, Syuta; Suemasu, Takashi

    2016-09-01

    The magnetic structure of the domain wall (DW) of a 30-nm-thick Fe4N epitaxial film with a negative spin polarization of the electrical conductivity is observed by magnetic force microscopy and is well explained by micromagnetic simulation. The Fe4N film is grown by molecular beam epitaxy on a SrTiO3(001) substrate and processed into arc-shaped ferromagnetic nanostrips 0.3 μm wide by electron beam lithography and reactive ion etching with Cl2 and BCl3 plasma. Two electrodes mounted approximately 12 μm apart on the nanostrip register an electrical resistance at 8 K. By changing the direction of an external magnetic field (0.2 T), the presence or absence of a DW positioned in the nanostrip between the two electrodes can be controlled. The resistance is increased by approximately 0.5 Ω when the DW is located between the electrodes, which signifies the negative anisotropic magnetoresistance effect of Fe4N. The electrical detection of the resistance change is an important step toward the electrical detection of current-induced DW motion in Fe4N.

  14. B4N and Fe3BN nitrides bands structure and theoretical determination of bulk modulus

    NASA Astrophysics Data System (ADS)

    dos Santos, A. V.

    2007-06-01

    With the evolution of material science there was some technological evolution as well as the need of finding new links which could be applied to diverse areas of knowledge. Thus, in this article, we study nitrides bands structures which contain boron, in two different stoichiometries Fe3BN and B4N. The choice of these compounds is meant to plan new links and to understand nitrides fundamental state properties facing these new crystalline structures. In order to resolve the compound band structure we used the method of linear Muffin Tin orbital (LMTO), with atomic sphere approximation (ASA). By using this method we obtained the energy of formation as a function of the lattice parameter as one of the results. We find the equilibrium lattice parameter of 6.9755 a.u., for the Fe3BN nitride, and in B4N, we have 6.8589 a.u. We also discuss in this article the charge transference between sites and the influence of pressure on the compound properties, as well as the Bulk modulus that is 239.82 GPa for Fe3BN and 105.48 GPa for B4N. We show the behaviour of the density of states (DOS) of the new band structure found for the proposed crystalline structure Fe3BN, in which the B atom replace the Fe atom in the corner of the structure γ‧- Fe4N.

  15. Transverse anisotropic magnetoresistance effects in pseudo-single-crystal γ'-Fe4N thin films

    NASA Astrophysics Data System (ADS)

    Kabara, Kazuki; Tsunoda, Masakiyo; Kokado, Satoshi

    2016-05-01

    Transverse anisotropic magnetoresistance (AMR) effects, for which magnetization is rotated in an orthogonal plane to the current direction, were investigated at various temperatures, in order to clarify the structural transformation from a cubic to a tetragonal symmetry in a pseudo-single-crystal Fe4N film, which is predicted from the usual in-plane AMR measurements by the theory taking into account the spin-orbit interaction and crystal field splitting of 3d bands. According to a phenomenological theory of AMR, which derives only from the crystal symmetry, a cos 2θ component ( C2 tr ) exists in transverse AMR curves for a tetragonal system but does not for a cubic system. In the Fe4N film, the C2 tr shows a positive small value (0.12%) from 300 K to 50 K. However, the C2 t r increases to negative value below 50 K and reaches to -2% at 5 K. The drastic increasing of the C2 tr demonstrates the structural transformation from a cubic to a tetragonal symmetry below 50 K in the Fe4N film. In addition, the out-of-plane and in-plane lattice constants (c and a) were precisely determined with X-ray diffraction at room temperature using the Nelson-Riely function. As a result, the positive small C2 t r above 50 K is attributed to a slightly distorted Fe4N lattice (c/a = 1.002).

  16. C4N2 ice in Titan’s atmosphere: reality or myth?

    NASA Astrophysics Data System (ADS)

    Anderson, Carrie; Samuelson, Robert E.; Achterberg, Richard K.; Flasar, F. M.

    2014-11-01

    Voyager 1 IRIS detected a spectral emission feature at 478 cm-1 in Titan’s atmosphere at high northern latitudes. Now one Titan year later we rediscovered it in Cassini CIRS limb spectra at 70°N. Thus far the feature has always been associated with the lower polar stratosphere during early northern spring. No known trace organic vapor in Titan’s atmosphere has a spectral feature at 478 cm-1, and the only known or suspected condensate that does is C4N2 ice. However, the C4N2 ν8 and ν9 vapor features at 472 cm-1 and 108 cm-1, respectively, have never been observed in Titan’s atmosphere, leading to a C4N2 vapor upper limit at least 2 orders of magnitude lower than equilibrium with the ice phase would suggest. In this study we analyze the spectral shapes and strengths of the 478 cm-1 feature in the IRIS and CIRS data sets in an effort to determine particle sizes, mole fractions, and vertical distributions of the putative condensate cloud responsible for the feature, and then discuss the pros and cons of its identify with C4N2 ice.

  17. Characterization of muntjac DNA

    SciTech Connect

    Davis, R.C.

    1981-05-27

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  18. Endocrine-Disrupting Potential of Bisphenol A, Bisphenol A Dimethacrylate, 4-n-Nonylphenol, and 4-n-Octylphenol in Vitro: New Data and a Brief Review

    PubMed Central

    Bonefeld-Jørgensen, Eva C.; Long, Manhai; Hofmeister, Marlene V.; Vinggaard, Anne Marie

    2007-01-01

    Background An array of environmental compounds is known to possess endocrine disruption (ED) potentials. Bisphenol A (BPA) and bisphenol A dimethacrylate (BPA-DM) are monomers used to a high extent in the plastic industry and as dental sealants. Alkylphenols such as 4-n-nonylphenol (nNP) and 4-n-octylphenol (nOP) are widely used as surfactants. Objectives We investigated the effect in vitro of these four compounds on four key cell mechanisms including transactivation of a) the human estrogen receptor (ER), b) the human androgen receptor (AR), c) the aryl hydrocarbon receptor (AhR), and d) aromatase activity. Results All four compounds inhibited aromatase activity and were agonists and antagonists of ER and AR, respectively. nNP increased AhR activity concentration-dependently and further increased the 2,3,7,8-tetrachlorodibenzo-p-dioxin AhR action. nOP caused dual responses with a weak increased and a decreased AhR activity at lower (10−8 M) and higher concentrations (10−5–10−4 M), respectively. AhR activity was inhibited with BPA (10−5–10−4 M) and weakly increased with BPA-DM (10−5 M), respectively. nNP showed the highest relative potency (REP) compared with the respective controls in the ER, AhR, and aromatase assays, whereas similar REP was observed for the four chemicals in the AR assay. Conclusion Our in vitro data clearly indicate that the four industrial compounds have ED potentials and that the effects can be mediated via several cellular pathways, including the two sex steroid hormone receptors (ER and AR), aromatase activity converting testosterone to estrogen, and AhR; AhR is involved in syntheses of steroids and metabolism of steroids and xenobiotic compounds. PMID:18174953

  19. Two new species of Limbodessus diving beetles from New Guinea - short verbal descriptions flanked by online content (digital photography, μCT scans, drawings and DNA sequence data)

    PubMed Central

    Ruthensteiner, Bernhard; Warikar, Evie Lilly; Neven, Katja; Hendrich, Lars

    2015-01-01

    Abstract Background To date only one species of Limbodessus diving beetles has been reported from the Island of New Guinea, L. compactus (Clark, 1862), which is widerspread in the Australian region. New information We describe two new species of microendemic New Guinea Limbodessus and use a compact descriptive format flanked by enriched online content in wiki powered species pages. Limbodessus baliem sp.n. is described from ca. 1,600 m altitude in the Baliem Valley of Papua and Limbodessus alexanderi sp.n. from >3,000 m altitude north of Sugapa, Papua. Based on our analysis, we also transfer three species from other genera to Limbodessus Guignot, 1939, with the following changes: Limbodessus deflectus (Ordish, 1966), new combination; Limbodessus leveri (J. Balfour-Browne, 1944), new combination; and Limbodessus plicatus (Sharp, 1882), new combination. PMID:26752969

  20. Laser Spectroscopy of GdPO4 . nH2O:Eu Nanomaterials.

    PubMed

    Lu, Shaozhe; Zhang, Jiahua; Zhang, Jishen; Shulin, Zhang E; Zhao, Haifeng; Luo, Yongshi

    2016-04-01

    One-dimensional GdPO4 . nH2O:Eu nanowires and nanorods of different sizes and the same structure were synthesized by hydrothermal method. Nanowire and nanorods had width and length of about 10 nm/50 nm and 80 nm/1 µm, respectively. Adjusting reaction system PH value by adding alkali metal NaOH, the size and shape of the product can be tuned. The high resolution spectra, excitation spectra, and laser selective excitation spectra at low temperature were determined. Nanorod compared with nanowire, photoluminescence was enhanced, and the excitation spectrum and laser selective excitation spectra were broadened. These results suggest that Eu3+ in GdPO4 . nH20 nanorod and nanowire were located in different local environments. PMID:27451675

  1. Extrinsic anomalous Hall effect in epitaxial Mn{sub 4}N films

    SciTech Connect

    Meng, M.; Wu, S. X. Ren, L. Z.; Zhou, W. Q.; Wang, Y. J.; Wang, G. L.; Li, S. W.

    2015-01-19

    Anomalous Hall effect (AHE) in ferrimagnetic Mn{sub 4}N epitaxial films grown by molecular-beam epitaxy is investigated. The longitudinal conductivity σ{sub xx} is within the superclean regime, indicating Mn{sub 4}N is a highly conducting material. We further demonstrate that the AHE signal in 40-nm-thick films is mainly due to the extrinsic contributions based on the analysis fitted by ρ{sub AH}=a′ρ{sub xx0}+bρ{sub xx}{sup 2} and σ{sub AH}∝σ{sub xx}. Our study not only provide a strategy for further theoretical work on antiperovskite manganese nitrides but also shed promising light on utilizing their extrinsic AHE to fabricate spintronic devices.

  2. Search for coupling in ferromagnetic/superconducting multilayers: Fe{sub 4}N/NbN

    SciTech Connect

    Mattson, J.E.; Potter, C.D.; Conover, M.J.; Sowers, C.H.; Bader, S.D.

    1997-09-01

    Structural, magnetic, and superconducting properties of ferromagnetic/superconducting multilayers of Fe{sub 4}N/NbN are examined. The onset of superconductivity occurs at NbN layer thickness of {approximately}100 {Angstrom}. Below this thickness ferromagnetism of the Fe{sub 4}N layers is observed. Above this thickness superconductivity of the NbN is also observed, but there is no evidence for interlayer magnetic or superconductive coupling. The results are used in the formulation of guidelines for future searches of novel interlayer coupling phenomena. The superconducting critical field curves are reasonably well described within the framework of the theory for ferromagnetic/superconducting multilayers. {copyright} {ital 1997 American Vacuum Society.}

  3. Structure determination of (Fe3O4)n+(n = 1 - 3) clusters via DFT

    NASA Astrophysics Data System (ADS)

    Li, Yanhua; Cai, Congzhong; Zhao, Chengjun; Gu, Yonghong

    2016-07-01

    In virtue of the particle swarm optimization (PSO) algorithm, the global minimum candidate structures with the lowest energy for (Fe3O4)n(n = 1 - 3) clusters were obtained by first-principles structural searches. The geometric structures and spin configurations of three cationic (Fe3O4)n+(n = 1 - 3) clusters have been identified for the first time by comparing the experimental IR spectra with the calculated results from density functional theory by using different exchange-correlation functionals. It is found that the lowest energy structures of these clusters are of a shape of hat, boat and tower, respectively, with a ferrimagnetic arrangement of spins, and M06L functional is more suitable for Fe3O4 clusters than other ones.

  4. Using DNA looping to measure sequence dependent DNA elasticity

    NASA Astrophysics Data System (ADS)

    Kandinov, Alan; Raghunathan, Krishnan; Meiners, Jens-Christian

    2012-10-01

    We are using tethered particle motion (TPM) microscopy to observe protein-mediated DNA looping in the lactose repressor system in DNA constructs with varying AT / CG content. We use these data to determine the persistence length of the DNA as a function of its sequence content and compare the data to direct micromechanical measurements with constant-force axial optical tweezers. The data from the TPM experiments show a much smaller sequence effect on the persistence length than the optical tweezers experiments.

  5. Role of nitrogen in the formation of HC-N films by CH(4)/N(2) barrier discharge plasma: aliphatic tendency.

    PubMed

    Majumdar, Abhijit; Das, Gobind; Basvani, Kaleswara Rao; Heinicke, Joachim; Hippler, Rainer

    2009-12-01

    We have studied the influence of nitrogen on the chemical properties of the hydrogenated carbon nitride (a-CN(x):H) film deposited by CH(4)/N(2) dielectric barrier discharge (DBD) plasma. X-ray photoelectron spectroscopy (XPS) indicates that carbon and nitrogen form an unpolarized covalent bond in these C-N(x) materials, and the observed chemical shift in the C 1s and N 1s binding energy is explained with respect to N 1s incorporation. Furthermore, the average nitrogen content (N/C approximately 0.76) in the films was systematically varied by changing the nitrogen partial pressure (CH(4)/N(2) approximately from 5:1 to 1:7) which is well supported by the elemental analysis. Fourier transform infrared (FTIR) absorption spectra exhibit significant changes in different C-N, C identical withN, and NH/OH molecular bands at higher nitrogen concentration in the film. The isonitrile and nitrile groups (-NC and -CN) are increased with the increase of deposition time. In addition, the elemental analysis, proton NMR, and thermolysis mass spectrum show that the composition of the film with the ratio CH(4)/N(2) approximately 1:1 is C, 67.68; H, 9.88; N, 16.53 (in wt %) and that the film is composed of polymers, probably containing linear chains which are cleaved off on heating in vacuum. PMID:19894689

  6. Structural and magnetic properties of ferrimagnetic ε-phase Mn4N and antiferromagnetic ζ-phase Mn10N thin films on MgO(001)

    NASA Astrophysics Data System (ADS)

    Foley, Andrew; Corbett, Joseph; Richard, Andrea L.; Alam, Khan; Ingram, David C.; Smith, Arthur R.

    2016-07-01

    Single phase ε-Mn4N and ζ-Mn10N thin films are grown on MgO(001) using molecular beam epitaxy. The films are identified and characterized using reflection high-energy electron diffraction, x-ray diffraction, back scattered electron scanning electron microscopy, atomic/magnetic force microscopy and Rutherford backscattering spectrometry. These films are found to be highly smooth with root-mean-squared roughnesses 3.39 nm and below. The quality of ε-Mn4N grown is strongly dependent on substrate temperature during growth. Epitaxial growth of substantial grains composed of the antiferromagnetic η-phase Mn3N2 side by side with ferrimagnetic ε-phase grains is observed when growth temperature is below 480 °C. Ising domains isolated within areas roughly 0.5 μm across are observed in the ferrimagnetic ε-phase grains of samples consisting of a mix of η- and ε-phase grains. Magnetic domains following semi-continuous paths, which are 0.7-7.2 μm across, are observed in single phase ε-Mn4N. Measurements of the ζ-phase detail the structure and magnetism of the material as high Mn content γ-type ζ-phase with a regular surface corrugation along the [100]-direction and antiferromagnetic.

  7. 4'''-N-demethylspiramycin derivatives: synthesis and evaluation of effectiveness against drug-resistant bacteria.

    PubMed

    Sunazuka, Toshiaki; Shudo, Hiroko; Nagai, Kenichiro; Yoshida, Kiminari; Yamaguchi, Yukie; Hanaki, Hideaki; Omura, Satoshi

    2008-03-01

    18-amino-4''-O-benzoyl-4'''-N-demethyl-18-deoxospiramycins were designed and synthesized. Synthetic strategy involved selective demethylation of the dimethylamino group in forosamine, benzoylation of the hydroxyl group at the C4'' position and reductive N-amination of the formyl group. Antibacterial characteristics of spiramycin derivatives were tested. The derivatives exhibited promising activity against drug-resistant bacterial strains. PMID:18503196

  8. Bu4N+ alkoxide-initiated/autocatalytic addition reactions with organotrimethylsilanes.

    PubMed

    Das, Manas; O'Shea, Donal F

    2014-06-20

    The use of Me3SiO(-)/Bu4N(+) as a general activator of organotrimethylsilanes for addition reactions has been established. The broad scope of the method offers trimethylsilanes (including acetate, allyl, propargyl, benzyl, dithiane, heteroaryl, and aryl derivatives) as bench-stable organometallics that can be readily utilized as carbanion equivalents for synthesis. Reactions are achieved at rt without the requirement of specialized precautions that are commonplace for other organometallics.

  9. Nqrs Data for C8H12BCuF4N4 (Subst. No. 1102)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C8H12BCuF4N4 (Subst. No. 1102)

  10. Anomalous Hall effects in pseudo-single-crystal γ'-Fe4N thin films

    NASA Astrophysics Data System (ADS)

    Kabara, Kazuki; Tsunoda, Masakiyo; Kokado, Satoshi

    2016-05-01

    The anomalous Hall effects (AHE) were investigated at various temperatures for the pseudo-single-crystal Fe4N films, deposited on MgO substrates with changing the degree of order (S) of the nitrogen site. Both the anomalous Hall resistivity and the longitudinal resistivity simply decrease with lowering temperature for all the specimens. The AHE of the Fe4N films is presumed to arise from an intrinsic mechanism because of the relationship between the anomalous Hall resistivity and longitudinal resistivity. The anomalous Hall conductivity, σAH, exhibits a specific behavior at low temperature. In the case of the film with S = 0.93, the σAH drastically drops below 50 K, while it simply increases with lowering temperature in the range of 50-300 K. This low-temperature anomaly decays with decreasing S of the film and nearly vanishes in the films with low S. The threshold temperature and the dependence on S of the low-temperature anomaly of the σAH well correspond to those of the anisotropic magnetoresistance effects in the Fe4N films, reported in the literatures. From these results, it is suggested that the low-temperature anomaly of the σAH originates from the crystal field effect which reflects the structural transformation from a cubic to a tetragonal symmetry below 50 K and provides a modulation of the orbital angular momentum of the 3d orbitals at the Fermi level.

  11. Nano-crystalline silicon solar cell architecture with absorption at the classical 4n2 limit

    SciTech Connect

    Biswas, Rana; Xu, Chun

    2011-07-04

    We develop a periodically patterned conformal photonic-plasmonic crystal based solar architecture for a nano-crystalline silicon solar cell, through rigorous scattering matrix simulations. The solar cell architecture has a periodic array of tapered silver nano-pillars as the back-reflector coupled with a conformal periodic structure at the top of the cell. The absorption and maximal current, averaged over the entire range of wavelengths, for this solar cell architecture is at the semi-classical 4n{sup 2} limit over a range of common thicknesses (500-1500 nm) and slightly above the 4n{sup 2} limit for a 500 nm nc-Si cell. The absorption exceeds the 4n{sup 2} limit, corrected for reflection loss at the top surface. The photonic crystal cell current is enhanced over the flat Ag back-reflector by 60%, for a thick 1000 nm nc-Si layer, where predicted currents exceed 31 mA/cm{sup 2}. The conformal structure at the top surface focuses light within the absorber layer. There is plasmonic concentration of light, with intensity enhancements exceeding 7, near the back reflector that substantially enhances absorption.

  12. Fully automated TV-image analysis of the cell-cycle: comparison of the PLM method with determinations of the percentage and the DNA content of labelled cells.

    PubMed

    Wachsmuth, E D; van Golitschek, M; Macht, F; Maurer-Schultze, B

    1988-01-01

    A cell-cycle analysis based on a fully automated TV-image scanning system is proposed to replace the laborious PLM method. To compare the efficiency of the two procedures, cell-cycle parameters were assessed in Ehrlich (diploid and hyperdiploid), L-1210, and JB-1 mouse ascites tumours and in rat jejunal crypts. The percentages of labelled mitoses (PLM) were counted visually on Feulgen-stained autoradiographs obtained at various times after a single 3H-thymidine pulse. The fraction of labelled cells (P) and the DNA ratio of labelled and unlabelled cells were measured by TV-image analysis in the same slides and plotted against time. Within practical limits, TV-image analysis using the P-curve gives the same results as the PLM method. Using the P-curve has the important advantage that its first part, beginning at the time of 3H-thymidine injection and ending at the first maximum, furnishes more information about the cell cycle than the corresponding part of the PLM curve. It can be used to compute tG2M tS and the ratio of the growth faction index to the cell-cycle time (IP/tC) whereas the first part of the PLM-curve reveals only the length of the S-phase (tS). The IP/tC ratio is a readily accessible measure of growth and increases when the cells divide more frequently. Cell death rates may be neglected since the ratio is determined within less than the duration of one cell cycle. Moreover, the data from the first part of the P curve indicate whether there is a large non-growth fraction. If the non-growth fraction is small, i.e. if IP approximately 1, the P curve need only be measured until the first maximum is reached so that fewer samples and animals are required. If the non-growth fraction is large or unknown, the cell-cycle parameters are calculated by reference to the position and size not only of the first minimum and the first maximum, but also of the second minimum of the P curve.

  13. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.

    PubMed

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela; Gamba, Cristina; Barnett, Ross; Samaniego, José Alfredo; Madrigal, Jazmín Ramos; Orlando, Ludovic; Gilbert, M Thomas P

    2015-12-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained <3% endogenous DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.

  14. Search for evidence of C4N2 on Titan with new spectroscopic data

    NASA Astrophysics Data System (ADS)

    Jolly, A.; Benilan, Y.; Fayt, A.; Nixon, C.; Jennings, D.; Anderson, C.; Bjoraker, G.

    2013-09-01

    The Composite Infrared Spectrometer (CIRS) onboard Cassini has recorded spectra in the far and mid-infrared since 2004 with a spectral resolution of up to 0.5 cm-1. Mismatch between observed spectra and model spectra obtained from the available line lists has led us to study the spectroscopic parameters of HC3N, C4H2 and C2N2, the longest gas phase carbon chains observed so far on Titan. Band intensities, hot band intensities, and line lists were systematically verified by comparison with new laboratory spectra. Erroneous band intensities as well as an absence or shortage of hot band transitions in the line lists leading to model-data mismatches and inaccurate quantifications have been found. Improvement in the spectroscopic parameters has led to the detection of 13C isotopologues of HC3N [1] and C4H2 [2]. The study on C2N2 opens the way to the detection of 15N isotopologues whose abundances could give some clues to understand the origin and the evolution of Titan's atmosphere [3]. Also, the higher accuracy of spectroscopic data used to model CIRS spectra will facilitate the search for longer carbon chains on Titan such as HC5N, C6H2 and C4N2. Our recent measurements obtained at the SOLEIL synchrotron far infrared beam line of band intensities of C4N2 in the far and mid infrared domain have shown strong discrepancies with previous results [4]. Following the intensity measurements, a careful analysis of high resolution data has led to the first line lists for C4N2, which gives us the chance to determine precise abundance upper limits of this molecule in Titan's atmosphere.

  15. Vibrational and multinuclear NMR spectra of anionic mercuriomethanes [CH 4-n(HgX) n] n-

    NASA Astrophysics Data System (ADS)

    Breitinger, D. K.; Krumphanzl, U.; Moll, M.

    1990-03-01

    Vibrational spectra of solid sodium sulfitomercuriomethanates Na n[CH 4-n(HgSO 3) n]·nH 2O (2 ≤ and ≤ 4) exhibit high frequencies of the valence vibrations ν as(SO 3) > ν s(SO 3) (average 1057 cm -1) with big differences ν as - ν s (mean 104 cm -1), and ν(HgS) vibrations in the 200 to 230 cm -1 range, thus indicating S-coordinated sulfite ligands. Force field calculations for the ion [C(HgSO 3) 4] 4- yield high force constants K(S-O) = 605 N/m, K(Hg-S) = 258 N/m, and even K(C-Hg) = 181 N/m.- For thiosulfatomercuriomethanates [CH 4-n(HgS 2O 3] n- (1 ≤ n ≤ 4) in aqueous solutions Raman spectra suggest S-coordination with high ν as(SO 3) and ν s(SO 3) (average 1130 cm -1), and low ν(S-S) (˜420 cm -1) frequencies, and strong ν(Hg-S) bands (˜250 cm -1). From 1H, 13C and 199Hg NMR data is concluded that the CHg bond strengths in the series decrease on a lower level than in other mercuriomethanes.- On the whole, the electronic properties of the peripheral ligands X in the mercuriomethanes CH 4-n(HgX) n seem to be more important for the CHg bond strengths than the total charge.

  16. The Radiative Transfer Of CH{sub 4}-N{sub 2} Plasma Arc

    SciTech Connect

    Benallal, R.; Liani, B.

    2008-09-23

    Any physical modelling of a circuit-breaker arc therefore requires an understanding of the radiated energy which is taken into account in the form of a net coefficient. The evaluation of the net emission coefficient is performed by the knowledge of the chemical plasma composition and the resolution of the radiative transfer equation. In this paper, the total radiation which escapes from a CH{sub 4}-N{sub 2} plasma is calculated in the temperature range between 5000 and 30000K on the assumption of a local thermodynamic equilibrium and we have studied the nitrogen effect in the hydrocarbon plasmas.

  17. Critical fields of Fe{sub 4}N/NbN ferromagnetic/superconducting multilayers

    SciTech Connect

    Mattson, J.E.; Potter, C.D.; Conover, M.J.; Sowers, C.H.; Bader, S.D.

    1997-01-01

    Structural, magnetic, and superconducting properties of ferromagnetic/superconducting multilayers of Fe{sub 4}N/NbN are explored for a variety of thickness combinations. The superconducting properties show that 11 {Angstrom} ferromagnetic layers are sufficient to decouple the superconducting layers and to yield anisotropic behavior. The upper critical field data are well described by theory for ferromagnetic/superconducting multilayers. This analysis yields an interfacial parameter which characterizes the electron scattering at the ferromagnetic/superconducting boundary. {copyright} {ital 1997} {ital The American Physical Society}

  18. 4-N,N-Dimethylaminopyridine promoted selective oxidation of methyl aromatics with molecular oxygen.

    PubMed

    Zhang, Zhan; Gao, Jin; Wang, Feng; Xu, Jie

    2012-03-30

    4-N,N-Dimethylaminopyridine (DMAP) as catalyst in combination with benzyl bromide was developed for the selective oxidation of methyl aromatics. DMAP exhibited higher catalytic activity than other pyridine analogues, such as 4-carboxypyridine, 4-cyanopyridine and pyridine. The sp3 hybrid carbon-hydrogen (C-H) bonds of different methyl aromatics were successfully oxygenated with molecular oxygen. The real catalyst is due to the formation of a pyridine onium salt from the bromide and DMAP. The onium salt was well characterized by NMR and the reaction mechanism was discussed.

  19. Diffusion and separation of CH4/N2 in pillared graphene nanomaterials: A molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Zhou, Sainan; Lu, Xiaoqing; Wu, Zhonghua; Jin, Dongliang; Guo, Chen; Wang, Maohuai; Wei, Shuxian

    2016-09-01

    Diffusion and separation of CH4/N2 in pillared graphene were investigated by molecular dynamics. The pillared graphene with (6, 6) carbon nanotube (CNT) exhibited the higher diffusion and selectivity of CH4 over N2 than that with (7, 7) CNT due to the cooperative effect of pore topological characteristics and interaction energy. The stronger interaction facilitated CH4 to enter CNT prior to N2, and higher pressure promoted CH4 to pass CNT more easily. The relative concentrations profiles showed that CH4 reached equilibrium state faster than N2 at low pressure. Our results highlight potential use of pillared graphene in gas purification and separation.

  20. Laser pyrolysis fabrication of ferromagnetic gamma'-Fe4N and FeC nanoparticles

    NASA Technical Reports Server (NTRS)

    Grimes, C. A.; Qian, D.; Dickey, E. C.; Allen, J. L.; Eklund, P. C.

    2000-01-01

    Using the laser pyrolysis method, single phase gamma'-Fe4N nanoparticles were prepared by a two step method involving preparation of nanoscale iron oxide and a subsequent gas-solid nitridation reaction. Single phase Fe3C and Fe7C3 could be prepared by laser pyrolysis from Fe(CO)5 and 3C2H4 directly. Characterization techniques such as XRD, TEM and vibrating sample magnetometer were used to measure phase structure, particle size and magnetic properties of these nanoscale nitride and carbide particles. c2000 American Journal of Physics.

  1. Static hyperpolarizability of the van der Waals complex CH(4)-N(2).

    PubMed

    Kalugina, Yulia N; Buldakov, Mikhail A; Cherepanov, Victor N

    2012-12-15

    The static first hyperpolarizability of the van der Waals CH(4)-N(2) complex was calculated. The calculations were carried out in the approximation of the rigid interacting molecules for a broad range of intermolecular separations (R = 6-40 a(0)) and for six configurations at CCSD(T) level of theory using the correlation consistent aug-cc-pVTZ basis set with the basis set superposition error correction. It was shown that the long-range classical approximation, including the terms up to R(-6), is in a good agreement with ab initio calculations for R > 11 a(0). It was found out that for the family of most stable configurations of the complex, the first hyperpolarizability invariants practically do not change (the changes are less than 0.1%). Under forming the stable van der Waals CH(4)-N(2) complex, the intensity and degree of depolarization of the hyper-Rayleigh scattering are noticeable decreased (by ∼10%) to be compared with the free CH(4) and N(2) molecules. PMID:22903865

  2. Biodegradation and utilization of 4-n-nonylphenol by Aspergillus versicolor as a sole carbon and energy source.

    PubMed

    Krupiński, Mariusz; Janicki, Tomasz; Pałecz, Bartłomiej; Długoński, Jerzy

    2014-09-15

    4-n-Nonylphenol (4-n-NP) is an environmental pollutant with endocrine-disrupting activities that is formed during the degradation of nonylphenol polyethoxylates, which are widely used as surfactants. Utilization of 4-n-NP by the filamentous fungus Aspergillus versicolor as the sole carbon and energy source was investigated. By means of gas chromatography-mass spectrometry, we showed that in the absence of any carbon source other than 4-n-NP in the medium, A. versicolor completely removed the xenobiotic (100 mg L(-1)) after 3 d of cultivation. Moreover, mass spectrometric analysis of intracellular extracts led to the identification of eight intermediates. The mineralization of the xenobiotic in cultures supplemented with 4-n-NP [ring-(14)C(U)] as a growth substrate was also assessed. After 3 d of incubation, approximately 50% of the initially applied radioactivity was recovered in the form of (14)CO2, proving that this xenobiotic was completely metabolized and utilized by A. versicolor as a carbon source. Based on microscopic analysis, A. versicolor is capable of germinating spores under such conditions. To confirm these observations, a microcalorimetric method was used. The results show that even the highest amount of 4-n-NP initiates heat production in the fungal samples, proving that metabolic processes were affected by the use of 4-n-NP as an energetic substrate. PMID:25222932

  3. Induction of mouthpart deformities in Chironomus riparius larvae exposed to 4-n-nonylphenol.

    PubMed

    Meregalli, G; Pluymers, L; Ollevier, F

    2001-01-01

    Chironomid mouthpart deformities have often been associated with sediment contamination and are, therefore, currently used to assess sediment quality. Deformities were only occasionally induced in laboratory bioassays. Mouthpart deformities results from a physiological disturbance during larval molting. In the past few years it has been shown that some chemicals can exert negative effects on both vertebrates and invertebrates at the level of endocrine regulation. As insect molting is hormonally regulated, we wanted to test the hypothesis that deformities are induced due to a hormonal disruption in the developmental process. The aim of the present study was to test whether the endocrine disrupter, 4-n-nonylphenol (4NP), induces mouthpart deformities in chironomids. A laboratory bioassay was performed exposing Chironomus riparius larvae to 10, 50 and 100 micrograms l-1 4NP. Survival of the larvae was not affected by the tested concentrations, but the frequency of mentum deformities increased significantly (P < 0.01) after exposure to 4NP. PMID:11202727

  4. Nitrogen Incorporation in CH4-N2 Photochemical Aerosol Produced by Far Ultraviolet Irradiation

    PubMed Central

    Jimenez, Jose L.; Yung, Yuk L.; Toon, Owen B.; Tolbert, Margaret A.

    2012-01-01

    Abstract Nitrile incorporation into Titan aerosol accompanying hydrocarbon chemistry is thought to be driven by extreme UV wavelengths (λ<120 nm) or magnetospheric electrons in the outer reaches of the atmosphere. Far UV radiation (120–200 nm), which is transmitted down to the stratosphere of Titan, is expected to affect hydrocarbon chemistry only and not initiate the formation of nitrogenated species. We examined the chemical properties of photochemical aerosol produced at far UV wavelengths, using a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS), which allows for elemental analysis of particle-phase products. Our results show that aerosol formed from CH4/N2 photochemistry contains a surprising amount of nitrogen, up to 16% by mass, a result of photolysis in the far UV. The proportion of nitrogenated organics to hydrocarbon species is shown to be correlated with that of N2 in the irradiated gas. The aerosol mass greatly decreases when N2 is removed, which indicates that N2 plays a major role in aerosol production. Because direct dissociation of N2 is highly improbable given the immeasurably low cross section at the wavelengths studied, the chemical activation of N2 must occur via another pathway. Any chemical activation of N2 at wavelengths >120 nm is presently unaccounted for in atmospheric photochemical models. We suggest that reaction with CH radicals produced from CH4 photolysis may provide a mechanism for incorporating N into the molecular structure of the aerosol. Further work is needed to understand the chemistry involved, as these processes may have significant implications for how we view prebiotic chemistry on early Earth and similar planets. Key Words: Titan—Photochemical aerosol—CH4-N2 photolysis—Far UV—Nitrogen activation. Astrobiology 12, 315–326. PMID:22519972

  5. The use of dimorphic Alu insertions in human DNA fingerprinting

    SciTech Connect

    Novick, G.E.; Gonzalez, T.; Garrison, J.; Novick, C.C.; Herrera, R.J.; Batzer, M.A.; Deininger, P.L.

    1992-12-04

    We have characterized certain Human Specific Alu Insertions as either dimorphic (TPA25, PV92, APO), sightly dimorphic (C2N4 and C4N4) or monomorphic (C3N1, C4N6, C4N2, C4N5, C4N8), based on studies of Caucasian, Asian, American Black and African Black populations. Our approach is based upon: (1) PCR amplification using primers directed to the sequences that flank the site of insertion of the different Alu elements studied; (2) gel electrophoresis and scoring according to the presence or absence of an Alu insertion in one or both homologous chromosomes; (3) allelic frequencies calculated and compared according to Hardy-Weinberg equilibrium. Our DNA fingerprinting procedure using PCR amplification of dimorphic Human Specific Alu insertions, is stable enough to be used not only as a tool for genetic mapping but also to characterize populations, study migrational patterns and track the inheritance of human genetic disorders.

  6. Epitaxial V{sub 0.6}W{sub 0.4}N/MgO(001): Evidence for ordering on the cation sublattice

    SciTech Connect

    Kindlund, H.; Lu, J.; Jensen, J.; Hultman, L.; Petrov, I.; Greene, J. E.

    2013-07-15

    V{sub 0.6}W{sub 0.4}N alloys are grown on MgO(001) by ultrahigh vacuum reactive magnetron sputtering from V and W targets in 10 mTorr pure-N{sub 2} atmospheres at temperatures T{sub s} ranging from 600 to 900 Degree-Sign C. Based on x-ray diffraction and transmission electron microscopy results, all films have the B1-NaCl crystal structure and grow with a cube-on-cube epitaxial relationship to the substrate, (001){sub VWN} Double-Vertical-Line (001){sub MgO} and [100]{sub VWN} Double-Vertical-Line [100]{sub MgO}. Rutherford backscattering spectrometry analyses show that the N content in V{sub 0.6}W{sub 0.4}N{sub x} alloys decreases with increasing T{sub s} from overstoichiometric with x = 1.13 at 600 Degree-Sign C, to approximately stoichiometric with x = 1.08 at 700 Degree-Sign C, to understoichiometric at 800 Degree-Sign C (x = 0.80) and 900 Degree-Sign C (x = 0.75). High-resolution scanning transmission electron microscopy, Z-contrast, and selected-area electron diffraction investigations of V{sub 0.6}W{sub 0.4}N(001) alloys grown at 600 and 700 Degree-Sign C reveal the onset of W ordering on adjacent 111 planes of the metal sublattice; no ordering is observed for understoichiometric films grown at higher temperatures.

  7. [DNA fingerprinting structure of plankton community and its relations to environmental physical-chemical factors in Donghu Lake].

    PubMed

    Song, Xiao-Hong; Yu, Yu-He; Feng, Wei-Song; Yan, Qing-Yun; Deng, Wen-Na

    2007-12-01

    By the method of RAPD fingerprinting, this paper studied the DNA fingerprinting structure of plankton community and its relations to the main environmental physical-chemical factors at five sites in Donghu Lake. From the screened 9 random primers, a total of 210 observable bands with a length of 150-2 000 bp were amplified, 93.3% of which were polymorphic. At the five sites, the average number of amplified bands was 42, with the maximum (53) at site IV and the minimum (35) at site V. The PO4(3-)-P and TP contents were the highest at site I, NH4(+)-N, TN and NO2(-)-N contents were the highest at site V, while the values of all test physical-chemical parameters were the lowest at site IV. No obvious differences in COD, alkalinity, rigidity, and calcium content were observed among the study sites. Similarity clustering analysis showed that the DNA fingerprinting of plankton community based on RAPD marker could cluster the five sites into two groups, i. e., sites I, II and III could be clustered into one group, while sites IV and V could be clustered into another group, which was consistent with the clustering analysis based on the main environmental physical-chemical factors. In conclusion, there was a close relation between the DNA fingerprinting structure of plankton community and the main environmental physical-chemical factors in Donghu Lake.

  8. Cationic motions and phase transitions in [(CH 3) 4N] 2SO 4·4H 2O, [(CH 3) 4N] 2SO 4, and [(CH 3) 4N] 2SeO 4 as studied by 1H NMR, differential thermal analysis, and X-ray powder diffraction techniques

    NASA Astrophysics Data System (ADS)

    Sato, Setsuko; Endo, Midori; Hara, Naoki; Nakamura, Daiyu; Ikeda, Ryuichi

    1995-02-01

    Cationic reorientations have been studied in solid [(CH 3) 4N] 2SO 4·4H 2O, [(CH 3) 4N] 2SO 4, and [(CH 3) 4N] 2SeO 4 by measuring 1H NMR spin-lattice relaxation times, T1. These motions have been discussed in association with the crystal structures and the phase transitions examined by X-ray powder diffraction and differential thermal analysis, respectively. In crystals of [(CH 3) 4N] 2SO 4·4H 2O, there are two kinds of cations distorted from regular tetrahedra. T1 is calculated according to the interpretation that two T1 minima are due to the two inequivalent (NH 3) 4N + ions reorienting at different frequencies. The result shows that at the phase transition temperatures, the correlation times to those cationic reorientations are very different from each other in this compound in contrast with (NH 4) 2SO 4 and [(CH 3) 4N] 2CdX 4 (X = Cl and Br). For the sulfate and selenate, there is a single kind of cation which can be considered tetrahedral, and the phase transitions occur in the temperature region where the narrowing of the resonance line owing to the overall cationic reorientations starts.

  9. Spherically symmetric solutions of a (4 + n)-dimensional Einstein Yang Mills model with cosmological constant

    NASA Astrophysics Data System (ADS)

    Brihaye, Yves; Hartmann, Betti

    2005-01-01

    We construct solutions of an Einstein Yang Mills system including a cosmological constant in 4 + n spacetime dimensions, where the n-dimensional manifold associated with the extra dimensions is taken to be Ricci flat. Assuming the matter and metric fields to be independent of the n extra coordinates, a spherical symmetric ansatz for the fields leads to a set of coupled ordinary differential equations. We find that for n > 1 only solutions with either one non-zero Higgs field or with all Higgs fields constant and zero gauge field function (corresponding to a Wu Yang-type ansatz) exist. We give the analytic solutions available in this model. These are 'embedded' Abelian solutions with a diverging size of the manifold associated with the extra n dimensions. Depending on the choice of parameters, these latter solutions either represent naked singularities or they possess a single horizon. We also present solutions of the effective four-dimensional Einstein Yang Mills Higgs-dilaton model, where the higher-dimensional cosmological constant induces a Liouville-type potential. The solutions are non-Abelian solutions with diverging Higgs fields, which exist only up to a maximal value of the cosmological constant.

  10. Structure, conformation and hydrogen bonding of 4-( N-methylpiperidinium)-butyric acid bromide

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Z.; Dulewicz, E.; Szafran, M.; Thaimattam, R.; Jaskolski, M.

    2007-02-01

    A 1:1 complex between 4-( N-methylpiperidinium)-butyrate inner salt (betaine) and hydrobromide, MPBUH·Br, has been characterized by single crystal X-ray analysis. The crystals are monoclinic, space group P2 1/c, with a = 8.284(1), b = 10.369(1), c = 13.809(2) Å, β = 92.26(1)°. The piperidine ring adopts a chair conformation with the (CH 2) 3COOH substituent in the axial and the CH 3 group in the equatorial positions. In the crystal, the Br - anion is engaged in a medium-strong hydrogen bond with the COOH group (O sbnd H⋯Br - = 3.141(1) Å), N +⋯Br - electrostatic interactions and in several C sbnd H⋯Br - contacts with the aliphatic groups forming a cavity in which it is enclosed. Three conformers ( 2- 4) were optimized by the B3LYP/6-31G (d, p) level of theory. The most stable is conformer 4 with the (CH 2) 3COOH substituent in the equatorial position and the CH 3 group in the axial position. The stability of the investigated conformers is controlled by electrostatic interactions between the oppositely charged groups. The FTIR spectrum of MPBUH·Br shows a strong band at 2941 cm -1 due to νOH and the νC dbnd O band at 1712 cm -1.

  11. Purification and characterization of 4-N-trimethylamino-1-butanol dehydrogenase from Fusarium merismoides var. acetilereum.

    PubMed

    Fujimitsu, Hiroshi; Taniyama, Yuko; Tajima, Sae; Mohamed Ahmed, Isam A; Arima, Jiro; Mori, Nobuhiro

    2016-09-01

    From investigation of 60 filamentous fungi, we identified Fusarium merismoides var. acetilereum, which uses 4-N-trimethylamino-1-butanol (TMA-butanol) as the sole source of carbon and nitrogen. The fungus produced NAD(+)-dependent TMA-butanol dehydrogenase (DH) when it was cultivated in medium containing TMA-butanol. The enzyme showed molecular mass of 40 kDa by SDS-PAGE and 160 kDa by gel filtration, suggesting that it is a homotetramer. TMA-butanol DH is stable at pH 7.5-9.0. It exhibits moderate stability with respect to temperature (up to 30 °C). Additionally, it has optimum activity at 45 °C and at pH 9.5. The enzyme has broad specificity to various alkyl alcohols and amino alkyl alcohols, and the carbon chains of which are longer than butanol. Moreover, the activity is strongly inhibited by oxidizing agents, carbonyl and thiol modulators, and chelating agents. This report is the first study examining TMA-butanol DH from eukaryotic microbes. PMID:27121905

  12. Can Moral Hazard Be Resolved by Common-Knowledge in S4n-Knowledge?

    NASA Astrophysics Data System (ADS)

    Matsuhisa, Takashi

    This article investigates the relationship between common-knowledge and agreement in multi-agent system, and to apply the agreement result by common-knowledge to the principal-agent model under non-partition information. We treat the two problems: (1) how we capture the fact that the agents agree on an event or they get consensus on it from epistemic point of view, and (2) how the agreement theorem will be able to make progress to settle a moral hazard problem in the principal-agents model under non-partition information. We shall propose a solution program for the moral hazard in the principal-agents model under non-partition information by common-knowledge. Let us start that the agents have the knowledge structure induced from a reflexive and transitive relation associated with the multi-modal logic S4n. Each agent obtains the membership value of an event under his/her private information, so he/she considers the event as fuzzy set. Specifically consider the situation that the agents commonly know all membership values of the other agents. In this circumstance we shall show the agreement theorem that consensus on the membership values among all agents can still be guaranteed. Furthermore, under certain assumptions we shall show that the moral hazard can be resolved in the principal-agent model when all the expected marginal costs are common-knowledge among the principal and agents.

  13. Cation-Cation Interactions in [(UO2)2(OH)n](4-n) Complexes

    SciTech Connect

    Odoh, Samuel O.; Govind, Niranjan; Schreckenbach, Georg; De Jong, Wibe A.

    2013-10-07

    The structures and bonding of gas-phase [(UO2)2(OH)n]4-n (n=2-6) complexes have been studied using density functional theory (DFT), MP2 and CCSD(T) methods with particular emphasis on ground state structures featuring cation-cation interactions (CCIs) between the uranyl groups. An interesting trend is observed in the stabilities of members of this series of complexes. The structures of [(UO2)2(OH)2]2+, [(UO2)2(OH)4] and [(UO2)2(OH)6]2- featuring CCIs are found at higher energies (by 3-20 kcal/mol) in comparison to their conventional μ2-dihydroxo structures. In contrast, the CCI structures of [(UO2)2(OH)3]+ and [(UO2)2(OH)5]- are respectively almost degenerate with and lower in energy than the structures with the μ2-dihydroxo format. The origin of this trend lies in the ‘symmetry’-based need to balance the coordination numbers and effective atomic charges of each uranium center. The calculated IR vibrational frequencies provide signature probes that can be used in differentiating the lowenergy structures and in experimentally confirming the existence of the structures featuring CCIs. Analysis of the bonding in the structures of [(UO2)2(OH)3]+ and [(UO2)2(OH)5]- shows that the CCIs and bridging hydroxo between the dioxo-uranium units are mainly electrostatic in nature.

  14. Early Events in the Nonadiabatic Relaxation Dynamics of 4-(N,N-Dimethylamino)benzonitrile.

    PubMed

    Kochman, Michał A; Tajti, Attila; Morrison, Carole A; Miller, R J Dwayne

    2015-03-10

    4-(N,N-Dimethylamino)benzonitrile (DMABN) is the archetypal system for dual fluorescence. Several past studies, both experimental and theoretical, have examined the mechanism of its relaxation in the gas phase following photoexcitation to the S2 state, without converging to a single description. In this contribution, we report first-principles simulations of the early events involved in this process performed using the nonadiabatic trajectory surface hopping (TSH) approach in combination with the ADC(2) electronic structure method. ADC(2) is verified to reproduce the ground- and excited-state structures of DMABN in reasonably close agreement with previous theoretical benchmarks. The TSH simulations predict that internal conversion from the S2 state to the S1 takes place as early as 8.5 fs, on average, after the initial photoexcitation, and with no significant torsion of the dimethylamino group relative to the aromatic ring. As evidenced by supporting EOM-CCSD calculations, the population transfer from S2 to S1 can be attributed to the skeletal deformation modes of the aromatic ring and the stretching of the ring-dimethylamino nitrogen bond. The non- or slightly twisted locally excited structure is the predominant product of the internal conversion, and the twisted intramolecular charge transfer structure is formed through equilibration with the locally excited structure with no change of adiabatic state. These findings point toward a new interpretation of data from previous time-resolved experiments. PMID:26579762

  15. Structural and biological evaluation of some metal complexes of vanillin-4N-(2-pyridyl) thiosemicarbazone

    NASA Astrophysics Data System (ADS)

    Yousef, T. A.; Abu El-Reash, G. M.; Al-Jahdali, M.; El-Rakhawy, El-Bastawesy R.

    2013-12-01

    The synthesis and characterization of Mn(II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II), Hg(II) and U(VI)O2 complexes of vanillin-4N-(2-pyridyl) thiosemicarbazone (H2PVT) are reported. Theoretical calculations have been performed to obtain IR spectra of ligand and its complexes using AM1, Zindo/1, MM+ and PM3, methods. The Schiff base and its metal complexes have been screened for antibacterial Pseudomonas aeruginosa, Escherichia coli, Bacillus subtilis and Staphylococcus saprophyticus. H2VPT shows no apparent digestion effect on the egg albumin while Mn(II), Hg(II) and Cu(II) complexes exhibited a considerable digestion effect following the order Cu(II) > Mn(II) > Hg(II). Moreover, Ni(II) and Co(II) complexes revealed strong digestion effect. Fe(II), Mn(II), Cu(II), Zn(II) and Ni(II) acted as metal co- SOD enzyme factors, which are located in different compartments of the cell.

  16. Transport Properties of a Rarefied Ch4-N2 Gas Mixture

    NASA Astrophysics Data System (ADS)

    Fokin, L. R.; Kalashnikov, A. N.

    2016-01-01

    The area of application of the rarefied neutral methane-nitrogen gas mixture is considered. Experimental data on the transport properties of this mixture and its components were analyzed and generalized on the basis of molecular-kinetic theory relations with the use of the potentials of pair uniform and cross interactions of CH4 and N2 molecules. The parameters of three spherical symmetric three-parameter m-6 Lennard-Jones interaction potentials with a repulsive branch of varying rigidity were determined with the use of the nonlinear weight method of least squares. Tables of reference data on the viscosity of the indicated mixture and the coefficients of interdiffusion of its components were calculated for the concentration range 0-1 at temperatures 100-1150 K. Estimates of the confidential errors in determining the properties of this mixture have been made with the use of the error matrix of parameters of the indicated potentials. The results of calculations were compared with the corresponding reference data obtained earlier for the CH4-N2 gas mixture.

  17. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting

    PubMed Central

    Vlijm, Rifka; v.d. Torre, Jaco; Dekker, Cees

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix. PMID:26513573

  18. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting.

    PubMed

    Vlijm, Rifka; V D Torre, Jaco; Dekker, Cees

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix.

  19. The diverse electronic properties of C4N3 monolayer under biaxial compressive strain: a theoretical study

    NASA Astrophysics Data System (ADS)

    Wu, Haiping; Liu, Yuzhen; Kan, Erjun; Ma, Yanming; Xu, Wenjie; Li, Jie; Yan, Meichen; Lu, Ruifeng; Wei, Jianfeng; Qian, Yan

    2016-07-01

    Because of the observation of half-metallicity in graphitic carbon nitride C4N3 (g-C4N3), extensive research has recently been focused on this compound. Using density-functional calculations, herein diverse electronic properties of g-C4N3 were engineered by applying biaxial compressive strain. The calculated results demonstrate that g-C4N3 preserves ferromagnetic half-metallicity when the strain is lower than  -2%, accompanied by a decrease of the half-metallic gap. When the compressive strain ranges from  -5 to  -3%, the compound turns into nonmagnetic metal. By increasing the strain on the end, it becomes a nonmagnetic semiconductor. Further investigations show that all nonmagnetic semiconductors possess a direct band gap with a value of around 1.6 eV. This fact indicates that g-C4N3 can be applied in spintronic or photovoltaic fields under a strain environment.

  20. The diverse electronic properties of C4N3 monolayer under biaxial compressive strain: a theoretical study

    NASA Astrophysics Data System (ADS)

    Wu, Haiping; Liu, Yuzhen; Kan, Erjun; Ma, Yanming; Xu, Wenjie; Li, Jie; Yan, Meichen; Lu, Ruifeng; Wei, Jianfeng; Qian, Yan

    2016-07-01

    Because of the observation of half-metallicity in graphitic carbon nitride C4N3 (g-C4N3), extensive research has recently been focused on this compound. Using density-functional calculations, herein diverse electronic properties of g-C4N3 were engineered by applying biaxial compressive strain. The calculated results demonstrate that g-C4N3 preserves ferromagnetic half-metallicity when the strain is lower than  ‑2%, accompanied by a decrease of the half-metallic gap. When the compressive strain ranges from  ‑5 to  ‑3%, the compound turns into nonmagnetic metal. By increasing the strain on the end, it becomes a nonmagnetic semiconductor. Further investigations show that all nonmagnetic semiconductors possess a direct band gap with a value of around 1.6 eV. This fact indicates that g-C4N3 can be applied in spintronic or photovoltaic fields under a strain environment.

  1. Nitrogen Incorporation in CH4-N2 Photochemical Aerosol Produced by Far UV Irradiation

    NASA Technical Reports Server (NTRS)

    Trainer, Melissa G.; Jimenez, Jose L.; Yung, Yuk L.; Toon, Owen B.; Tolbert, Margaret A.

    2012-01-01

    Nitrile incorporation into Titan aerosol accompanying hydrocarbon chemistry is thought to be driven by extreme UV wavelengths (lambda < 120 nm) or magnetospheric electrons in the outer reaches of the atmosphere. Far UV radiation (120 - 200 nm), which is transmitted down to the stratosphere of Titan, is expected to affect hydrocarbon chemistry only and not initiate the formation of nitrogenated species. We have examined the chemical properties of photochemical aerosol produced at far UV wavelengths using a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS), which allows for elemental analysis of particle-phase products. Our results show that aerosol formed from CH4/N2 photochemistry contains a surprising amount of nitrogen, up to 16% by mass, a result of photolysis in the far UV. The proportion of nitrogenated organics to hydrocarbon species is shown to be correlated with that of N2 in the irradiated gas. The aerosol mass greatly decreases when N2 is removed, indicating that N2 plays a major role in aerosol production. Because direct dissociation of N2 is highly improbable given the immeasurably low cross-section at the wavelengths studied, the chemical activation of N2 must occur via another pathway. Any chemical activation of N2 at wavelengths > 120 nm is presently unaccounted for in atmospheric photochemical models. We suggest that reaction with CH radicals produced from CH4 photolysis may provide a mechanism for incorporating N into the molecular structure of the aerosol. Further work is needed to understand the chemistry involved, as these processes may have significant implications for prebiotic chemistry on the early Earth and similar planets.

  2. Effects of Picoxystrobin and 4-n-Nonylphenol on Soil Microbial Community Structure and Respiration Activity

    PubMed Central

    Stenrød, Marianne; Klemsdal, Sonja S.; Norli, Hans Ragnar; Eklo, Ole Martin

    2013-01-01

    There is widespread use of chemical amendments to meet the demands for increased productivity in agriculture. Potentially toxic compounds, single or in mixtures, are added to the soil medium on a regular basis, while the ecotoxicological risk assessment procedures mainly follow a chemical by chemical approach. Picoxystrobin is a fungicide that has caused concern due to studies showing potentially detrimental effects to soil fauna (earthworms), while negative effects on soil microbial activities (nitrification, respiration) are shown to be transient. Potential mixture situations with nonylphenol, a chemical frequently occurring as a contaminant in sewage sludge used for land application, infer a need to explore whether these chemicals in mixture could alter the potential effects of picoxystrobin on the soil microflora. The main objective of this study was to assess the effects of picoxystrobin and nonylphenol, as single chemicals and mixtures, on soil microbial community structure and respiration activity in an agricultural sandy loam. Effects of the chemicals were assessed through measurements of soil microbial respiration activity and soil bacterial and fungal community structure fingerprints, together with a degradation study of the chemicals, through a 70 d incubation period. Picoxystrobin caused a decrease in the respiration activity, while 4-n-nonylphenol caused an increase in respiration activity concurring with a rapid degradation of the substance. Community structure fingerprints were also affected, but these results could not be directly interpreted in terms of positive or negative effects, and were indicated to be transient. Treatment with the chemicals in mixture caused less evident changes and indicated antagonistic effects between the chemicals in soil. In conclusion, the results imply that the application of the fungicide picoxystrobin and nonylphenol from sewage sludge application to agricultural soil in environmentally relevant concentrations, as

  3. Spin-polarization inversion at small organic molecule/Fe{sub 4}N interfaces: A first-principles study

    SciTech Connect

    Zhang, Qian; Mi, Wenbo

    2015-09-21

    We report the first-principles calculations on the electronic structure and simulation of the spin-polarized scan tunneling microscopy graphic of the small organic molecules (benzene, thiophene, and cyclopentadienyl)/Fe{sub 4}N interfaces. It is found that the plane of benzene and thiophene keeps parallel to Fe{sub 4}N surface, while that of cyclopentadienyl does not. For all the systems, the organic molecules bind strongly with Fe{sub 4}N. Due to the hybridization between molecule p{sub z} orbitals and d orbitals of Fe, i.e., Zener interaction, all the three systems realize the spin-polarization inversion, whereas the spatial spin-polarization inversion distribution shows different intensities influenced by the competition between the spin polarization of C p{sub z} and Fe d states.

  4. Sunscreens and T4N5 liposomes differ in their ability to protect against ultraviolet-induced sunburn cell formation, alterations of dendritic epidermal cells, and local suppression of contact hypersensitivity.

    PubMed

    Wolf, P; Cox, P; Yarosh, D B; Kripke, M L

    1995-02-01

    Exposure of skin to ultraviolet (UV) radiation can lead to diverse biologic effects, including inflammation, sunburn cell formation, alterations of cutaneous immune cells, and impaired induction of contact hypersensitivity responses. The molecular mechanisms of these UV-induced effects are not completely understood. We investigated the ability of sunscreens and liposomes containing the DNA excision repair enzyme T4 endonuclease V to prevent these effects of UV radiation. The use of T4N5 liposomes, which increase the repair of cyclobutyl pyrimidine dimers, provides an approach for assessing the role of DNA damage in the effects of UV radiation on the skin. Exposing C3H mice to 500 mJ/cm2 UVB radiation from FS40 sunlamps resulted in skin edema, sunburn cell formation, and morphologic alterations and decreased numbers of Langerhans cells and Thy-1+ dendritic epidermal T cells. In addition, the induction of contact hypersensitivity after application of 2,4-dinitrofluorobenzene on UV-irradiated skin was diminished by 80%. Applying sunscreens containing octyl-N-dimethyl-p-aminobenzoate, 2-ethylhexyl-p-methoxycinnamate, or benzophenone-3 before this dose of UV irradiation gave nearly complete protection against all of these effects of UV irradiation. In contrast, topical application of T4N5 liposomes after UV irradiation had no effect on UV-induced skin edema and only partially protected against sunburn cell formation and local suppression of contact hypersensitivity, although its ability to protect against alterations in dendritic immune cells was comparable to that of the sunscreens. These results suggest that DNA damage is involved in only some of the local effects of UV radiation on the skin. In addition, T4N5 liposomes may be a useful adjunct to sunscreens because they can reduce some of the deleterious effects of UV radiation on skin even after a sunburn has been initiated. PMID:7829886

  5. Mitochondrial DNA.

    ERIC Educational Resources Information Center

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  6. Characterization of an H4N2 avian influenza virus isolated from domestic duck in Dongting Lake wetland in 2009.

    PubMed

    Zhang, Hongbo; Chen, Quanjiao; Chen, Ze

    2012-02-01

    In January 2009, an H4N2 subtype of avian influenza virus [A/duck/Hunan/8-19/2009 (H4N2)] was isolated from domestic ducks in Dongting Lake wetland. The whole genome of the virus was sequenced and the results indicated that multiple gene segments of the virus had a high homology with viruses isolated from wild waterfowl, which indicated that the virus was probably transmitted from wild waterfowl to domestic ducks. Phylogenetic analysis revealed that the each gene belonged to the Eurasian lineage of avian influenza viruses, but genetic reassortment occurs between viruses of different subtypes.

  7. DNA Banking

    SciTech Connect

    Reilly, P.R. )

    1992-11-01

    The author is involved in the ethical, legal, and social issues of banking of DNA and data from DNA analysis. In his attempt to determine the extent of DNA banking in the U.S., the author surveyed some commercial companies performing DNA banking services. This article summarizes the results of that survey, with special emphasis on the procedures the companies use to protect the privacy of individuals. 4 refs.

  8. Amine templating effect absent in uranyl sulfates synthesized with 1,4-n-butyldiamine

    SciTech Connect

    Jouffret, Laurent J.; Wylie, Ernest M.; Burns, Peter C.

    2013-01-15

    Two new uranyl sulfates, (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2}){sub 2}(SO{sub 4}){sub 3}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS2) and (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2})(SO{sub 4}){sub 2}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS3), were synthesized and their crystal structures determined. NDUS2 was obtained in highly acidic media heat-treated at 373 K and subsequently maintained at 278 K until crystals formed after two months. NDUS3 results from the degradation of NDUS2 over the course of a few days. NDUS2 and NDUS3 crystallize in the monoclinic space group P2{sub 1}/n, a=10.9075(4) A, b=10.4513(4) A, c=17.7881(7) A, {beta}=97.908(2) Degree-Sign , V=2008.52(13) A{sup 3}, Z=4, at 140 K and a=8.8570(4) A, b=7.3299(3) A, c=20.4260(9) A, {beta}=95.140(2) Degree-Sign , V=1320.74(10) A{sup 3}, Z=4, at 140 K, respectively. The compounds contain interlayer 1,4-n-butyldiammonium cations that charge-balance the anionic structural units. - Graphical abstract: Amine templating effect absent in uranyl sulfates synthesized with 1,4-diaminobutane, as shown by the synthesis of two new uranyl sulfates, (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2}){sub 2}(SO{sub 4}){sub 3}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS2) and (C{sub 4}H{sub 14}N{sub 2})[(UO{sub 2})(SO{sub 4}){sub 2}(H{sub 2}O)]{center_dot}2H{sub 2}O (NDUS3). Highlights: Black-Right-Pointing-Pointer Two layered uranyl sulfates were synthesized. Black-Right-Pointing-Pointer Amine molecules are located in the interlayers of the compounds. Black-Right-Pointing-Pointer No templating effect of the amine was observed. Black-Right-Pointing-Pointer Amine molecules are only charge balancing cations in the structures.

  9. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  10. AF4 and AF4N protein complexes: recruitment of P-TEFb kinase, their interactome and potential functions

    PubMed Central

    Scholz, Bastian; Kowarz, Eric; Rössler, Tanja; Ahmad, Khalil; Steinhilber, Dieter; Marschalek, Rolf

    2015-01-01

    AF4/AFF1 and AF5/AFF4 are the molecular backbone to assemble “super-elongation complexes” (SECs) that have two main functions: (1) control of transcriptional elongation by recruiting the positive transcription elongation factor b (P-TEFb = CyclinT1/CDK9) that is usually stored in inhibitory 7SK RNPs; (2) binding of different histone methyltransferases, like DOT1L, NSD1 and CARM1. This way, transcribed genes obtain specific histone signatures (e.g. H3K79me2/3, H3K36me2) to generate a transcriptional memory system. Here we addressed several questions: how is P-TEFb recruited into SEC, how is the AF4 interactome composed, and what is the function of the naturally occuring AF4N protein variant which exhibits only the first 360 amino acids of the AF4 full-length protein. Noteworthy, shorter protein variants are a specific feature of all AFF protein family members. Here, we demonstrate that full-length AF4 and AF4N are both catalyzing the transition of P-TEFb from 7SK RNP to their N-terminal domain. We have also mapped the protein-protein interaction network within both complexes. In addition, we have first evidence that the AF4N protein also recruits TFIIH and the tumor suppressor MEN1. This indicate that AF4N may have additional functions in transcriptional initiation and in MEN1-dependend transcriptional processes. PMID:26171280

  11. Structure, phase transitions, and isotope effects in [(CH3)4N]2PuCl6

    SciTech Connect

    Wilson, Richard E.

    2015-11-02

    The single crystal X-ray diffraction structure of [(CH3)4N]2PuCl6 is presented for the first time, resolving long standing confusion and speculation regarding the structure of this compound in the literature. A temperature dependent study of this compound shows that the structure of [(CH3)4N]2PuCl6 undergoes no fewer than two phase transitions between 100 and 360 K. The phase of [(CH3)4N]2PuCl6 at room temperature is Fd-3c a = 26.012(3) Å. At 360 K, the structure is in space group Fm-3m with a = 13.088(1) Å. The plutonium octahedra and tetramethylammonium cations undergo a rotative displacement and the degree of rotation varies with temperature, giving rise to the phase transition from Fm-3m to Fd-3c as the crystal is cooled. Synthesis and structural studies of the deuterated salt [(CD3)4N]2PuCl6 suggest that there is an isotopic effect associated with this phase transition as revealed by a changing transition temperature in the deuterated versus protonated compound indicating that the donor-acceptor interactions between the tetramethylammonium cations and the hexachloroplutonate anions are driving the phase transformation.

  12. DNA denaturation in ionic solution

    NASA Astrophysics Data System (ADS)

    Maity, Arghya; Singh, Amar; Singh, Navin

    2016-05-01

    Salt or cations, present in solution play an important role in DNA denaturation and folding kinetics of DNA helix. In this work we study the thermal melting of double stranded DNA (dsDNA) molecule using Peyrard Bishop Dauxois (PBD) model. We modify the potential of H-bonding between the bases of the complimentary strands to introduce the salt and solvent effect. We choose different DNA sequences having different contents of GC pairs and calculate the melting temperatures. The melting temperature increases logarithmically with the salt concentration of the solution. The more GC base pairs in the chain enhance the stability of DNA chain at a fix salt concentration. The obtained results are in good accordance with experimental findings.

  13. Metastatic Neuroblastoma Confined to Distant Lymph Nodes (stage 4N) Predicts Outcome in Patients With Stage 4 Disease: A Study From the International Neuroblastoma Risk Group Database

    PubMed Central

    Morgenstern, Daniel A.; London, Wendy B.; Stephens, Derek; Volchenboum, Samuel L.; Hero, Barbara; Di Cataldo, Andrea; Nakagawara, Akira; Shimada, Hiroyuki; Ambros, Peter F.; Matthay, Katherine K.; Cohn, Susan L.; Pearson, Andrew D.J.; Irwin, Meredith S.

    2014-01-01

    Purpose The presence of distant metastases is one of the most powerful predictors of outcome in patients with neuroblastoma. However, the pattern of metastatic spread is not incorporated into current risk stratification systems. Small case series have suggested that patients with neuroblastoma who have metastatic disease limited to distant lymph nodes (4N disease) may have improved outcomes. Patients and Methods We analyzed retrospective data from the International Neuroblastoma Risk Group database for patients diagnosed from 1990 to 2002. 4N patients were compared with the remaining stage 4 patients (non-4N), excluding those with missing metastatic site data. Results In all, 2,250 International Neuroblastoma Staging System stage 4 patients with complete data were identified, of whom 146 (6.5%) had 4N disease. For 4N patients, event-free survival (EFS; 5-year, 77% ± 4%) and overall survival (OS; 5-year, 85% ± 3%) were significantly better than EFS (5-year, 35% ± 1%) and OS (5-year, 42% ± 1%) for non-4N stage 4 patients (P < .001). 4N patients were more likely to be younger (P < .001) and have tumors with favorable characteristics, including absence of MYCN amplification (89% v 69%; P < .001). In a multivariable analysis, 4N disease remained a significant predictor of outcome (hazard ratio for non-4N v 4N: 3.40 for EFS and 3.69 for OS). Within subgroups defined by age at diagnosis and tumor MYCN status, 4N disease was significantly associated with improved outcomes. Conclusion 4N represents a subgroup with better outcome than that of other patients with metastatic disease. These findings suggest that the biology and treatment response of 4N tumors differ from other stage 4 tumors, and less intensive therapy should be considered for this cohort. Future exploration of biologic factors determining the pattern of metastatic spread is warranted. PMID:24663047

  14. Tetrabutylammonium cation in a homoleptic environment of borohydride ligands: [(n-Bu){sub 4}N][BH{sub 4}] and [(n-Bu){sub 4}N][Y(BH{sub 4}){sub 4}

    SciTech Connect

    Jaron, T.; Wegner, W.; Cyranski, M.K.; Dobrzycki, L.; Grochala, W.

    2012-07-15

    A novel solvent-free dual-cation organic-inorganic derivative, tetrabutylammonium yttrium borohydride (TBAYB), has been prepared for the first time and structurally characterized together with its organic precursor, tetrabutylammonium borohydride (TBAB). Both compounds crystallize in monoclinic unit cells (TBAYB: P2{sub 1}/c, TBAB: P2/c) and they contain [(n-Bu){sub 4}N]{sup +} in a homoleptic environment consisting of BH{sub 4}{sup -} ligands. Presence of large and lightweight Bu{sub 4}N{sup +} cations results in loose packing and low densities of both solids close to 1 g cm{sup -3}. TBAB melts at ca. 130 Degree-Sign C and it decomposes thermally above 160 Degree-Sign C while TBAYB melts at temperature as low as 78 Degree-Sign C, and the melt is stable over an appreciable temperature range of ca. 150 Degree-Sign C. The low melting point of TBAYB is the second lowest among derivatives of yttrium rendering this compound a new ionic liquid above 78 Degree-Sign C. - Graphical abstract: A novel organic-inorganic hybrid material for hydrogen storage, where (n-Bu){sub 4}N{sup +} cation is found in homoleptic environment of BH{sub 4}{sup -} ligands, was synthesised. Highlights: Black-Right-Pointing-Pointer Novel organic-inorganic hybrid material for hydrogen storage was synthesised. Black-Right-Pointing-Pointer (n-Bu){sub 4}N{sup +} cation is found in a homoleptic environment of BH{sub 4}{sup -} ligands. Black-Right-Pointing-Pointer TBAYB derivative is a novel ionic liquid with melting point of 78 Degree-Sign C..

  15. A-DNA and B-DNA: Comparing Their Historical X-Ray Fiber Diffraction Images

    ERIC Educational Resources Information Center

    Lucas, Amand A.

    2008-01-01

    A-DNA and B-DNA are two secondary molecular conformations (among other allomorphs) that double-stranded DNA drawn into a fiber can assume, depending on the relative water content and other chemical parameters of the fiber. They were the first two forms to be observed by X-ray fiber diffraction in the early 1950s, respectively by Wilkins and…

  16. DNA-directed aniline mustards based on 9-aminoacridine: interaction with DNA.

    PubMed

    O'Connor, C J; Denny, W A; Fan, J Y; Gamage, R S

    1992-11-30

    A series of 4-substituted aniline mustards ArNH(CH2)nOpC6H4N(CH2CH2Cl)2, where Ar is an acridine and n varies from 2 to 5, interact with DNA. Scatchard analysis shows the compounds bind tightly, with a binding site size similar to that of 9-aminoacridine. The rate of hydrolysis of the mustards, measured by HPLC, is essentially constant across the series. With increasing length of the polymethylene linker, non-covalent binding becomes less strong, but the rate of DNA alkylation increases. Viscometric helix extension measurements and electrophoretic analyses using closed circular supercoiled DNA show that all the compounds are DNA intercalating ligands. Despite these similarities, the compounds are known to have quite different patterns of DNA alkylation, switching from guanine to adenine alkylation as the chain length is extended.

  17. Metallic transport and large anomalous Hall effect at room temperature in ferrimagnetic Mn{sub 4}N epitaxial thin film

    SciTech Connect

    Shen, Xi; Shigematsu, Kei; Chikamatsu, Akira Fukumura, Tomoteru; Hirose, Yasushi; Hasegawa, Tetsuya

    2014-08-18

    We report the electrical transport properties of ferrimagnetic Mn{sub 4}N (001) epitaxial thin films grown by pulsed laser deposition on MgO (001) substrates. The Mn{sub 4}N thin films were tetragonally distorted with a ratio of out-of-plane to in-plane lattice constants of 0.987 and showed perpendicular magnetic anisotropy with an effective magnetic anisotropy constant of 0.16 MJ/m{sup 3}, which is comparable with that of a recently reported molecular-beam-epitaxy-grown film. The thin films exhibited metallic transport with a room temperature resistivity of 125 μΩ cm in addition to a large anomalous Hall effect with a Hall angle tangent of 0.023.

  18. Solid-state photochemistry as a formation mechanism for Titan's stratospheric C4N2 ice clouds

    NASA Astrophysics Data System (ADS)

    Anderson, C. M.; Samuelson, R. E.; Yung, Y. L.; McLain, J. L.

    2016-04-01

    We propose that C4N2 ice clouds observed in Titan's springtime polar stratosphere arise due to solid-state photochemistry occurring within extant ice cloud particles of HCN-HC3N mixtures. This formation process resembles the halogen-induced ice particle surface chemistry that leads to condensed nitric acid trihydrate (NAT) particles and ozone depletion in Earth's polar stratosphere. As our analysis of the Cassini Composite Infrared Spectrometer 478 cm-1 ice emission feature demonstrates, this solid-state photochemistry mechanism eliminates the need for the relatively high C4N2 saturation vapor pressures required (even though they are not observed) when the ice is produced through the usual procedure of direct condensation from the vapor.

  19. The investigation of the electrical properties of Fe3O4/n-Si heterojunctions in a wide temperature range.

    PubMed

    Deniz, Ali Rıza; Çaldıran, Zakir; Metin, Önder; Meral, Kadem; Aydoğan, Şakir

    2016-07-01

    Monodisperse 8nm Fe3O4 nanoparticles (NPs) were synthesized by the thermal decomposition of iron(III) acetylacetonate in oleylamine and then were deposited onto n-type silicon wafer having the Al ohmic contact. Next, the morphology of the Fe3O4 NPs were characterized by using TEM and XRD. The optical properties of Fe3O4 NPs film was studied by UV-Vis spectroscopoy and its band gap was calculated to be 2.16eV. Au circle contacts with 7.85×10(-3)cm(2) area were provided on the Fe3O4 film via evaporation at 10(-5)Torr and the Au/Fe3O4 NPs/n-Si/Al heterojunction device were fabricated. The temperature-dependent junction parameters of Au/Fe3O4/n-Si/Al device including ideality factor, barrier height and series resistance were calculated by using the I-V characteristics in a wide temperature range of 40-300K. The results revealed that the ideality factor and series resistance increased by the decreasing temperature while the barrier height decreases. The Richardson constant of Au/Fe3O4/n-Si/Al device was calculated to be 2.17A/K(2)cm(2) from the I-V characteristics. The temperature dependence of Au/Fe3O4/n-Si/Al heterojunction device showed a double Gaussian distribution, which is caused by the inhomogeneities characteristics of Fe3O4/n-Si heterojunction.

  20. Spinel ZnCo2O4/N-doped carbon nanotube composite: A high active oxygen reduction reaction electrocatalyst

    NASA Astrophysics Data System (ADS)

    Pu, Zonghua; Liu, Qian; Tang, Chun; Asiri, Abdullah M.; Qusti, Abdullah H.; Al-Youbi, Abdulrahman O.; Sun, Xuping

    2014-07-01

    In this communication, we report on the solvothermal preparation of spinel ZnCo2O4/N-doped carbon nanotube (ZnCo2O4/NCNT) composite. As a novel oxygen reduction reaction (ORR) electrocatalyst, the ZnCo2O4/NCNT composite shows high activity via a four-electron pathway in alkaline solution. Such catalyst also exhibits superior methanol tolerance ability and durability over commercial Pt/C catalyst.

  1. DDX6 transfers P-TEFb kinase to the AF4/AF4N (AFF1) super elongation complex

    PubMed Central

    Mück, Fabian; Bracharz, Silvia; Marschalek, Rolf

    2016-01-01

    AF4/AFF1 and AF5/AFF4 are both backbones for the assembly of “super elongation complexes” (SECs) that exert 2 distinct functions after the recruitment of P-TEFb from the 7SK snRNP: (1) initiation and elongation of RNA polymerase II gene transcription, and (2) modification of transcribed gene regions by distinct histone methylation patterns. In this study we aimed to investigate one of the initial steps, namely how P-TEFb is transferred from 7SK snRNPs to the SECs. In particular, we were interested in the role of DDX6 that we have recently identified as part of the AF4 complex. DDX6 is an evolutionarily conserved member of the DEAD-box RNA helicase family that is known to control miRNA and mRNA biology (translation, storage and degradation). Overexpressed DDX6 is associated with different cancer types and with c-Myc protein overexpression. We could demonstrate that DDX6 binds to 7SK snRNA and causes the release and transfer of P-TEFb to the AF4/AF4N SEC. DDX6 also binds stably to AF4 and AF4N as demonstrated by GST pull-down and co-immunoprecipitation experiments. As a consequence, overexpression of either AF4/AF4N or DDX6 resulted in a strong increase of mRNA production (5-6 fold), while their simultaneous expression increased the cellular mRNA production by 11-fold. Conversely, the corresponding knockdown of DDX6 decreased mRNA production by 70%. In conclusion, AF4/AF4N and DDX6 represent key molecules for the elongation process of gene transcription and a model will be proposed for the hand-over process of P-TEFb to SECs. PMID:27679741

  2. Etch characteristics of magnetic tunnel junction materials using bias pulsing in the CH4/N2O inductively coupled plasma.

    PubMed

    Jeon, Min Hwan; Youn, Ji Youn; Yang, Kyung Chae; Yun, Deok Hyun; Lee, Du Yeong; Shim, Tae Hun; Park, Jea Gun; Yeom, Geun Young

    2014-12-01

    The etch characteristics of magnetic tunneling junction (MTJ) related materials such as CoFeB, MgO, FePt, Ru, and W as hard mask have been investigated as functions of rf pulse biasing, substrate heating, and CH4/N2O gas combination in an inductively coupled plasma system. When CH4/N2O gas ratio was varied, at CH4/N2O gas ratio of 2:1, not only the highest etch rates but also the highest etch selectivity over W could be obtained. By increasing the substrate temperature, the linear increase of both the etch rates of MTJ materials and the etch selectivity over W could be obtained. The use of the rf pulse biasing improved the etch selectivity of the MTJ materials over hard mask such as W further. The surface roughness and residual thickness remaining on the etched surface of the CoFeB were also decreased by using rf pulse biasing and with the decrease of rf duty percentage. The improvement of etch characteristics by substrate heating and rf pulse biasing was possibly related to the formation of more stable and volatile etch compounds and the removal of chemically reacted compounds more easily on the etched CoFeB surface. Highly selective etching of MTJ materials over the hard mask could be obtained by using the rf pulse biasing of 30% of duty ratio and by increasing the substrate temperature to 200 degrees C in the CH4/N2O (2:1) plasmas. PMID:25971096

  3. Stereotactic body radiotherapy for T3 and T4N0M0 non–small cell lung cancer

    PubMed Central

    Eriguchi, Takahisa; Takeda, Atsuya; Sanuki, Naoko; Nishimura, Shuichi; Takagawa, Yoshiaki; Enomoto, Tatsuji; Saeki, Noriyuki; Yashiro, Kae; Mizuno, Tomikazu; Aoki, Yousuke; Oku, Yohei; Yokosuka, Tetsuya; Shigematsu, Naoyuki

    2016-01-01

    To evaluate the outcomes and feasibility of stereotactic body radiotherapy (SBRT) for cT3 and cT4N0M0 non–small cell lung cancer (NSCLC), 25 patients with localized primary NSCLC diagnosed as cT3 or cT4N0M0, given SBRT between May 2005 and July 2013, were analyzed. All patients had inoperable tumors. The major reasons for tumors being unresectable were insufficient respiratory function for curative resection, advanced age (>80 years old) or technically inoperable due to invasion into critical organs. The median patient age was 79 years (range; 60–86). The median follow-up duration was 25 months (range: 5–100 months). The 2-year overall survival rates for T3 and T4 were 57% and 69%, respectively. The 2-year local control rates for T3 and T4 were 91% and 68%, respectively. As for toxicities, Grade 0–1, Grade 2 and Grade 3 radiation pneumonitis occurred in 23, 1 and 1 patient, respectively. No other acute or symptomatic late toxicities were reported. Thirteen patients who had no local, mediastinal or intrapulmonary progression at one year after SBRT underwent pulmonary function testing. The median variation in pre-SBRT and post-SBRT forced expiratory volume in 1 s (FEV1) values was –0.1 (–0.8–0.8). This variation was not statistically significant (P = 0.56). Forced vital capacity (FVC), vital capacity (VC), %VC and %FEV1 also showed no significant differences. SBRT for cT3 and cT4N0M0 NSCLC was both effective and feasible. Considering the favorable survival and low morbidity rate, SBRT is a potential treatment option for cT3 and cT4N0M0 NSCLC. PMID:26983978

  4. DDX6 transfers P-TEFb kinase to the AF4/AF4N (AFF1) super elongation complex.

    PubMed

    Mück, Fabian; Bracharz, Silvia; Marschalek, Rolf

    2016-01-01

    AF4/AFF1 and AF5/AFF4 are both backbones for the assembly of "super elongation complexes" (SECs) that exert 2 distinct functions after the recruitment of P-TEFb from the 7SK snRNP: (1) initiation and elongation of RNA polymerase II gene transcription, and (2) modification of transcribed gene regions by distinct histone methylation patterns. In this study we aimed to investigate one of the initial steps, namely how P-TEFb is transferred from 7SK snRNPs to the SECs. In particular, we were interested in the role of DDX6 that we have recently identified as part of the AF4 complex. DDX6 is an evolutionarily conserved member of the DEAD-box RNA helicase family that is known to control miRNA and mRNA biology (translation, storage and degradation). Overexpressed DDX6 is associated with different cancer types and with c-Myc protein overexpression. We could demonstrate that DDX6 binds to 7SK snRNA and causes the release and transfer of P-TEFb to the AF4/AF4N SEC. DDX6 also binds stably to AF4 and AF4N as demonstrated by GST pull-down and co-immunoprecipitation experiments. As a consequence, overexpression of either AF4/AF4N or DDX6 resulted in a strong increase of mRNA production (5-6 fold), while their simultaneous expression increased the cellular mRNA production by 11-fold. Conversely, the corresponding knockdown of DDX6 decreased mRNA production by 70%. In conclusion, AF4/AF4N and DDX6 represent key molecules for the elongation process of gene transcription and a model will be proposed for the hand-over process of P-TEFb to SECs. PMID:27679741

  5. Growth and electrical properties on NLO crystal: 4-N,N-dimethylamino 4′-N′-methylstilbazolium iodide

    SciTech Connect

    Kumar, M. Krishna Sudhahar, S. Kumar, R. Mohan

    2014-04-24

    4-N,N-Dimethylamino-4′-N′-methylstilbazolium tosylate single crystals were grown by solution crystal growth method. The cell parameters of grown crystal have been estimated using single crystal-X-ray diffraction analysis. The variation of real (´ε) and imaginary (´ε) part of dielectric constants and dielectric loss were observed for different frequencies and temperatures. The ac and dc electrical conductivities and activation energy were determined for DMSI crystal using dielectric studies.

  6. Stereotactic body radiotherapy for T3 and T4N0M0 non-small cell lung cancer.

    PubMed

    Eriguchi, Takahisa; Takeda, Atsuya; Sanuki, Naoko; Nishimura, Shuichi; Takagawa, Yoshiaki; Enomoto, Tatsuji; Saeki, Noriyuki; Yashiro, Kae; Mizuno, Tomikazu; Aoki, Yousuke; Oku, Yohei; Yokosuka, Tetsuya; Shigematsu, Naoyuki

    2016-06-01

    To evaluate the outcomes and feasibility of stereotactic body radiotherapy (SBRT) for cT3 and cT4N0M0 non-small cell lung cancer (NSCLC), 25 patients with localized primary NSCLC diagnosed as cT3 or cT4N0M0, given SBRT between May 2005 and July 2013, were analyzed. All patients had inoperable tumors. The major reasons for tumors being unresectable were insufficient respiratory function for curative resection, advanced age (>80 years old) or technically inoperable due to invasion into critical organs. The median patient age was 79 years (range; 60-86). The median follow-up duration was 25 months (range: 5-100 months). The 2-year overall survival rates for T3 and T4 were 57% and 69%, respectively. The 2-year local control rates for T3 and T4 were 91% and 68%, respectively. As for toxicities, Grade 0-1, Grade 2 and Grade 3 radiation pneumonitis occurred in 23, 1 and 1 patient, respectively. No other acute or symptomatic late toxicities were reported. Thirteen patients who had no local, mediastinal or intrapulmonary progression at one year after SBRT underwent pulmonary function testing. The median variation in pre-SBRT and post-SBRT forced expiratory volume in 1 s (FEV1) values was -0.1 (-0.8-0.8). This variation was not statistically significant (P = 0.56). Forced vital capacity (FVC), vital capacity (VC), %VC and %FEV1 also showed no significant differences. SBRT for cT3 and cT4N0M0 NSCLC was both effective and feasible. Considering the favorable survival and low morbidity rate, SBRT is a potential treatment option for cT3 and cT4N0M0 NSCLC. PMID:26983978

  7. DDX6 transfers P-TEFb kinase to the AF4/AF4N (AFF1) super elongation complex

    PubMed Central

    Mück, Fabian; Bracharz, Silvia; Marschalek, Rolf

    2016-01-01

    AF4/AFF1 and AF5/AFF4 are both backbones for the assembly of “super elongation complexes” (SECs) that exert 2 distinct functions after the recruitment of P-TEFb from the 7SK snRNP: (1) initiation and elongation of RNA polymerase II gene transcription, and (2) modification of transcribed gene regions by distinct histone methylation patterns. In this study we aimed to investigate one of the initial steps, namely how P-TEFb is transferred from 7SK snRNPs to the SECs. In particular, we were interested in the role of DDX6 that we have recently identified as part of the AF4 complex. DDX6 is an evolutionarily conserved member of the DEAD-box RNA helicase family that is known to control miRNA and mRNA biology (translation, storage and degradation). Overexpressed DDX6 is associated with different cancer types and with c-Myc protein overexpression. We could demonstrate that DDX6 binds to 7SK snRNA and causes the release and transfer of P-TEFb to the AF4/AF4N SEC. DDX6 also binds stably to AF4 and AF4N as demonstrated by GST pull-down and co-immunoprecipitation experiments. As a consequence, overexpression of either AF4/AF4N or DDX6 resulted in a strong increase of mRNA production (5-6 fold), while their simultaneous expression increased the cellular mRNA production by 11-fold. Conversely, the corresponding knockdown of DDX6 decreased mRNA production by 70%. In conclusion, AF4/AF4N and DDX6 represent key molecules for the elongation process of gene transcription and a model will be proposed for the hand-over process of P-TEFb to SECs.

  8. The first quaternary lanthanide(III) nitride iodides: Na M4N 2I 7 ( M=La-Nd)

    NASA Astrophysics Data System (ADS)

    Schurz, Christian M.; Schleid, Thomas

    2010-10-01

    In attempts to synthesize lanthanide(III) nitride iodides with the formula M2NI 3 ( M=La-Nd), moisture-sensitive single crystals of the first quaternary sodium lanthanide(III) nitride iodides Na M4N 2I 7 (orthorhombic, Pna2 1; Z=4; a=1391-1401, b=1086-1094, c=1186-1211 pm) could be obtained. The dominating structural features are {[}∞1 chains of trans-edge linked [N M4] 9+ tetrahedra, which run parallel to the polar 2 1-axis [001]. Between the chains, direct bonding via special iodide anions generates cages, in which isolated [NaI 6] 5- octahedra are embedded. The IR spectrum of NaLa 4N 2I 7 recorded from 100 to 1000 cm -1 shows main bands at υ=337, 373 and 489 cm -1. With decreasing radii of the lanthanide trications these bands, which can be assigned as an influence of the vibrations of the condensed [N M4] 9+ tetrahedra, are shifted toward higher frequencies for the Na M4N 2I 7 series ( M=La-Nd), following the lanthanide contraction.

  9. Characterization of an H4N2 Influenza Virus from Quails with a Multibasic Motif in the Hemagglutinin Cleavage Site

    PubMed Central

    Wong, Sook-San; Yoon, Sun-Woo; Zanin, Mark; Song, Min-Suk; Oshansky, Christine; Zaraket, Hassan; Sonnberg, Stephanie; Rubrum, Adam; Seiler, Patrick; Ferguson, Angela; Krauss, Scott; Cardona, Carol; Webby, Richard J.; Crossley, Beate

    2014-01-01

    The cleavage motif in the hemagglutinin (HA) protein of highly pathogenic H5 and H7 subtypes of avian influenza viruses is characterized by a peptide insertion or a multibasic cleavage site (MBCS). Here, we isolated an H4N2 virus from quails (Quail/CA12) with two additional arginines in the HA cleavage site, PEKRRTR/G, forming an MBCS-like motif. Quail/CA12 is a reassortant virus with the HA and neuraminidase (NA) gene most similar to a duck-isolated H4N2 virus, PD/CA06 with a monobasic HA cleavage site. Quail/CA12 required exogenous trypsin for efficient growth in culture and caused no clinical illness in infected chickens. Quail/CA12 had high binding preference for α2,6-linked sialic acids and showed higher replication and transmission ability in chickens and quails than PD/CA06. Although the H4N2 virus remained low pathogenic, these data suggests that the acquisition of MBCS in the field is not restricted to H5 or H7 subtypes. PMID:25151061

  10. Efficient hypoxic activation of the anticancer agent AQ4N by CYP2S1 and CYP2W1.

    PubMed

    Nishida, Clinton R; Lee, Melody; de Montellano, Paul R Ortiz

    2010-09-01

    AQ4N [1,4-bis{[2-(dimethylamino-N-oxide)ethyl]amino}-5,8-dihydroxyanthracene-9,10-dione], a prodrug with two dimethylamino N-oxide groups, is converted to the topoisomerase II inhibitor AQ4 [1,4-bis{[2-(dimethylamino)ethyl]amino}-5,8-dihydroxy-anthracene-9,10-dione] by reduction of the N-oxides to dimethylamino substituents. Earlier studies showed that several drug-metabolizing cytochrome P450 (P450) enzymes can catalyze this reductive reaction under hypoxic conditions comparable with those in solid tumors. CYP2S1 and CYP2W1, two extrahepatic P450 enzymes identified from the human genome whose functions are unknown, are expressed in hypoxic tumor cells at much higher levels than in normal tissue. Here, we demonstrate that CYP2S1, contrary to a published report (Mol Pharmacol 76:1031-1043, 2009), is efficiently reduced by NADPH-P450 reductase. Most importantly, both CYP2S1 and CYP2W1 are better catalysts for the reductive activation of AQ4N to AQ4 than all previously examined P450 enzymes. The overexpression of CYP2S1 and CYP2W1 in tumor tissues, together with their high catalytic activities for AQ4N activation, suggests that they may be exploited for the localized activation of anticancer prodrugs.

  11. Master curve characterization of the fracture toughness behavior in SA508 Gr.4N low alloy steels

    NASA Astrophysics Data System (ADS)

    Lee, Ki-Hyoung; Kim, Min-Chul; Lee, Bong-Sang; Wee, Dang-Moon

    2010-08-01

    The fracture toughness properties of the tempered martensitic SA508 Gr.4N Ni-Mo-Cr low alloy steel for reactor pressure vessels were investigated by using the master curve concept. These results were compared to those of the bainitic SA508 Gr.3 Mn-Mo-Ni low alloy steel, which is a commercial RPV material. The fracture toughness tests were conducted by 3-point bending with pre-cracked charpy (PCVN) specimens according to the ASTM E1921-09c standard method. The temperature dependency of the fracture toughness was steeper than those predicted by the standard master curve, while the bainitic SA508 Gr.3 steel fitted well with the standard prediction. In order to properly evaluate the fracture toughness of the Gr.4N steels, the exponential coefficient of the master curve equation was changed and the modified curve was applied to the fracture toughness test results of model alloys that have various chemical compositions. It was found that the modified curve provided a better description for the overall fracture toughness behavior and adequate T0 determination for the tempered martensitic SA508 Gr.4N steels.

  12. DNA nanomachines.

    PubMed

    Bath, Jonathan; Turberfield, Andrew J

    2007-05-01

    We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specific signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.

  13. A DNA machine for sensitive and homogeneous DNA detection via lambda exonuclease assisted amplification.

    PubMed

    Liu, Lin; Lei, Jianping; Gao, Fenglei; Ju, Huangxian

    2013-10-15

    This work designs a DNA machine with three assistant DNAs and lambda exonuclease (Exo-λ) for sensitive and homogeneous fluorescent detection of DNA. The selective digestion of Exo-λ to blunt or recessed 5'-phosphorylated strand of probe 1-probe 2 duplex results in the release of target DNA and probe 2 to produce the fluorescence restoring of fluorophore labeled to probe 1. The released target DNA could hybridize with another probe 1-probe 2 duplex to trigger the target recycling for signal amplification, while the released probe 2 hybridized with molecular beacon to restore its fluorescence for signal enhancement. This DNA machine showed a fast response to target DNA with a linear concentration range from 0.4 pM to 4 nM. The limit of detection was 68 fM at a signal-to-noise ratio of 3. The high selectivity of the method may result from the Exo-λ's specific recognition-site of double-stranded DNA and the specific hybridization of target DNA with probe 1-probe 2 duplex. This DNA machine with the homogenous detection, rapid response as well as simplicity provides a new approach for sensitive detection of DNA.

  14. [DNA computing].

    PubMed

    Błasiak, Janusz; Krasiński, Tadeusz; Popławski, Tomasz; Sakowski, Sebastian

    2011-01-01

    Biocomputers can be an alternative for traditional "silicon-based" computers, which continuous development may be limited due to further miniaturization (imposed by the Heisenberg Uncertainty Principle) and increasing the amount of information between the central processing unit and the main memory (von Neuman bottleneck). The idea of DNA computing came true for the first time in 1994, when Adleman solved the Hamiltonian Path Problem using short DNA oligomers and DNA ligase. In the early 2000s a series of biocomputer models was presented with a seminal work of Shapiro and his colleguas who presented molecular 2 state finite automaton, in which the restriction enzyme, FokI, constituted hardware and short DNA oligomers were software as well as input/output signals. DNA molecules provided also energy for this machine. DNA computing can be exploited in many applications, from study on the gene expression pattern to diagnosis and therapy of cancer. The idea of DNA computing is still in progress in research both in vitro and in vivo and at least promising results of these research allow to have a hope for a breakthrough in the computer science. PMID:21735816

  15. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOEpatents

    Dolbeare, Frank A.; Gray, Joe W.

    1986-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as bromodeoxyuridine (BrdU) is used as a probe for the measurement of BrdU uptake by the cells as a measure of DNA synthesis.

  16. Dancing DNA.

    ERIC Educational Resources Information Center

    Pennisi, Elizabeth

    1991-01-01

    An imaging technique that uses fluorescent dyes and allows scientists to track DNA as it moves through gels or in solution is described. The importance, opportunities, and implications of this technique are discussed. (KR)

  17. DNA Dynamics.

    ERIC Educational Resources Information Center

    Warren, Michael D.

    1997-01-01

    Explains a method to enable students to understand DNA and protein synthesis using model-building and role-playing. Acquaints students with the triplet code and transcription. Includes copies of the charts used in this technique. (DDR)

  18. DNA Adductomics

    PubMed Central

    2015-01-01

    Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the 32P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC–MSn), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC–MSn instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology. PMID:24437709

  19. Pea amyloplast DNA is qualitatively similar to pea chloroplast DNA

    NASA Technical Reports Server (NTRS)

    Gaynor, J. J.

    1984-01-01

    Amyloplast DNA (apDNA), when subjected to digestion with restriction endonucleases, yields patterns nearly identical to that of DNA from mature pea chloroplasts (ctDNA). Southern transfers of apDNA and ctDNA, probed with the large subunit (LS) gene of ribulose-1,5-bisphosphate carboxylase (Rubisco), shows hybridization to the expected restriction fragments for both apDNA and ctDNA. However, Northern transfers of total RNA from chloroplasts and amyloplasts, probed again with the LS gene of Rubisco, shows that no detectable LS meggage is found in amyloplasts although LS expression in mature chloroplasts is high. Likewise, two dimensional polyacrylamide gel electrophoresis of etiolated gravisensitive pea tissue shows that both large and small subunits of Rubisco are conspicuously absent; however, in greening tissue these two constitute the major soluble proteins. These findings suggest that although the informational content of these two organelle types is equivalent, gene expression is quite different and is presumably under nuclear control.

  20. Electron attachment and detachment, and the electron affinities of C5F5N and C5HF4N.

    PubMed

    Van Doren, Jane M; Kerr, Donna M; Miller, Thomas M; Viggiano, A A

    2005-09-15

    Rate constants have been measured for electron attachment to C5F5N (297-433 K) and to 2, 3, 5, 6-C5HF4N (303 K) using a flowing-afterglow Langmuir-probe apparatus (at a He gas pressure of 133 Pa). In both cases only the parent anion was formed in the attachment process. The attachment rate constants measured at room temperature are 1.8 +/- 0.5 X 10(-7) and 7 +/- 3 X 10(-10) cm(-3) s(-1), respectively. Rate constants were also measured for thermal electron detachment from the parent anions of these molecules. For C5F5N- detachment is negligible at room temperature, but increases to 2530 +/- 890 s(-1) at 433 K. For 2, 3, 5, 6-C5HF4N-, the detachment rate at 303 K was 520 +/- 180 s(-1). The attachment/detachment equilibrium yielded experimental electron affinities EA(C5F5N)=0.70 +/- 0.05 eV and EA(2, 3, 5, 6-C5HF4N)=0.40 +/- 0.08 eV. Electronic structure calculations were carried out for these molecules and related C5HxF5-xN using density-functional theory and the G3(MP2)//B3LYP compound method. The EAs are found to decrease by 0.25 eV, on average, with each F substitution by H. The calculated EAs are in good agreement with the present experimental results.

  1. mtDNA/nDNA ratio in 14484 LHON mitochondrial mutation carriers.

    PubMed

    Nishioka, Tomoki; Soemantri, Augustinus; Ishida, Takafumi

    2004-01-01

    Leber's hereditary optic neuropathy (LHON) is a maternally inherited disease caused by mitochondrial DNA (mtDNA) mutations. In this study, the mtDNA/nuclear DNA ratio was evaluated in 11 LHON patients with the 14484 mutation, 13 asymptomatic carriers and 18 non-carrier relatives as controls, to reveal possible relationships between the disease and mtDNA content. DNAs from peripheral blood lymphocytes were subjected to quantitative PCR. Gender differences and age-dependent changes in the mtDNA content were not observed. Significant increase in the mtDNA content was observed only in the asymptomatic carriers (P<0.05). This indicated that individuals whose mtDNA content had increased and been maintained at certain levels were free from LHON development, whereas those whose levels had not, had developed LHON. Since the asymptomatic carriers are the stock of the future LHON patients, monitoring the mtDNA content in patients and their relatives may help to predict the prognosis of the disease.

  2. Electronic structure and pair potential energy analysis of 4-n-methoxy-4'-cyanobiphenyl: A nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Sharma, Dipendra; Dwivedi, M. K.; Tiwari, S. N.

    2016-05-01

    Electronic structure properties of 4-n-methoxy-4'-cyanobiphenyl, a pure nematic liquid crystal have been examined using an ab‒initio, HF/6‒31G(d,p) technique with GAMESS program. Conformational and charge distribution analysis have been carried out. MEP, HOMO and LUMO surfaces have been scanned. Ionization potential, electron affinity, electronegativity, global hardness and softness of the liquid crystal molecule have been calculated. Further, stacking, side by side and end to end interactions between a molecular pair have been evaluated. Results have been used to elucidate the physico-chemical and liquid crystalline properties of the system.

  3. Molecular characterization of an influenza A virus (H4N2) isolated from waterfowl habitats in the State of Mexico.

    PubMed

    Ornelas-Eusebio, Erika; Obregón-Ascencio, Alejandro; Chávez-Maya, Fernando; García-Espinosa, Gary

    2015-03-01

    Wild waterfowl and their habitats are the main reservoirs of influenza A virus (IAV) mainly during the breeding season and prior to migration. This study describes the molecular characterization of an IAV isolated from 240 water samples of a small wetland during non-breeding season of migratory wild ducks in the State of Mexico, Mexico. The results showed that the virus belongs to the H4N2 subtype and each of its eight segments of the viral genome has similarity to IAV isolated from ducks in North America. This study suggests that IAV can be isolated from small wetland during non-breeding season of migrating waterfowl. PMID:25482497

  4. Molecular characterization of an influenza A virus (H4N2) isolated from waterfowl habitats in the State of Mexico.

    PubMed

    Ornelas-Eusebio, Erika; Obregón-Ascencio, Alejandro; Chávez-Maya, Fernando; García-Espinosa, Gary

    2015-03-01

    Wild waterfowl and their habitats are the main reservoirs of influenza A virus (IAV) mainly during the breeding season and prior to migration. This study describes the molecular characterization of an IAV isolated from 240 water samples of a small wetland during non-breeding season of migratory wild ducks in the State of Mexico, Mexico. The results showed that the virus belongs to the H4N2 subtype and each of its eight segments of the viral genome has similarity to IAV isolated from ducks in North America. This study suggests that IAV can be isolated from small wetland during non-breeding season of migrating waterfowl.

  5. Molecular characterization of an influenza A virus (H4N2) isolated from waterfowl habitats in the State of Mexico

    PubMed Central

    ORNELAS-EUSEBIO, Erika; OBREGÓN-ASCENCIO, Alejandro; CHÁVEZ-MAYA, Fernando; GARCÍA-ESPINOSA, Gary

    2014-01-01

    Wild waterfowl and their habitats are the main reservoirs of influenza A virus (IAV) mainly during the breeding season and prior to migration. This study describes the molecular characterization of an IAV isolated from 240 water samples of a small wetland during non-breeding season of migratory wild ducks in the State of Mexico, Mexico. The results showed that the virus belongs to the H4N2 subtype and each of its eight segments of the viral genome has similarity to IAV isolated from ducks in North America. This study suggests that IAV can be isolated from small wetland during non-breeding season of migrating waterfowl. PMID:25482497

  6. catena-Poly[[aqua-{4-[N'-(2,4-dioxo-3-pentyl-idene)-hydrazino]-benzoato}-copper(II)]-μ-acetato].

    PubMed

    Hao, Lujiang; Mu, Chunhua; Wang, Ridong

    2008-01-01

    In the title compound, [Cu(CH(3)CO(2))(C(12)H(11)N(2)O(4))(H(2)O)](n), the Cu(II) cation is tetra-coordinated by three carboxyl-ate O atoms from one 4-[N'-(2,4-dioxo-3-pentyl-idene)-hydrazino]-benzoate ligand and two acetate bridges, and by one water mol-ecule. The acetate bridges link adjacent Cu(II) cations, forming a chain. The crystal structure involves O-H⋯O hydrogen bonds. PMID:21202784

  7. The mitigating effect of calcification-dependent of utilization of inorganic carbon of Chara vulgaris Linn on NH4-N toxicity.

    PubMed

    Wang, Heyun; Ni, Leyi; Xie, Ping

    2013-09-01

    Increased ammonium (NH4-N) concentrations in water bodies have been reported to adversely affect the dominant species of submersed vegetation in meso-eutrophic waters worldwide. However calcareous plants were lowly sensitive to NH4-N toxicity. In order to make clear the function of calcification in the tolerance of calcareous plants to NH4-N stress, we studied the effects of increased HCO3(-) and additional NH4-N on calcification and utilization of dissolve inorganic carbon (DIC) in Chara vulgaris Linn in a 7-d sub-acute experiment (light:dark 12:12h) carried out in an open experimental system in lab. Results revealed that calcification was dependent of utilization of dissolve inorganic carbon. Additional HCO3(-) significantly decreased the increase of pH while additional NH4-N did not. And additional HCO3(-) significantly improved calcification while NH4-N did in versus in relation to the variation of DIC concentration. However, addition of both HCO3(-) and NH4-N increased utilization of DIC. This resulted in calcification to utilization of DIC ratio decreased under additional NH4-N condition while increased under additional HCO3(-) conditions in response to the variation of solution pH. In the present study, external HCO3(-) decreased the increase of solution pH by increasing calcification, which correspondingly mitigated the toxic effect of high NH4-N. And we argue that the mitigating effect of increased HCO3(-) on NH4-N toxicity is dependent of plant calcification, and it is a positive feedback mechanism, potentially leading to the dominance of calcareous plants in meso-eutrophic water bodies.

  8. The mitigating effect of calcification-dependent of utilization of inorganic carbon of Chara vulgaris Linn on NH4-N toxicity.

    PubMed

    Wang, Heyun; Ni, Leyi; Xie, Ping

    2013-09-01

    Increased ammonium (NH4-N) concentrations in water bodies have been reported to adversely affect the dominant species of submersed vegetation in meso-eutrophic waters worldwide. However calcareous plants were lowly sensitive to NH4-N toxicity. In order to make clear the function of calcification in the tolerance of calcareous plants to NH4-N stress, we studied the effects of increased HCO3(-) and additional NH4-N on calcification and utilization of dissolve inorganic carbon (DIC) in Chara vulgaris Linn in a 7-d sub-acute experiment (light:dark 12:12h) carried out in an open experimental system in lab. Results revealed that calcification was dependent of utilization of dissolve inorganic carbon. Additional HCO3(-) significantly decreased the increase of pH while additional NH4-N did not. And additional HCO3(-) significantly improved calcification while NH4-N did in versus in relation to the variation of DIC concentration. However, addition of both HCO3(-) and NH4-N increased utilization of DIC. This resulted in calcification to utilization of DIC ratio decreased under additional NH4-N condition while increased under additional HCO3(-) conditions in response to the variation of solution pH. In the present study, external HCO3(-) decreased the increase of solution pH by increasing calcification, which correspondingly mitigated the toxic effect of high NH4-N. And we argue that the mitigating effect of increased HCO3(-) on NH4-N toxicity is dependent of plant calcification, and it is a positive feedback mechanism, potentially leading to the dominance of calcareous plants in meso-eutrophic water bodies. PMID:23755986

  9. What Is Mitochondrial DNA?

    MedlinePlus

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  10. Determining a Structural Distortion and Anion Ordering in La2Si4N6C via Computation and Experiment.

    PubMed

    Hermus, Martin; Mansouri Tehrani, Aria; Brgoch, Jakoah

    2016-09-19

    A structural instability in the orthorhombic carbonitridosilicate La2Si4N6C arises when calculating the ab initio phonon dispersion curves. The presence of imaginary modes indicates the compound reported in space group Pnma is dynamically unstable with the eigenvectors showing a monoclinic distortion pathway leading to space group P21/c. Synthesizing La2Si4N6C using a high-temperature route and conducting a co-refinement with high-resolution synchrotron X-ray and neutron powder diffraction shows the predicted peak splitting confirming the predicted lower symmetry crystal structure. Further, the combination of ab initio computation, neutron diffraction, and a total scattering analysis based on a neutron pair distribution function analysis supports that the anions are fully ordered and that carbon is only found on the central position of a star-shaped C(SiN3)4 unit. These results illustrate the power of combining computation and experiment to unequivocally solve crystal structures from polycrystalline powders.

  11. Determination of 2-ethylhexyl 4-(N-methyl-N-nitrosamino) benzoate in commercial sunscreens and cosmetic products.

    PubMed

    Chou, H J; Yates, R L; Havery, D C; Wenninger, J A

    1995-01-01

    An analytical method has been developed for determination of 2-ethylhexyl 4-(N-methyl-N-nitrosamino) benzoate (NMPABAO), a nitrosamine contaminant in sunscreen products containing 2-ethylhexyl 4-(N,N-dimethylamino) benzoate (Padimate O). The method involves extraction of NMPABAO by column chromatography followed by liquid chromatographic separation and analysis wit a nitric oxide detector. To confirm the presence of NMPABAO in sunscreen products, the N-nitrosamine was synthesized and its structure was determined by infrared spectrophotometry, nuclear magnetic resonance spectrometry, and mass spectrometry (MS). For method validation, recovery studies were performed on a commercial suntan lotion, cream, and gel. Recoveries of NMPABAO added to representative test samples averaged 83%. The method has an estimated detection limit of 30 ppb. The method was used to analyze 25 commercial cosmetic and sunscreen products containing Padimate O. Eleven products contained NMPABAO at levels ranging from 160 to 21000 ppb. NMPABAO presence in 4 products was confirmed by MS at levels > or = 4000 ppb. The highest levels of NMPABAO were associated with products that contained the nitrite-releasing preservative 2-bromo-2-nitro-1,3-propanediol.

  12. Decrease of NH4+-N by bacterioplankton accelerated the removal of cyanobacterial blooms in aerated aquatic ecosystem.

    PubMed

    Yang, Xi; Xie, Ping; Ma, Zhimei; Wang, Qing; Fan, Huihui; Shen, Hong

    2013-11-01

    We used aerated systems to assess the influence of the bacterioplankton community on cyanobacterial blooms in algae/post-bloom of Lake Taihu, China. Bacterioplankton community diversity was evaluated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting. Chemical analysis and nitrogen dynamic changes illustrated that NH4+-N was nitrified to NO2--N and NO3--N by bacterioplankton. Finally, NH4+-N was exhausted and NO3--N was denitrified to NO2--N, while the accumulation of NO2--N indicated that bacterioplankton with completely aerobic denitrification ability were lacking in the water samples collected from Lake Taihu. We suggested that adding completely aerobic denitrification bacteria (to denitrify NO2--N to N2) would improve the water quality. PCR-DGGE and sequencing results showed that more than1/3 of the bacterial species were associated with the removal of nitrogen, and Acidovorax temperans was the dominant one. PCR-DGGE, variation of nitrogen, removal efficiencies of chlorophyll-a and canonical correspondence analysis indicated that the bacterioplanktonsignificantly influenced the physiological and biochemical changes of cyanobacteria. Additionally, the unweighted pair-group method with arithmetic means revealed there was no obvious harm to the microecosystem from aeration. The present study demonstrated that bacterioplankton can play crucial roles in aerated ecosystems, which could control the impact of cyanobacterial blooms in eutrophicated fresh water systems.

  13. Determining a Structural Distortion and Anion Ordering in La2Si4N6C via Computation and Experiment.

    PubMed

    Hermus, Martin; Mansouri Tehrani, Aria; Brgoch, Jakoah

    2016-09-19

    A structural instability in the orthorhombic carbonitridosilicate La2Si4N6C arises when calculating the ab initio phonon dispersion curves. The presence of imaginary modes indicates the compound reported in space group Pnma is dynamically unstable with the eigenvectors showing a monoclinic distortion pathway leading to space group P21/c. Synthesizing La2Si4N6C using a high-temperature route and conducting a co-refinement with high-resolution synchrotron X-ray and neutron powder diffraction shows the predicted peak splitting confirming the predicted lower symmetry crystal structure. Further, the combination of ab initio computation, neutron diffraction, and a total scattering analysis based on a neutron pair distribution function analysis supports that the anions are fully ordered and that carbon is only found on the central position of a star-shaped C(SiN3)4 unit. These results illustrate the power of combining computation and experiment to unequivocally solve crystal structures from polycrystalline powders. PMID:27598316

  14. Transparent half metallic g-C4N3 nanotubes: potential multifunctional applications for spintronics and optical devices.

    PubMed

    Hu, Tao; Hashmi, Arqum; Hong, Jisang

    2014-08-14

    Multifunctional material brings many interesting issues because of various potential device applications. Using first principles calculations, we predict that the graphitic carbon nitride (g-C4N3) nanotubes can display multifunctional properties for both spintronics and optical device applications. Very interestingly, armchair tubes (n, n) with n = 2, 3, 4, 5, 6 and (5, 0) zigzag tubes are found to be half metallic, while zigzag tubes (n, 0) with n = 4, 6 show an antiferromagnetic ground state with band gaps. However, larger zigzag tubes of (7, 0), (8, 0), and (10, 0) are turned out to be half metallic. Along with the half metallic behavior of the tubes, those tubes seem to be optically transparent in the visible range. Due to these magnetic and optical properties, we suggest that the g-C4N3 nanotubes (CNNTs) can be used for both ideal spintronics and transparent electrode materials. We also explored the stability of magnetic state and nanotube structure using ab initio molecular dynamics. The CNNTs were found to be thermally stable and the magnetic moment was robust against the structural deformation at 300 K. Overall, our theoretical prediction in one dimensional CNNTs may provide a new physics in spintronics and also in other device applications because of potential multifunctional properties.

  15. Ancient DNA.

    PubMed

    Willerslev, Eske; Cooper, Alan

    2005-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

  16. Ancient DNA

    PubMed Central

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets. PMID:15875564

  17. DNA vaccines

    NASA Astrophysics Data System (ADS)

    Gregersen, Jens-Peter

    2001-12-01

    Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

  18. Bottom-up substitution assembly of AuF4-n0,-+nPO3 (n = 1-4): a theoretical study of novel oxyfluoride hyperhalogen molecules and anions AuF4-n(PO3)n0,-

    NASA Astrophysics Data System (ADS)

    Yang, Yi-fan; Cui, Zhong-hua; Ding, Yi-hong

    2014-06-01

    Compounds with high electron affinity, i.e. superhalogens, have continued to attract chemists' attention, due to their potential importance in fundamental chemistry and materials science. It has now proven very effective to build up novel superhalogens with multi-positively charged centres, which are usually called 'hyperhalogens'. Herein, using AuF4- and PO3 as the model building blocks, we made the first attempt to design the Au,P-based hyperhalogen anions AuF4-n(PO3)n- (n = 1-4) at the B3LYP/6-311+G(d)&SDD and CCSD(T)/6-311+G(d)&SDD (single-point) levels (6-311+G(d) for O, F, P and SDD for Au). Notably, for all the considered Au,P systems, the ground state bears a dioxo-bonded structure with n ≤ 3, which is significantly more stable than the usually presumed mono-oxo-bonded one. Moreover, the clustering of the -PO3 moieties becomes energetically favoured for n ≥ 3. The ground states of AuP4O120,- are the first reported cage-like oxide hyperhalogens. Thus, the -PO3 moiety cannot be retained during the 'bottom-up' assembly. The vertical detachment energy (VDE) value of the most stable AuF4-n(PO3)n- (n = 1-4) ranges from 7.16 to 8.20 eV, higher than the VDE values of the corresponding building blocks AuF4- (7.08 eV) and PO3- (4.69 eV). The adiabatic detachment energy values of these four hyperhalogens exceed 6.00 eV. Possible generation routes for AuF4-n(PO3)n- (n = 1-4) were discussed. The presently designed oxyfluorides not only enriches the family of hyperhalogens, but also demonstrates the great importance of considering the structural transformation during the superhalogen → hyperhalogen design such as for the present Au-P based systems.

  19. DNA topoisomerases.

    PubMed

    Wang, J C

    1996-01-01

    The various problems of disentangling DNA strands or duplexes in a cell are all rooted in the double-helical structure of DNA. Three distinct subfamilies of enzymes, known as the DNA topoisomerases, have evolved to solve these problems. This review focuses on work in the past decade on the mechanisms and cellular functions of these enzymes. Newly discovered members and recent biochemical and structural results are reviewed, and mechanistic implications of these results are summarized. The primary cellular functions of these enzymes, including their roles in replication, transcription, chromosome condensation, and the maintenance of genome stability, are then discussed. The review ends with a summary of the regulation of the cellular levels of these enzymes and a discussion of their association with other cellular proteins.

  20. Inhibitory effect of high NH4(+)-N concentration on anaerobic biotreatment of fresh leachate from a municipal solid waste incineration plant.

    PubMed

    Liu, Zhao; Dang, Yan; Li, Caihua; Sun, Dezhi

    2015-09-01

    Fresh leachate from municipal solid waste (MSW) incineration plants generally contains extremely high NH4(+)-N concentration which could inhibit the bioactivity of microorganisms. The inhibitory effect of high NH4(+)-N concentration on anaerobic biotreatment of fresh leachate from a MSW incineration plant in China has been investigated in this study. The inhibition processes was studied by both static tests and a laboratory-scale expanded granular sludge bed (EGSB) reactor. The specific methanogenic activity (SMA) of the microorganisms in anaerobic granular sludge was inhibited with the NH4(+)-N concentration increasing to 1000mg/L in static tests. As well the chemical oxygen demand (COD) removal efficiency and the methane yield decreased in the EGSB reactor, while the volatile fatty acids (VFAs) accumulated and extracellular polymeric substances (EPS) of the anaerobic granular sludge increased with NH4(+)-N concentration rising to 1000mg/L, without any rebounding during 30days of operation. Decreasing NH4(+)-N concentration to 500mg/L in influent, the COD removal efficiency recovered to about 85% after 26days. 1000mg/L of NH4(+)-N in leachate was suggested to be the inhibition threshold in EGSB reactor. High-throughput sequencing results showed little changes in microbial communities of the sludge for a high NH4(+)-N concentration, indicating that the survival of most microorganisms was not affected under such a condition. It inhibited the bioactivity of the microorganisms, resulting in decrease of the COD removal efficiency.

  1. Content identification: binary content fingerprinting versus binary content encoding

    NASA Astrophysics Data System (ADS)

    Ferdowsi, Sohrab; Voloshynovskiy, Svyatoslav; Kostadinov, Dimche

    2014-02-01

    In this work, we address the problem of content identification. We consider content identification as a special case of multiclass classification. The conventional approach towards identification is based on content fingerprinting where a short binary content description known as a fingerprint is extracted from the content. We propose an alternative solution based on elements of machine learning theory and digital communications. Similar to binary content fingerprinting, binary content representation is generated based on a set of trained binary classifiers. We consider several training/encoding strategies and demonstrate that the proposed system can achieve the upper theoretical performance limits of content identification. The experimental results were carried out both on a synthetic dataset with different parameters and the FAMOS dataset of microstructures from consumer packages.

  2. Human Immunodeficiency Virus Type 1 Vpr Induces DNA Replication Stress In Vitro and In Vivo▿

    PubMed Central

    Zimmerman, Erik S.; Sherman, Michael P.; Blackett, Jana L.; Neidleman, Jason A.; Kreis, Christophe; Mundt, Pamela; Williams, Samuel A.; Warmerdam, Maria; Kahn, James; Hecht, Frederick M.; Grant, Robert M.; de Noronha, Carlos M. C.; Weyrich, Andrew S.; Greene, Warner C.; Planelles, Vicente

    2006-01-01

    The human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) causes cell cycle arrest in G2. Vpr-expressing cells display the hallmarks of certain forms of DNA damage, specifically activation of the ataxia telangiectasia mutated and Rad3-related kinase, ATR. However, evidence that Vpr function is relevant in vivo or in the context of viral infection is still lacking. In the present study, we demonstrate that HIV-1 infection of primary, human CD4+ lymphocytes causes G2 arrest in a Vpr-dependent manner and that this response requires ATR, as shown by RNA interference. The event leading to ATR activation in CD4+ lymphocytes is the accumulation of replication protein A in nuclear foci, an indication that Vpr likely induces stalling of replication forks. Primary macrophages are refractory to ATR activation by Vpr, a finding that is consistent with the lack of detectable ATR, Rad17, and Chk1 protein expression in these nondividing cells. These observations begin to explain the remarkable resilience of macrophages to HIV-1-induced cytopathicity. To study the in vivo consequences of Vpr function, we isolated CD4+ lymphocytes from HIV-1-infected individuals and interrogated the cell cycle status of anti-p24Gag-immunoreactive cells. We report that infected cells in vivo display an aberrant cell cycle profile whereby a majority of cells have a 4N DNA content, consistent with the onset of G2 arrest. PMID:16956949

  3. Ion Competition in Condensed DNA Arrays in the Attractive Regime

    PubMed Central

    Qiu, Xiangyun; Giannini, John; Howell, Steven C.; Xia, Qi; Ke, Fuyou; Andresen, Kurt

    2013-01-01

    Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt3+ Hexammine, or Co3+Hex) and one nonDNA-condensing ion (Mg2+) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations are shown to significantly underestimate the number of Co3+Hex ions, consistent with the deficiencies of nonlinear Poisson-Boltzmann approaches in describing multivalent cations. Upon increasing the concentration of Mg2+, the Co3+Hex-condensed DNA array expands and eventually redissolves as a result of ion competition weakening DNA-DNA attraction. Although the DNA-DNA spacing depends on both Mg2+ and Co3+Hex concentrations in the bath solution, it is observed that the spacing is largely determined by a single parameter of the DNA array, the fraction of DNA charges neutralized by Co3+Hex. It is also observed that only ∼20% DNA charge neutralization by Co3+Hex is necessary for spontaneous DNA condensation. We then show that the bath ion conditions can be reduced to one variable with a simplistic ion binding model, which is able to describe the variations of both ion contents and DNA-DNA spacings reasonably well. Finally, we discuss the implications on the nature of interstitial ions and cation-mediated DNA-DNA interactions. PMID:23972850

  4. DNA Methylation

    PubMed Central

    Marinus, M.G.; Løbner-Olesen, A.

    2014-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential and in C. crescentus, it is important for temporal gene expression which, in turn, is required for coordinating chromosome initiation, replication and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage; decrease transformation frequency in certain bacteria; decrease the stability of short direct repeats; are necessary for site-directed mutagenesis; and to probe eukaryotic structure and function. PMID:26442938

  5. DNA Investigations.

    ERIC Educational Resources Information Center

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  6. Feature Scale Simulation of PECVD of SiO2 in SiH4/N2O Mixture

    NASA Astrophysics Data System (ADS)

    Liu, Xuan; Ge, Jie; Yang, Yi; Song, Yixu; Ren, Tianling

    2014-04-01

    In this paper, to simulate the process of PECVD (plasma enhanced chemical vapor deposition) of SiO2, the plasma chemistry and plasma density of SiH4/N2O mixture have been studied with an inductive coupled plasma model, and the level set methodology has been used to obtain the feature scale variation during the process. In this simulation, the goal is to fill a trench. We studied how ion sputtering and chamber pressure affect the feature scale model. After the simulation, we found that the trench will close up at the top after a few steps, and if we add the ion sputtering into the surface reactions, the trench top will close up a little later. When the chamber pressure is improved, the plasma density will increase, so the trench top will close up earlier. In semiconductor device manufacture, people can control the trench's feature scale through adjusting these two parameters.

  7. Synthesis and aromatase inhibitory evaluation of 4-N-nitrophenyl substituted amino-4H-1,2,4-triazole derivatives.

    PubMed

    Song, Zhidan; Liu, Yanchun; Dai, Zhoutong; Liu, Wei; Zhao, Kai; Zhang, Tongcun; Hu, Yanying; Zhang, Xiuli; Dai, Yujie

    2016-10-01

    In this paper, 13 4-N-nitrophenyl substituted amino-4H-1,2,4-triazole derivatives were synthesized and their aromatase inhibitory activities were measured. The results show that the substitution of the groups on benzyl group can further improve their bioactivity and the compound with Cl on the para position of benzyl has the highest bioactivity (IC50=9.02nM). A QSAR model was constructed from the 13 compounds with genetic function approximation using DS 2.1 package. This model can explain 90.09% of the variance (R(2)Adj), while it can predict 84.95% of the variance (R(2)cv) with the confidence interval of 95%. PMID:27567077

  8. Cross section limits for the Cm248(Mg25,4n-5n)Hs268,269 reactions

    NASA Astrophysics Data System (ADS)

    Dvorak, J.; Brüchle, W.; Düllmann, Ch. E.; Dvorakova, Z.; Eberhardt, K.; Eichler, R.; Jäger, E.; Nagame, Y.; Qin, Z.; Schädel, M.; Schausten, B.; Schimpf, E.; Schuber, R.; Semchenkov, A.; Thörle, P.; Türler, A.; Wegrzecki, M.; Yakushev, A.

    2009-03-01

    We report on an attempt to produce and detect Hs268 and Hs269 in the nuclear fusion reaction Mg25+Cm248 using the gas phase chemistry apparatus COMPACT. No decay chains attributable to the decay of hassium isotopes were observed during the course of this experiment. From the nonobservation of Hs269 we derive a cross section limit of 0.4 pb (63% confidence limit) for the reaction Cm248(Mg25,4n)Hs269 at a center-of-target beam energy of 140 MeV. The evaluated cross section limit for the Cm248(Mg25,5n)Hs268 reaction depends on the assumed half-life of unknown Hs268. Current systematics of the half-lives for even-even Hs isotopes suggests a value of 0.5 s, resulting in a cross section limit of 1.3 pb.

  9. Electronic structure and magnetism in g-C{sub 4}N{sub 3} controlled by strain engineering

    SciTech Connect

    Liu, L. Z.; Liu, X. X.; Wu, X. L. E-mail: paul.chu@cityu.edu.hk; Chu, Paul K. E-mail: paul.chu@cityu.edu.hk

    2015-03-30

    Regulation of magnetism and half-metallicity has attracted much attention because of its potential in spintronics. The magnetic properties and electronic structure of graphitic carbon nitride (g-C{sub 4}N{sub 3}) with external strain are determined theoretically based on the density function theory and many-body perturbation theory (G{sub 0}W{sub 0}). Asymmetric deformation induced by uniaxial strain not only regulates the magnetic characteristics but also leads to a transformation from half-metallicity to metallicity. However, this transition cannot occur in the structure with symmetric deformation induced by biaxial strain. Our results suggest the use of strain engineering in metal-free spintronics applications.

  10. Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

    PubMed

    Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

    2014-05-01

    Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. PMID:24531108

  11. Measurements of the dielectric and viscoelastic constants in mixtures of 4,4'-n-octyl-cyanobiphenyl and biphenyl.

    PubMed

    Oswald, Patrick; Scalliet, Camille

    2014-03-01

    We performed measurements of the dielectric constants, splay elastic constant, and rotational viscosity of the nematic phase of mixtures of 4,4'-n-octyl-cyanobiphenyl (8CB) and biphenyl (BP). In contrast with previous results of DasGupta et al. [Phys. Rev. E 63, 041703 (2001); Phys. Lett. A 288, 323 (2001)], we do not find any anomaly of these constants when the smectic-A phase is approached at all concentrations of BP. These results are compatible with recent calorimetric measurements of Denolf et al. [Phys. Rev. Lett. 97, 107801 (2006); Phys. Rev. E 76, 051702 (2007)] and the absence of a tricritical point in the phase diagram. The origin of the anomalies observed by DasGupta et al. at large concentration of BP is also briefly discussed and a likely explanation in terms of biphenyl evaporation is proposed.

  12. Optimizing Phytoplasma DNA purification for genome analysis.

    PubMed

    Tran-Nguyen, L T T; Gibb, K S

    2007-04-01

    Genome analysis of uncultivable plant pathogenic phytoplasmas is hindered by the difficulty in obtaining sufficient quantities of phytoplasma enriched DNA. We investigated a combination of conventional enrichment techniques such as cesium chloride (CsCl) buoyant gradient centrifugation, and new methods such as rolling circle amplification (RCA), suppression subtractive hybridization (SSH), and mirror orientation selection (MOS) to obtain DNA with a high phytoplasma:host ratio as the major first step in genome analysis of Candidatus Phytoplasma australiense. The phytoplasma:host ratio was calculated for five different plasmid libraries. Based on sequence data, 90% of clones from CsCl DNA enrichment contained chromosomal phytoplasma DNA, compared to 60% from RCA CsCl DNA and 20% from SSH subtracted libraries. Based on an analysis of representative libraries, none contained plant DNA. A high percentage of clones (80-100%) from SSH libraries contained extrachromosomal DNA (eDNA), and we speculate that eDNA in the original DNA preparation was amplified in subsequent SSH manipulations. Despite the availability of new techniques for nucleic acid amplification, we found that conventional CsCl gradient centrifugation was the best enrichment method for obtaining chromosomal phytoplasma DNA with low host DNA content.

  13. A Termolecular Reaction Mechanism for Nitrogen Incorporation in Aerosol Produced by Far UV Irradiation of CH4-N2 Atmospheres

    NASA Astrophysics Data System (ADS)

    Hicks, R. K.; Trainer, M. G.; Jimenez, J. L.; Yung, Y. L.; Toon, O. B.; Tolbert, M. A.

    2012-12-01

    Results from the Aerosol Collector and Pyrolyser located onboard the Huygens lander reveal the presence of carbon and nitrogen in Titan's aerosols. Nitrogen incorporation is thought to be initiated by energy sources strong enough to break the N-N triple bond of molecular nitrogen (9.8eV). Such energy sources include extreme UV photons (λ <120 nm) and electrons from Saturn's magnetosphere. Less energetic photons in the far UV (120-200 nm) penetrate to the stratosphere of Titan and are only expected to affect hydrocarbon photochemistry there. However, recent results from our laboratory indicate a surprising amount of nitrogen incorporation- up to 16% by mass- in Titan aerosol analog produced by photochemistry initiated by far UV irradiation of CH4/N2 mixtures. The termolecular reaction CH + N2 + M --> HCN2 has been proposed to account for this observation. Here, we test this hypothesis by using a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) to measure the mass loading and chemical composition of aerosol produced at a range of pressures from roughly 0.1 to 1 atm. Even though these gas mixtures spanned an order of magnitude in pressure, they experienced the same residence time in the photochemical chamber and had the same methane optical depth. We report a 150% increase in aerosol mass loading across the range of pressures studied, indicating that the mechanism controlling the total mass produced depends on pressure. We also report an overall increase with pressure in the ratio of nitrogen-bearing organic species to hydrocarbon-only species. These observations support the hypothesis that the termolecular reaction above is responsible for the incorporation of nitrogen into Titan aerosol analog produced from CH4/N2 gas mixtures irradiated in the far UV. These findings have implications for our understanding of the evolution of Titan's atmosphere, and the atmospheric synthesis of biologically relevant N-containing molecules.

  14. Improvement of RNA-SIP by pyrosequencing to identify putative 4-n-nonylphenol degraders in activated sludge.

    PubMed

    Zemb, O; Lee, M; Gutierrez-Zamora, M L; Hamelin, J; Coupland, K; Hazrin-Chong, N H; Taleb, I; Manefield, M

    2012-03-01

    Nonylphenols (NP) have estrogenic potential because of their phenolic ring, but the organisms involved in the degradation of this alkylated phenol remain unidentified. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP) and a new method based on pyrosequencing, we identified the bacteria involved in the degradation of the aromatic ring of [U-ring-(13)C] 4-n-NP in aerobic sludge. The first order degradation rate of 4-n-NP was 5.5d(-1). Single strand conformation polymorphism of density-separated labeled and unlabeled 16S rRNA showed significant differences and enabled selection of four representative fractions for pyrosequencing. Nineteen phylotypes showed a significant enrichment in the heavy fraction in the labeled pulse. The relative abundances of these phylotypes were combined with the RNA concentration of each fraction to yield a simple model of the distribution of each phylotype across the gradient. This model was used to estimate the percentage of labeling for each phylotype. The sequences showing the highest labeling (11%) were closely related to Afipia sp. but represented only 2 % of the RNA in the heavy fraction of the labeled pulse. The sequences representing the largest proportion of the RNA in the heavy fraction were related to Propionibacterium acnes and Frateuria aurantia, which are known to possess enzymes for phenol degradation. The model shows that despite Afipia having the highest (13)C enrichment, other species encoding phenol degradation pathways are responsible for more (13)C incorporation. Last, we showed that some species represent 12% of the total RNA but contain only 1% (13)C above natural abundance.

  15. Working with DNA & Bacteria in Precollege Science Classrooms.

    ERIC Educational Resources Information Center

    Horn, Toby Mogollon; Frame, Kathy, Ed.

    This document describes ways to work with DNA and host organisms in precollege classrooms. The guidelines are intended to assist the teacher who already has training in working with microbes, DNA, and associated chemicals. The contents of the guidelines include: (1) Permitted DNA molecules, vectors, and recommended host organisms for constructing…

  16. [DNA in koilocytotic dysplasia of the cervix uteri, cytophotometric studies].

    PubMed

    Christov, K; Karageosov, I; Makaveeva, V; Kristeva, K

    1987-01-01

    In koilocytotic dysplasia of the uterine cervix the DNA content in squamous cells was quantitated by cytophotometry in histological preparations stained according to Feulgen. Three patterns of DNA distribution in the squamous cells were found. In type one (21.4%) the cells had DNA content in the diploid and paradiploid zone of the histogram. In type two (35.7%) cells with triploid and tetraploid DNA values were found, but with a conspicuous modal class of cells. In type three no modal class cells were found (42.9%). The quantitative DNA changes in squamous cells show that some of the HPV induced alterations may be regarded as precancerous.

  17. Adsorption of 4-n-Nonylphenol and Bisphenol-A on Magnetic Reduced Graphene Oxides: A Combined Experimental and Theoretical Studies.

    PubMed

    Jin, Zhongxiu; Wang, Xiangxue; Sun, Yubing; Ai, Yuejie; Wang, Xiangke

    2015-08-01

    Adsorption of 4-n-nonylphenol (4-n-NP) and bisphenol A (BPA) on magnetic reduced graphene oxides (rGOs) as a function of contact time, pH, ionic strength and humic acid were investigated by batch techniques. Adsorption of 4-n-NP and BPA were independent of pH at 3.0- 8.0, whereas the slightly decreased adsorption was observed at pH 8.0-11.0. Adsorption kinetics and isotherms of 4-n-NP and BPA on magnetic rGOs can be satisfactorily fitted by pseudo-second-order kinetic and Freundlich model, respectively. The maximum adsorption capacities of magnetic rGOs at pH 6.5 and 293 K were 63.96 and 48.74 mg/g for 4-n-NP and BPA, respectively, which were significantly higher than that of activated carbon. Based on theoretical calculations, the higher adsorption energy of rGOs + 4-n-NP was mainly due to π-π stacking and flexible long alkyl chain of 4-n-NP, whereas adsorption of BPA on rGOs was energetically favored by a lying-down configuration due to π-π stacking and dispersion forces, which was further demonstrated by FTIR analysis. These findings indicate that magnetic rGOs is a promising adsorbent for the efficient elimination of 4-n-NP/BPA from aqueous solutions due to its excellent adsorption performance and simple magnetic separation, which are of great significance for the remediation of endocrine-disrupting chemicals in environmental cleanup. PMID:26161689

  18. A novel yellow-emitting SrAlSi4N7:Ce3+ phosphor for solid state lighting: Synthesis, electronic structure and photoluminescence properties

    NASA Astrophysics Data System (ADS)

    Ruan, Jian; Xie, Rong-Jun; Funahashi, Shiro; Tanaka, Yoshinori; Takeda, Takashi; Suehiro, Takayuki; Hirosaki, Naoto; Li, Yuan-Qiang

    2013-12-01

    Ce3+-doped and Ce3+/Li+-codoped SrAlSi4N7 phosphors were synthesized by gas pressure sintering of powder mixtures of Sr3N2, AlN, α-Si3N4, CeN and Li3N. The phase purity, electronic crystal structure, photoluminescence properties of SrAlSi4N7:Ce3+(Ce3+/Li+) were investigated in this work. The band structure calculated by the DMol3 code shows that SrAlSi4N7 has a direct band gap of 3.87 eV. The single crystal analysis of Ce3+-doped SrAlSi4N7 indicates a disordered Si/Al distribution and nitrogen vacnacy defects. SrAlSi4N7 was identified as a major phase of the fired powders, and Sr5Al5Si21N35O2 and AlN as minor phases. Both Ce3+ and Ce3+/Li+ doped SrAlSi4N7 phosphors can be efficiently excited by near-UV or blue light and show a broadband yellow emission peaking around 565 nm. A highest external quantum efficiency of 38.3% under the 450 nm excitation was observed for the Ce3+/Li+-doped SrAlSi4N7 (5 mol%). A white light LED lamp with color temperature of 6300 K and color rendering index of Ra=78 was achieved by combining Sr0.97Al1.03Si3.997N\\94\\maccounttest14=t0005_18193 7:Ce3+0.03 with a commercial blue InGaN chip. It indicates that SrAlSi4N7:Ce3+ is a promising yellow emitting down-conversion phosphor for white LEDs.

  19. Mitochondrial DNA plasticity is an essential inducer of tumorigenesis

    PubMed Central

    Lee, W T Y; Cain, J E; Cuddihy, A; Johnson, J; Dickinson, A; Yeung, K-Y; Kumar, B; Johns, T G; Watkins, D N; Spencer, A; St John, J C

    2016-01-01

    Although mitochondrial DNA has been implicated in diseases such as cancer, its role remains to be defined. Using three models of tumorigenesis, namely glioblastoma multiforme, multiple myeloma and osteosarcoma, we show that mitochondrial DNA plays defining roles at early and late tumour progression. Specifically, tumour cells partially or completely depleted of mitochondrial DNA either restored their mitochondrial DNA content or actively recruited mitochondrial DNA, which affected the rate of tumorigenesis. Nevertheless, non-depleted tumour cells modulated mitochondrial DNA copy number at early and late progression in a mitochondrial DNA genotype-specific manner. In glioblastoma multiforme and osteosarcoma, this was coupled with loss and gain of mitochondrial DNA variants. Changes in mitochondrial DNA genotype affected tumour morphology and gene expression patterns at early and late progression. Importantly, this identified a subset of genes that are essential to early progression. Consequently, mitochondrial DNA and commonly expressed early tumour-specific genes provide novel targets against tumorigenesis. PMID:27551510

  20. Mitochondrial DNA plasticity is an essential inducer of tumorigenesis.

    PubMed

    Lee, W T Y; Cain, J E; Cuddihy, A; Johnson, J; Dickinson, A; Yeung, K-Y; Kumar, B; Johns, T G; Watkins, D N; Spencer, A; St John, J C

    2016-01-01

    Although mitochondrial DNA has been implicated in diseases such as cancer, its role remains to be defined. Using three models of tumorigenesis, namely glioblastoma multiforme, multiple myeloma and osteosarcoma, we show that mitochondrial DNA plays defining roles at early and late tumour progression. Specifically, tumour cells partially or completely depleted of mitochondrial DNA either restored their mitochondrial DNA content or actively recruited mitochondrial DNA, which affected the rate of tumorigenesis. Nevertheless, non-depleted tumour cells modulated mitochondrial DNA copy number at early and late progression in a mitochondrial DNA genotype-specific manner. In glioblastoma multiforme and osteosarcoma, this was coupled with loss and gain of mitochondrial DNA variants. Changes in mitochondrial DNA genotype affected tumour morphology and gene expression patterns at early and late progression. Importantly, this identified a subset of genes that are essential to early progression. Consequently, mitochondrial DNA and commonly expressed early tumour-specific genes provide novel targets against tumorigenesis. PMID:27551510

  1. Comparative study on the inclusion behavior between meso-tetrakis(4- N-ethylpyridiniurmyl)porphyrin and β-cyclodextrin derivatives

    NASA Astrophysics Data System (ADS)

    Xiliang, Guo; Shaomin, Shuang; Chuan, Dong; Feng, Feng; Wong, M. S.

    2005-01-01

    5,10,15,20-Tetrakis(4- N-ethylpyridiniurmyl)porphyrin (TEPyP) formed 1:1 stoichiometry inclusion complexes with β-cyclodextrin (β-CD) and its derivatives including hydroxypropyl-β-cyclodextrin (HP-β-CD), sulfobutylether-β-cyclodextrin (SBE-β-CD) in basic aqueous solution. The supramolecular system was investigated by the methods of fluorescence, UV-vis absorption spectroscopy, nuclear magnetic resonance (NMR) technique. The inclusion ability of cyclodextrins exhibited remarkable difference for β-CD, HP-β-CD and SBE-β-CD. Association constants as high as K=1.1×10 4 M -1 in the case of HP-β-CD/TEPyP and 2.0×10 5 M -1 in the case of SBE-β-CD/TEPyP complexes were determined, whereas a lower value ( K=550 M -1) was given in the case of β-CD/TEPyP. The results showed that hydrogen bonding and charge attraction play important roles in the processes of host-guest interaction. The interaction mechanism of inclusion processes could be explained by the analysis of NMR spectroscopy. The supramolecular assembly was formed. β-CD and HP-β-CD approached from the primary face of cavities of CDs.

  2. Comparative study on the inclusion behavior between meso-tetrakis(4-N-ethylpyridiniurmyl)porphyrin and beta-cyclodextrin derivatives.

    PubMed

    Xiliang, Guo; Shaomin, Shuang; Chuan, Dong; Feng, Feng; Wong, M S

    2005-01-14

    5,10,15,20-Tetrakis(4-N-ethylpyridiniurmyl)porphyrin (TEPyP) formed 1:1 stoichiometry inclusion complexes with beta-cyclodextrin (beta-CD) and its derivatives including hydroxypropyl-beta-cyclodextrin (HP-beta-CD), sulfobutylether-beta-cyclodextrin (SBE-beta-CD) in basic aqueous solution. The supramolecular system was investigated by the methods of fluorescence, UV-vis absorption spectroscopy, nuclear magnetic resonance (NMR) technique. The inclusion ability of cyclodextrins exhibited remarkable difference for beta-CD, HP-beta-CD and SBE-beta-CD. Association constants as high as K=1.1 x 10(4) M(-1) in the case of HP-beta-CD/TEPyP and 2.0 x 10(5) M(-1) in the case of SBE-beta-CD/TEPyP complexes were determined, whereas a lower value (K=550 M(-1)) was given in the case of beta-CD/TEPyP. The results showed that hydrogen bonding and charge attraction play important roles in the processes of host-guest interaction. The interaction mechanism of inclusion processes could be explained by the analysis of NMR spectroscopy. The supramolecular assembly was formed. beta-CD and HP-beta-CD approached from the primary face of cavities of CDs.

  3. A "high 4He/3He" mantle material detected under the East Pacific Rise (15°4'N)

    NASA Astrophysics Data System (ADS)

    Mougel, Berengere; Moreira, Manuel; Agranier, Arnaud

    2015-03-01

    We investigate in details helium isotope data reported in Mougel et al. (2014) for 14 basaltic samples collected on the East Pacific Rise by submersible (15°4'N) where the ridge interacts with the Mathematician seamounts. Samples locations are separated by only few hundred meters across a 15 km along-axis profile. The data reveal a strong geochemical variability that has never been observed at such high spatial resolution for helium isotope compositions. Moreover, they reveal an unusually high 4He/3He mantle component also characterized by unradiogenic lead, atypical in oceanic basalts. He-Pb systematics suggests a mixture between a nonradiogenic lead and radiogenic helium pyroxenitic component, recycled from the deep continental lithosphere and the ambient peridotitic mantle. The He isotope difference between these two end-members can be interpreted as a time evolution of two distinct mantle sources after a slight (U + Th)/3He fractionation, likely due to some ancient degassing during the formation of deep continental pyroxenites.

  4. Photodynamic Therapy of the Murine LM3 Tumor Using Meso-Tetra (4-N,N,N-Trimethylanilinium) Porphine

    PubMed Central

    Colombo, L. L.; Juarranz, A.; Cañete, M.; Villanueva, A.; Stockert, J. C.

    2007-01-01

    Photodynamic therapy (PDT) of cancer is based on the cytotoxicity induced by a photosensitizer in the presence of oxygen and visible light, resulting in cell death and tumor regression. This work describes the response of the murine LM3 tumor to PDT using meso-tetra (4-N,N,N-trimethylanilinium) porphine (TMAP). BALB/c mice with intradermal LM3 tumors were subjected to intravenous injection of TMAP (4 mg/kg) followed 24 h later by blue-red light irradiation (λmax: 419, 457, 650 nm) for 60 min (total dose: 290 J/cm2) on depilated and glycerol-covered skin over the tumor of anesthetized animals. Control (drug alone, light alone) and PDT treatments (drug + light) were performed once and repeated 48 h later. No significant differences were found between untreated tumors and tumors only treated with TMAP or light. PDT-treated tumors showed almost total but transitory tumor regression (from 3 mm to less than 1 mm) in 8/9 animals, whereas no regression was found in 1/9. PDT response was heterogeneous and each tumor showed different regression and growth delay. The survival of PDT-treated animals was significantly higher than that of TMAP and light controls, showing a lower number of lung metastasis but increased tumor-draining lymph node metastasis. Repeated treatment and reduction of tissue light scattering by glycerol could be useful approaches in studies on PDT of cancer. PMID:23675051

  5. Competitive sorption between 17alpha-ethinyl estradiol and bisphenol A/4-n-nonylphenol by soils.

    PubMed

    Li, Jianzhong; Jiang, Lu; Xiang, Xi; Xu, Shuang; Wen, Rou; Liu, Xiang

    2013-06-01

    The sorption of 17alpha-ethinyl estradiol (EE2), bisphenol A (BPA), and 4-n-nonylphenol (NP) in single systems and the sorption of EE2 with different initial aqueous concentrations of BPA or NP were examined using three soils. Results showed that all sorption isotherms were nonlinear and fit the Freundlich model. The degree of nonlinearity was in the order BPA (0.537-0.686) > EE2 (0.705-0.858) > NP (0.875-0.0.951) in single systems. The isotherm linearity index of EE2 sorption calculated by the Freundlich model for Loam, Silt Loam and Silt increased from 0.758, 0.705 and 0.858, to 0.889, 0.910 and 0.969, respectively, when BPA concentration increased from 0 to 1000 microg/L, but the effect of NP was comparably minimal. Additionally, EE2 significantly suppressed the sorption of BPA, but insignificantly suppressed that of NP. These findings can be attributed to the difference of sorption affinity of EE2, NP and BPA on the hard carbon (e.g., black carbon) of soil organic matter that dominated the sorption in the low equilibrium aqueous concentration range of endocrine-disrupting chemicals (EDCs). Competitive sorption among EDCs presents new challenges for predicting the transport and fate of EDCs under the influence of co-solutes.

  6. Transition metal complexes of Vanillin- 4N-(2-pyridyl) thiosemicarbazone (H 2VPT); thermal, structural and spectroscopic studies

    NASA Astrophysics Data System (ADS)

    El-Reash, Gaber Abu; El-Ayaan, Usama; Gabr, I. M.; El-Rachawy, El-Bastawesy

    2010-04-01

    The present work carried out a study on the ligational behavior of the new ligand, Vanillin- 4N-(2-pyridyl) thiosemicarbazone (H 2VPT) 1 towards some transition metal ions namely, Mn 2+, Co 2+, Ni 2+, Cu 2+, Zn 2+,Cd 2+, Hg 2+ and U 6+. These complexes namely [Mn(HVPT)Cl] 2, [Co(VPT)(H 2O)] 2H 2O 3, [Ni(HVPT)Cl(H 2O)] 4, [Cu(HVPT)Cl(H 2O)] 5, [Zn(VPT)(H 2O)]H 2O 6, [Cd(HVPT)Cl(H 2O)] 7, [Hg(VPT)(H 2O)]H 2O 8 and [UO 2(H 2VPT)(OAc) 2]H 2O 9, were characterized by elemental analysis, spectral (IR, 1H NMR and UV-vis) and magnetic moment measurements. The suggested structures were confirmed by applying geometry optimization and conformational analysis. Thermal properties and decomposition kinetics of all compounds are investigated. The interpretation, mathematical analysis and evaluation of kinetic parameters ( E, A, Δ H, Δ S and Δ G) of all thermal decomposition stages have been evaluated using Coats-Redfern equation. ESR spectra of [Cu(HVPT)Cl]H 2O at room temperature show broad signal, indicating spin-exchange interactions between copper(II) ions.

  7. Nuclear Magnetic Resonance Measurements and Electronic Structure of Pu(IV) in [(Me)4N]2PuCl6.

    PubMed

    Mounce, Andrew M; Yasuoka, Hiroshi; Koutroulakis, Georgios; Lee, Jeongseop A; Cho, Herman; Gendron, Frédéric; Zurek, Eva; Scott, Brian L; Trujillo, Julie A; Slemmons, Alice K; Cross, Justin N; Thompson, Joe D; Kozimor, Stosh A; Bauer, Eric D; Autschbach, Jochen; Clark, David L

    2016-09-01

    The synthesis, electronic structure, and characterization via single-crystal X-ray diffraction, nuclear magnetic resonance (NMR) spectroscopy, and magnetic susceptibility of (Me4N)2PuCl6 are reported. NMR measurements were performed to both search for the direct (239)Pu resonance and to obtain local magnetic and electronic information at the Cl site through (35)Cl and (37)Cl spectra. No signature of (239)Pu NMR was observed. The temperature dependence of the Cl spectra was simulated by diagonalizing the Zeeman and quadrupolar Hamiltonians for (35)Cl, (37)Cl, and (14)N isotopes. Electronic structure calculations predict a magnetic Γ5 triplet ground state of Pu(IV) in the crystalline electric field of the undistorted PuCl6 octahedron. A tetragonal distortion would result in a very small splitting (∼20 cm(-1)) of the triplet ground state into a nonmagnetic singlet and a doublet state. The Cl shifts have an inflection point at T ≈ 15 K, differing from the bulk susceptibility, indicating a nonmagnetic crystal field ground state. The Cl spin-lattice relaxation time is constant to T = 15 K, below which it rapidly increases, also supporting the nonmagnetic crystal field ground state.

  8. General transformation of α cluster model wave function to jj-coupling shell model in various 4N nuclei

    NASA Astrophysics Data System (ADS)

    Itagaki, N.; Matsuno, H.; Suhara, T.

    2016-09-01

    The antisymmetrized quasi-cluster model (AQCM) is a method to describe transitions from the α cluster wave functions to jj-coupling shell model wave functions. In this model, the cluster-shell transition is characterized by only two parameters: R representing the distance between α clusters and Λ describing the breaking of α clusters. The contribution of the spin-orbit interaction, very important in the jj-coupling shell model, can be taken into account starting with the α cluster model wave function. In this article we show the generality of AQCM by extending the application to heavier regions: various 4N nuclei from 4He to 100Sn. The characteristic magic numbers of the jj-coupling shell model, 28 and 50, are described starting with the α cluster model. The competition of two different configurations is discussed in 20Ne (16O + one quasi-cluster and 12C + two quasi-clusters) and 28Si (pentagon shape of five quasi-clusters and 12C + 16O). Also, we compare the energy curves for the α + 40Ca cluster configuration calculated with and without the α breaking effect in 44Ti.

  9. Distortion-sensitive insight into the pretransitional behavior of 4-n-octyloxy-4‧-cyanobiphenyl (8OCB)

    NASA Astrophysics Data System (ADS)

    Rzoska, Sylwester J.; Drozd-Rzoska, Aleksandra; Mukherjee, Prabir K.; Lopez, David O.; Martinez-Garcia, Julio C.

    2013-06-01

    Results of studies of the static and dynamic dielectric properties in rod-like 4-n-octyloxy-4‧-cyanobiphenyl (8OCB) with isotropic (I)-nematic (N)-smectic A (SmA)-crystal (Cr) mesomorphism, combined with measurements of the low-frequency nonlinear dielectric effect and heat capacity are presented. The analysis is supported by the derivative-based and distortion-sensitive transformation of experimental data. Evidence for the I-N and N-SmA pretransitional anomalies, indicating the influence of tricritical behavior, is shown. It has also been found that neither the N phase nor the SmA phase are uniform and hallmarks of fluid-fluid crossovers can be detected. The dynamics, tested via the evolution of the primary relaxation time, is clearly non-Arrhenius and described via τ(T) = τc(T-TC)-ϕ. In the immediate vicinity of the I-N transition a novel anomaly has been found: Δτ ∝ 1/(T - T*), where T* is the temperature of the virtual continuous transition and Δτ is the excess over the ‘background behavior’. Experimental results are confronted with the comprehensive Landau-de Gennes theory based modeling.

  10. DNA Microarrays

    NASA Astrophysics Data System (ADS)

    Nguyen, C.; Gidrol, X.

    Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

  11. DNA repair, immunosuppression, and skin cancer.

    PubMed

    Yarosh, Daniel B

    2004-11-01

    UV radiation (UVR) produces erythema within the first 24 hours of exposure, suppression of the immune system within the first 10 days, and, for many people, over the course of decades, skin cancer. Although UVR damages many skin targets, DNA damage in the form of cyclobutane pyrimidine dimers (CPDs) is an important mediator of these sequelae. The action spectrum for erythema parallels the action spectrum for CPD formation in skin, and in the absence of repair, as in the genetic disease xeroderma pigmentosum (XP), skin cancer rates are dramatically increased. DNA repair in skin can be enhanced by the delivery of DNA repair enzymes encapsulated in liposomes. Used in this way, photoreactivation of CPDs greatly diminishes erythema and the suppression of contact hypersensitivity (CHS). UV endonucleases delivered by liposomes also prevent UV-induced suppression of delayed-type hypersensitivity. In a clinical study of patients with XP, T4 endonuclease V (T4N5) liposome lotion applied for one year reduced the rates of actinic keratosis (AK) and skin cancer compared with placebo. These results showed that strategies to increase sun protection should include measures to reduce DNA damage and increase the rate of DNA repair.

  12. Optical DNA

    NASA Astrophysics Data System (ADS)

    Vijaywargi, Deepak; Lewis, Dave; Kirovski, Darko

    A certificate of authenticity (COA) is an inexpensive physical object with a random and unique structure S which is hard to near-exactly replicate. An inexpensive device should be able to scan object’s physical “fingerprint,” a set of features that represents S. In this paper, we explore one set of requirements that optical media such as DVDs should satisfy, to be considered as COAs. As manufacturing of such media produces inevitable errors, we use the locations and count of these errors as a “fingerprint” for each optical disc: its optical DNA. The “fingerprint” is signed using publisher’s private-key and the resulting signature is stored onto the optical medium using a post-production process. Standard DVD players with altered firmware that includes publisher’s public-key, should be able to verify the authenticity of DVDs protected with optical DNA. Our key finding is that for the proposed protocol, only DVDs with exceptional wear-and-tear characteristics would result in an inexpensive and viable anti-counterfeiting technology.

  13. Responses of biofilm characteristics to variations in temperature and NH4(+)-N loading in a moving-bed biofilm reactor treating micro-polluted raw water.

    PubMed

    Zhang, Shuangfu; Wang, Yayi; He, Weitao; Wu, Min; Xing, Meiyan; Yang, Jian; Gao, Naiyun; Yin, Daqiang

    2013-03-01

    A pilot-scale moving-bed biofilm reactor (MBBR) for biological treatment of micro-polluted raw water was operated over 400days to investigate the responses of biofilm characteristics and nitrification performance to variations in temperature and NH4(+)-N loading. The mean removal efficiency of NH4(+)-N in the MBBR reached 71.4±26.9%, and batch experiments were performed to study nitrification kinetics for better process understanding. Seven physical-chemical parameters, including volatile solids (VS), polysaccharides (PS) and phospholipids (PL) increased firstly, and then rapidly decreased with increasing temperature and NH4(+)-N loading, and properly characterized the attached biomass during biofilm development and detachment in the MBBR. The biofilm compositions were described by six ratios, e.g., PS/VS and PL/VS ratios showed different variation trends, indicating different responses of PS and PL to the changes in temperature and NH4(+)-N loading. Furthermore, fluorescent in situ hybridization (FISH) analysis revealed that increased NH4(+)-N loadings caused an enrichment of the nitrifying biofilm.

  14. DNA delivery systems based on complexes of DNA with synthetic polycations and their copolymers.

    PubMed

    Oupický, D; Konák, C; Ulbrich, K; Wolfert, M A; Seymour, L W

    2000-03-01

    Block and graft copolymers of N-(2-hydroxypropyl)methacrylamide (HPMA) with 2-(trimethylammonio)ethyl methacrylate were synthesised and used for preparation of polyelectrolyte complexes with calf thymus DNA intended for targeted delivery of genes in vivo. In this study the effects of the speed of component mixing, total concentration of polymers, ionic strength of solvents, copolymer structure and content of HPMA in the copolymers on parameters of the polyelectrolyte complexes was investigated. Static and dynamic light scattering methods were used as a main tool for characterising these complexes. The presence of HPMA units in the polycation had no significant effect on its ability to form complexes with DNA, but did affect molecular parameters and aggregation (precipitation) of the complexes. The size of the complexes increases whereas their molecular weight decreases with increasing content of HPMA units. The density of the complexes decreases with increasing HPMA content independently of the copolymer structure. In order to prepare stable DNA complexes containing single DNA molecule, the following rules should be observed: (1) copolymers should have a content of HPMA units higher than 40%; (2) the DNA concentrations in solutions should be kept below 4 x 10(-5) g/ml and (3) both components should be mixed together in deionized water. The stability of the complexes against precipitation in 0.15 M NaCl and the resistance of the complexed DNA to the action of nucleases was also studied. Whereas DNA complexes of all copolymers showed very good nuclease stability, the presence of a sufficiently high content of HPMA is necessary for their good stability in 0.15 M NaCl. The investigation of the stability and the interaction of DNA complexes in aqueous solutions of serum albumin and dilute human blood serum revealed adsorption of biomacromolecules on DNA complexes accompanied by significant changes in the zeta-potential which finally resulted in formation of a "protein

  15. A Transition to a Compact Form of DNA in Polymer Solutions

    PubMed Central

    Lerman, L. S.

    1971-01-01

    In the presence of over-threshold concentrations of simple neutral polymers and salts, DNA undergoes a cooperative change in its solution structure. Sedimentation studies at low DNA concentrations show that phage DNA molecules collapse into particles approaching the compactness of the contents of phage heads. The interaction between DNA and polymers is thought to be nonspecifically replusive. PMID:5288774

  16. The Richardson constant and barrier inhomogeneity at Au/Si3N4/n-Si (MIS) Schottky diodes

    NASA Astrophysics Data System (ADS)

    Tataroğlu, A.; Pür, F. Z.

    2013-07-01

    Si3N4 films were deposited on n-type silicon substrate by the radio frequency magnetron sputtering technique. The current-voltage (I-V) characteristics of Au/Si3N4/n-Si (metal-insulator-semiconductor) Schottky diodes were investigated in the temperature range of 160-400 K. Experimental results show an abnormal increase in the zero-bias barrier height (BH) (ΦBo) and a decrease in the ideality factor (n) with increasing temperature. This behavior is attributed to barrier inhomogeneities by assuming a Gaussian distribution (GD) of BHs. The conventional Richardson plot (ln(Io/T2) versus 1000/T) exhibits a linearity above about 300 K. The values of activation energy (Ea) and Richardson constant (A*) were found to be 0.350 eV and 1.242 × 10-3 A cm-2 K-2 from the slope and the intercept at the ordinate of the linear region of this plot, respectively. Also, we attempted to draw a ΦBo versus q/2kT plot to determine evidence of the GD of BHs, and the values of \\bar \\Phi _{{\\rm{Bo}}} = 0.999\\,{\\rm{eV}} and σs = 0.137 eV for the mean BH and zero-bias standard deviation, respectively, were obtained from this plot; then, a modified ln(Io/T2) - q2σs2/2k2T2 versus q/kT plot gives \\bar \\Phi _{{\\rm{Bo}}} and A* as 0.992 eV and 108.228 A cm-2 K-2, respectively. This value of A* is very close to the theoretical value of 112 A cm-2 K-2 for n-type Si.

  17. Capacitance and conductance characterization of nano-ZnGa{sub 2}Te{sub 4}/n-Si diode

    SciTech Connect

    Fouad, S.S.; Sakr, G.B.; Yahia, I.S.; Abdel-Basset, D.M.; Yakuphanoglu, F.

    2014-01-01

    Graphical abstract: - Highlights: • XRD and DTA micrographs were used to study the structure of ZnGa{sub 2}Te{sub 4}. • C–V, G–V and R{sub s}–V of the diode characteristics have been analyzed for the first time. • Dielectric constant, dielectric loss, loss tangent and ac conductivity were determined. • The interfaces states were determined using conductance–voltage technique. • ZnGa{sub 2}Te{sub 4} is a good candidate for electronic device applications. - Abstract: Capacitance–voltage (C–V) and conductance–voltage (G–V) characteristics of p-ZnGa{sub 2}Te{sub 4}/n-Si HJD were studied over a wide frequency and temperature. Both the interface states density N{sub ss} and series resistance R{sub s} were strongly frequency and temperature dependent. The interface states density N{sub ss} is decreased with increasing frequency and increase with increasing temperature. The values of the built-in potential (V{sub bi}) were calculated and found to increase with increasing temperature and frequency. The values of capacitance C, conductance G, series resistance R{sub s}, corrected capacitance C{sub ADJ}, corrected conductance G{sub ADJ}, dielectric constant (ε′), dielectric loss (ε″), loss tangent (tan δ) and the AC conductivity (σ{sub ac}) are strongly dependent on the applied frequency, voltage and temperature. The obtained results show that the locations of N{sub ss} and R{sub s} have a significant effect on the electrical characteristics of the studied diode.

  18. Solvent sensitive intramolecular charge transfer dynamics in the excited states of 4-N,N-dimethylamino-4'-nitrobiphenyl.

    PubMed

    Ghosh, Rajib; Nandi, Amitabha; Palit, Dipak K

    2016-03-21

    Organic molecules substituted with the nitro group show efficient nonlinear optical (NLO) properties, which are a consequence of the strong intramolecular charge transfer (ICT) character of the molecules because of the strong electron withdrawing nature of the nitro group and rapid responsiveness because of highly movable π-electrons. Dynamics of the ICT process in the excited states of a push-pull biphenyl derivative, namely, 4-N,N-dimethylamino-4'-nitrobiphenyl (DNBP), an efficient NLO material, has been investigated using ultrafast transient absorption spectroscopy. The experimental results have been corroborated with DFT and TDDFT calculations. In solvents of large polarity, e.g. acetonitrile, the ultrafast ICT process of DNBP is associated with the barrierless twisting of the N,N-dimethylaniline (DMA) group with respect to the nitrobenzene moiety to populate the twisted ICT (or TICT) state, and the rate of this process is solely governed by the viscosity of the medium. In solvents of moderate polarity, e.g. ethyl acetate, the rate of the twisting process is significantly slowed down and the LE and TICT states remain in equilibrium because of a low energy barrier for interconversion between these two states. By further lowering the polarity of the solvent, e.g. in dioxane, the twisting process is completely retarded. In nonpolar solvents, e.g. cyclohexane, a reverse twisting motion towards the planar geometry (i.e. the PICT process) has been evident in the excited state dynamics. In this solvent, the S1 state undergoes an ultrafast intersystem crossing to the triplet state because of its close proximity with the T2 state. PMID:26907751

  19. Magnetic properties of nanocrystalline ε-Fe{sub 3}N and Co{sub 4}N phases synthesized by newer precursor route

    SciTech Connect

    Theerthagiri, J.; Dalavi, Shankar B.; Manivel Raja, M.; Panda, R.N.

    2013-11-15

    Graphical abstract: Nanocrystalline ε-Fe{sub 3}N and Co{sub 4}N nitride phases are synthesized first time by newer chemical routes. The ε-Fe{sub 3}N phase crystallizes in hexagonal structure with unit cell parameters, a = 4.76 Å and c = 4.41 Å. The Co{sub 4}N phase crystallizes in face centred cubic (fcc) structure with unit cell parameters, a = 3.55 Å. The estimated crystallite size for ε-Fe{sub 3}N and Co{sub 4}N phases are 29 nm and 22 nm, respectively. The values of saturation magnetization for ε-Fe{sub 3}N and Co{sub 4}N phases are found to be 28.1 emu/g and 123.6 emu/g respectively. The reduction of magnetic moments in ultrafine materials compared to bulk materials has been explained by fine particle size and surface effects. We have synthesized the high moment ε-Fe{sub 3}N and Co{sub 4}N nitride with reduced coercivity which may find applications as soft magnetic materials. - Highlights: • Nanocrystalline ε-Fe{sub 3}N and Co{sub 4}N nitride phases are synthesized. • The ε-Fe{sub 3}N and Co{sub 4}N crystallizes in hexagonal and fcc structure respectively. • The observed magnetic parameters indicate soft magnetic properties. • The magnetic properties have been explained on the basis of fine particle magnetism. - Abstract: Nanocrystalline ε-Fe{sub 3}N and Co{sub 4}N nitride phases are synthesized first time by using tris(1,2-diaminoethane)iron(II) chloride and tris(1,2-diaminoethane)cobalt(III) chloride precursors, respectively. To prepare ε-Fe{sub 3}N and Co{sub 4}N nitride phases, the synthesized precursors were mixed with urea in 1:12 ratio and heat treated at various temperatures in the range of 450–900 °C under the ultrapure nitrogen gas atmosphere. The precursors are confirmed by FT-IR study. The ε-Fe{sub 3}N phase crystallizes in hexagonal structure with unit cell parameters, a = 4.76 Å and c = 4.41 Å. The Co{sub 4}N phase crystallizes in face centred cubic (fcc) structure with unit cell parameters, a = 3.55 Å. The

  20. Enhanced inverse spin-Hall voltage in (001) oriented Fe4N/Pt polycrystalline films without contribution of planar-Hall effect

    NASA Astrophysics Data System (ADS)

    Isogami, Shinji; Tsunoda, Masakiyo

    2016-04-01

    In this study, the output DC electric voltage (V out) generated by a Pt-capped Fe4N bilayer film (Fe4N/Pt) under ferromagnetic resonance conditions at room temperature was assessed. The contributions from the inverse spin-Hall effect (ISHE), the planar-Hall effect (PHE) and the anomalous-Hall effect (AHE) were separated from the output voltage by analysis of V out values determined at varying external field polar angles. The results showed that the polarity of the ISHE (V ISHE) component of V out was opposite to that of the PHE (V PHE). As a result, the magnitude of the intrinsic V ISHE was beyond V out by as much as the magnitude of V PHE. The X-ray diffraction structural analysis revealed the polycrystal of the Fe4N/Pt with (001) orientation, which might be one of the possible mechanisms for enhanced intrinsic V ISHE.

  1. Methods for sequencing GC-rich and CCT repeat DNA templates

    DOEpatents

    Robinson, Donna L.

    2007-02-20

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  2. PCR-based analysis of mitochondrial DNA copy number, mitochondrial DNA damage, and nuclear DNA damage

    PubMed Central

    Gonzalez-Hunt, Claudia P.; Rooney, John P.; Ryde, Ian T.; Anbalagan, Charumathi; Joglekar, Rashmi

    2016-01-01

    Because of the role DNA damage and depletion play in human disease, it is important to develop and improve tools to assess these endpoints. This unit describes PCR-based methods to measure nuclear and mitochondrial DNA damage and copy number. Long amplicon quantitative polymerase chain reaction (LA-QPCR) is used to detect DNA damage by measuring the number of polymerase-inhibiting lesions present based on the amount of PCR amplification; real-time PCR (RT-PCR) is used to calculate genome content. In this unit we provide step-by-step instructions to perform these assays in Homo sapiens, Mus musculus, Rattus norvegicus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Oryzias latipes, Fundulus grandis, and Fundulus heteroclitus, and discuss the advantages and disadvantages of these assays. PMID:26828332

  3. Structural characterisation of human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol, lactose, 3′-sulfo-lactose, and 2′-fucosyllactose

    PubMed Central

    Bum-Erdene, Khuchtumur; Leffler, Hakon; Nilsson, Ulf J.; Blanchard, Helen

    2016-01-01

    Galectin-4 is a tandem-repeat galectin with two distinct carbohydrate recognition domains (CRD). Galectin-4 is expressed mainly in the alimentary tract and is proposed to function as a lipid raft and adherens junction stabilizer by its glycan cross-linking capacity. Galectin-4 plays divergent roles in cancer and inflammatory conditions, either promoting or inhibiting each disease progression, depending on the specific pathological condition. The study of galectin-4’s ligand-binding profile may help decipher its roles under specific conditions. Here we present the X-ray structures of human galectin-4 N-terminal CRD (galectin-4N) bound to different saccharide ligands. Galectin-4’s overall fold and its core interactions to lactose are similar to other galectin CRDs. Galectin-4N recognises the sulfate cap of 3′-sulfated glycans by a weak interaction through Arg45 and two water-mediated hydrogen bonds via Trp84 and Asn49. When galectin-4N interacts with the H-antigen mimic, 2′-fucosyllactose, an interaction is formed between the ring oxygen of fucose and Arg45. The extended binding site of galectin-4N may not be well suited to the A/B-antigen determinants, α-GalNAc/α-Gal, specifically due to clashes with residue Phe47. Overall, galectin-4N favours sulfated glycans whilst galectin-4C prefers blood group determinants. However, the two CRDs of galectin-4 can, to a less extent, recognise each other’s ligands. PMID:26828567

  4. DNA mimicry by proteins.

    PubMed

    Dryden, D T F; Tock, M R

    2006-04-01

    It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins. PMID:16545103

  5. Further studies of infectious DNA extracted from mycobacteriophages.

    PubMed

    Sellers, M I; Tokunaga, T

    1966-02-01

    Results of the previous investigation in which it was found that DNA extracted from D29 mycobacteriophage was infectious for Mycobacterium smegmatis 607, have been extended. DNA extracted from mycobacteriophage D4 and D32 produced plaques when plated on their respective hosts; D28 DNA, extracted in the same manner and tested under similar conditions, failed to show infectivity. Species barriers were not crossed by mycobacteriophage DNA; bacteria resistant to intact phage were not infected with the phage DNA. The efficiency of plating of the DNA is very much lower than that of intact phage; infection of a given host was not accomplished by DNA when titration for plaque formation by the intact phage was less than 10(9) PFU. The base composition of DNA extracted from the four mycobacteriophages and the three propagating hosts was very similar. The bases were paired, adenine with thymine and guanine with cytosine. A relatively higher per cent of guanine-cytosine than of adenine-thymine, was found. The buoyant density of each DNA in CsCl was linearly related to its guanine-cytosine content whereas with the exception of D28 DNA, thermal denaturation temperatures failed to show this relationship. However, the thermal transition profiles were characteristic of double stranded DNA. Additional evidence that D29 DNA forms complexes with basic proteins was obtained. Binding between calf thymus histone and between RNAase and D29 DNA readily occurs with a resultant loss in DNA infectivity. Trypsin and D29 DNA are only weakly reactive.

  6. Drosophila RecQ4 Is Directly Involved in Both DNA Replication and the Response to UV Damage in S2 Cells

    PubMed Central

    Crevel, Gilles; Vo, Nicole; Crevel, Isabelle; Hamid, Sana; Hoa, Lily; Miyata, Seiji; Cotterill, Sue

    2012-01-01

    The RecQ4 protein shows homology to both the S.cerevisiae DNA replication protein Sld2 and the DNA repair related RecQ helicases. Experimental data also suggest replication and repair functions for RecQ4, but the precise details of its involvement remain to be clarified. Here we show that depletion of DmRecQ4 by dsRNA interference in S2 cells causes defects consistent with a replication function for the protein. The cells show reduced proliferation associated with an S phase block, reduced BrdU incorporation, and an increase in cells with a subG1 DNA content. At the molecular level we observe reduced chromatin association of DNA polymerase-alpha and PCNA. We also observe increased chromatin association of phosphorylated H2AvD - consistent with the presence of DNA damage and increased apoptosis. Analysis of DmRecQ4 repair function suggests a direct role in NER, as the protein shows rapid but transient nuclear localisation after UV treatment. Re-localisation is not observed after etoposide or H2O2 treatment, indicating that the involvement of DmRecQ4 in repair is likely to be pathway specific. Deletion analysis of DmRecQ4 suggests that the SLD2 domain was essential, but not sufficient, for replication function. In addition a DmRecQ4 N-terminal deletion could efficiently re-localise on UV treatment, suggesting that the determinants for this response are contained in the C terminus of the protein. Finally several deletions show differential rescue of dsRNA generated replication and proliferation phenotypes. These will be useful for a molecular analysis of the specific role of DmRecQ4 in different cellular pathways. PMID:23166690

  7. Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils.

    PubMed

    Mahmoudi, Nagissa; Slater, Greg F; Fulthorpe, Roberta R

    2011-08-01

    Molecular characterization of the microbial populations of soils and sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) is often a first step in assessing intrinsic biodegradation potential. However, soils are problematic for molecular analysis owing to the presence of organic matter, such as humic acids. Furthermore, the presence of contaminants, such as PAHs, can cause further challenges to DNA extraction, quantification, and amplification. The goal of our study was to compare the effectiveness of four commercial soil DNA extraction kits (UltraClean Soil DNA Isolation kit, PowerSoil DNA Isolation kit, PowerMax Soil DNA Isolation kit, and FastDNA SPIN kit) to extract pure, high-quality bacterial and eukaryotic DNA from PAH-contaminated soils. Six different contaminated soils were used to determine if there were any biases among the kits due to soil properties or level of contamination. Extracted DNA was used as a template for bacterial 16S rDNA and eukaryotic 18S rDNA amplifications, and PCR products were subsequently analyzed using denaturing gel gradient electrophoresis (DGGE). We found that the FastDNA SPIN kit provided significantly higher DNA yields for all soils; however, it also resulted in the highest levels of humic acid contamination. Soil texture and organic carbon content of the soil did not affect the DNA yield of any kit. Moreover, a liquid-liquid extraction of the DNA extracts found no residual PAHs, indicating that all kits were effective at removing contaminants in the extraction process. Although the PowerSoil DNA Isolation kit gave relatively low DNA yields, it provided the highest quality DNA based on successful amplification of both bacterial and eukaryotic DNA for all six soils. DGGE fingerprints among the kits were dramatically different for both bacterial and eukaryotic DNA. The PowerSoil DNA Isolation kit revealed multiple bands for each soil and provided the most consistent DGGE profiles among replicates for both

  8. DNA ligase I, the replicative DNA ligase

    PubMed Central

    Howes, Timothy R.L.; Tomkinson, Alan E.

    2013-01-01

    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication. PMID:22918593

  9. On the mechanism of photochromism of 4'-N,N-dimethylamino-7-hydroxyflavylium in pluronic F127.

    PubMed

    Gomes, Raquel; Laia, César A T; Pina, Fernando

    2009-08-13

    The photochromism of the compound 4'-N,N-dimethylamino-7-hydroxyflavylium incorporated in Pluronic F127 micelles and gels was studied in great detail. The red flavylium ion (AH(+)) or the quinoidal base (A), depending on pH, are the irradiation products of the colorless trans-chalcone (Ct). Absorption and fluorescence (steady-state, time-resolved, and anisotropy), pH jumps, and flash photolysis were used to characterize the system. At moderately acidic to neutral pH values, the Ct species is distributed between the core and corona of the Pluronic micelle, as well as in the aqueous phase. At acidic pH values, AH(+) remains most probably in the water phase. The Ct maximum absorption wavelength constitutes a good sensor for the critical micelle concentration (CMC) or critical micelle temperature (CMT). The apparent acidity constant pK'(a) was found to be a relatively good sensor for CMC and also for detection of the sol-gel critical temperature. The Ct photochromic mechanism was analyzed by comparing the photophysics in pure solvents and the pluronic media. Solvatochromic effects show a lack of solvent polarity dependence of the Stokes shift, indicating a low dipolar moment change between the ground and the locally excited state. An internal charge transfer nonradiative process (ICT) competes with Ct photoisomerization and is the dominant process in highly polar solvents, preventing the appearance of photochromism, in contrast with lower polar environments, such as micelles and ethanol. In high viscous environments as those found in the core of the Pluronic F127 micelles or glycerol, both ICT and photoisomerization are reduced, enhancing the Ct fluorescence quantum yield. According to the data from fluorescence measurements and pH jumps, evidence for the Ct distribution among different sites within the pluronic aggregate was found, (i) a hydrophilic/fluid region where Ct has poor fluorescence and isomerization yields, bulk region; (ii) the corona of the micelle where

  10. DNA modifications: Another stable base in DNA

    NASA Astrophysics Data System (ADS)

    Brazauskas, Pijus; Kriaucionis, Skirmantas

    2014-12-01

    Oxidation of 5-methylcytosine has been proposed to mediate active and passive DNA demethylation. Tracking the history of DNA modifications has now provided the first solid evidence that 5-hydroxymethylcytosine is a stable epigenetic modification.

  11. Detection of soy DNA in margarines.

    PubMed

    Gryson, N; Messens, K; Dewettinck, K

    2003-01-01

    The method in which to discriminate between genetically modified (GM) versus non-modified foodstuffs is based on the presence of newly introduced genes at the protein or DNA level. Current available methods are almost exclusively based on the polymerase chain reaction (PCR). This procedure consists of three steps: DNA isolation, the amplification of the desired DNA fragment and visualisation of the obtained amplification products. The first and crucial step is the DNA isolation. Due to several processing steps, the quality of the extracted DNA may be damaged, rendering PCR analysis, and therefore GMO detection, impossible. In this study, the DNA quality of soy lecithin in margarines has been evaluated by PCR. For this purpose, DNA was isolated from margarines with different levels of lecithin with two different extraction methods, including the CTAB method proposed by the European Committe for Standardization (CEN). The amplification of soy DNA by PCR resulted to be difficult, which could be explained by the difficult DNA extraction from margarine and the low lecithin content.

  12. Sperm DNA oxidative damage and DNA adducts.

    PubMed

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-12-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps=0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps=0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps=0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on sperm.

  13. Sperm DNA oxidative damage and DNA adducts.

    PubMed

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-12-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps=0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps=0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps=0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on sperm

  14. Synthesis of DNA

    DOEpatents

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  15. Phenylthiolate as a sigma- and pi- donor ligand: synthesis of a 3-D organometallic coordination polymer [K2Fe(SPh)4]n.

    PubMed

    Yu, Xiao-Yan; Jin, Guo-Xin; Weng, Lin-Hong

    2004-07-01

    The synthesis and crystal structure of the first mixed-metal organometallic polymer network containing phenylthiolato ligands, [K2Fe(SPh)4]n, are investigated. The simple phenylthiolate acts as a sigma- and pi-donor ligand to give a 3-D potassium iron coordination polymer with both metal-carbon and metal-sulfur coordination interactions.

  16. Inversion of exchange bias and complex magnetization reversal in full-nitride epitaxial γ‧-Fe4N/CoN bilayers

    NASA Astrophysics Data System (ADS)

    Li, Z. R.; Mi, W. B.; Wang, X. C.; Bai, H. L.

    2015-04-01

    Exchange bias has been observed in the full-nitride epitaxial γ‧-Fe4N/CoN bilayers. With the increase of temperature, the sign of exchange bias (EB) is inverse, which is independent on the cooling field and training effect. This novel behavior appears in the bilayers with different CoN and γ‧-Fe4N thicknesses. The inversion of EB sign not only occurs at low temperatures, but also takes place even at 200 K for the 10 and 12 nm thick CoN layer. With the decreased γ‧-Fe4N layer thickness, the inversion temperature of EB sign shows a roughly increased tendency. For the bilayer with a 4 nm-thick γ‧-Fe4N, the interfacial magnetization reversal presents a complex trend, which is considered as the combined actions of the disordered ferromagnetic spins and various competed magnetic structures. This new manifestation of EB has been discussed in terms of the complicated interfacial spin structures and frustration effects due to the competition between the ferromagnetic and antiferromagnetic exchange interactions at the interface.

  17. Development of ferret as a human lung cancer model by injecting4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Development of new animal lung cancer models that are relevant to human lung carcinogenesis is important for lung cancer research. Previously we have shown the induction of lung tumor in ferrets (Mustela putorius furo) exposed to both tobacco smoke and a tobacco carcinogen (4-(N-methyl-N-nitrosamino...

  18. Revealing the local properties of β-HP4N7, a promising candidate for high pressure synthesis of new materials

    NASA Astrophysics Data System (ADS)

    Morales-García, A.; del Corro, E.

    2015-04-01

    A computational investigation of β-HP4N7 system is accurately performed using the density functional theory formalism coupled with quantum theory of atoms in molecules. The aim of this work is to understand the behavior of β-HP4N7 under compression. At ambient conditions, the N atoms occupy around 81% of the unit cell volume; for this reason the N atoms are the ones contributing significantly to the bulk properties. The particular tetrahedron (PN4) connection promotes high flexibility to this structure. The atoms composing the solid show significant differences in their compressibilities. The high compressibility (or low resistence to pressure) of the N atoms indicates that the reorganization of these atoms is the key in the densification process that takes place when pressure is increased. When compresing the β-HP4N7 from 0 to 130 GPa the formation of PN6 units is observed, leading to a phase transition. The analysis of the elastic constants reveals the stability of this new phase at 110 GPa. This study shows that β-HP4N7 could be a potential candidate for high pressure synthesis of new phases where P atoms would be 6-fold coordinated.

  19. DNA encoding a DNA repair protein

    DOEpatents

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  20. Managing DNA polymerases: coordinating DNA replication, DNA repair, and DNA recombination.

    PubMed

    Sutton, M D; Walker, G C

    2001-07-17

    Two important and timely questions with respect to DNA replication, DNA recombination, and DNA repair are: (i) what controls which DNA polymerase gains access to a particular primer-terminus, and (ii) what determines whether a DNA polymerase hands off its DNA substrate to either a different DNA polymerase or to a different protein(s) for the completion of the specific biological process? These questions have taken on added importance in light of the fact that the number of known template-dependent DNA polymerases in both eukaryotes and in prokaryotes has grown tremendously in the past two years. Most notably, the current list now includes a completely new family of enzymes that are capable of replicating imperfect DNA templates. This UmuC-DinB-Rad30-Rev1 superfamily of DNA polymerases has members in all three kingdoms of life. Members of this family have recently received a great deal of attention due to the roles they play in translesion DNA synthesis (TLS), the potentially mutagenic replication over DNA lesions that act as potent blocks to continued replication catalyzed by replicative DNA polymerases. Here, we have attempted to summarize our current understanding of the regulation of action of DNA polymerases with respect to their roles in DNA replication, TLS, DNA repair, DNA recombination, and cell cycle progression. In particular, we discuss these issues in the context of the Gram-negative bacterium, Escherichia coli, that contains a DNA polymerase (Pol V) known to participate in most, if not all, of these processes.

  1. DNA polymerases and cancer

    PubMed Central

    Lange, Sabine S.; Takata, Kei-ichi; Wood, Richard D.

    2013-01-01

    There are fifteen different DNA polymerases encoded in mammalian genomes, which are specialized for replication, repair or the tolerance of DNA damage. New evidence is emerging for lesion-specific and tissue-specific functions of DNA polymerases. Many point mutations that occur in cancer cells arise from the error-generating activities of DNA polymerases. However, the ability of some of these enzymes to bypass DNA damage may actually defend against chromosome instability in cells and at least one DNA polymerase, POLζ, is a suppressor of spontaneous tumorigenesis. Because DNA polymerases can help cancer cells tolerate DNA damage, some of these enzymes may be viable targets for therapeutic strategies. PMID:21258395

  2. DNA-modified Electrodes Fabricated using Copper-Free Click Chemistry for Enhanced Protein Detection

    PubMed Central

    Furst, Ariel L.; Hill, Michael G.; Barton, Jacqueline K.

    2014-01-01

    A method of DNA monolayer formation has been developed using copper-free click chemistry that yields enhanced surface homogeneity and enables variation in the amount of DNA assembled; extremely low-density DNA monolayers, with as little as 5% of the monolayer being DNA, have been formed. These DNA-modified electrodes (DMEs) were characterized visually, with AFM, and electrochemically, and were found to facilitate DNA-mediated reduction of a distally bound redox probe. These low-density monolayers were found to be more homogeneous than traditional thiol-modified DNA monolayers, with greater helix accessibility through an increased surface area-to-volume ratio. Protein binding efficiency of the transcriptional activator TATA-binding protein (TBP) was also investigated on these surfaces and compared to that on DNA monolayers formed with standard thiol-modified DNA. Our low-density monolayers were found to be extremely sensitive to TBP binding, with a signal decrease in excess of 75% for 150 nM protein. This protein was detectable at 4 nM, on the order of its dissociation constant, with our low-density monolayers. The improved DNA helix accessibility and sensitivity of our low-density DNA monolayers to TBP binding reflects the general utility of this method of DNA monolayer formation for DNA-based electrochemical sensor development. PMID:24328347

  3. Cloning and comparative mapping of a human chromosome 4-specific alpha satellite DNA sequence

    SciTech Connect

    D'Aiuto, L.; Marzella, R.; Archidiacono, N.; Rocchi, M. ); Antonacci, R. )

    1993-11-01

    The authors have isolated and characterized two human alphoid DNA clones: p4n1/4 and pZ4.1. Clone p4n1/4 identifies specifically the centromeric region of chromosome 4; pZ4.1 recognizes a subset of alphoid DNA shared by chromosomes 4 and 9. The specificity was determined using fluorescence in situ hybridization experiments on metaphase spreads and Southern blotting analysis of human-hamster somatic cell hybrids. The genomic organization of both subsets was also investigated. Comparative mapping on chimpanzee and gorilla chromosomes was performed. p4n1/4 hybridizes to chimpanzee chromosomes 11 and 13, homologs of human chromosomes 9 and 2q, respectively. On gorilla metaphase spreads, p4n1/4 hybridizes exclusively to the centromeric region of chromosome 19, partially homologous to human chromosome 17. No hybridization signal was detected on chromosome 3 of both chimpanzee and gorilla, in both species homolog of human chromosome 4. Identical comparative mapping results were obtained using pZ4.1 probe, although the latter recognizes an alphoid subset distinct from the one recognized by p4n1/4. The implications of these results in the evolution of centromeric regions of primate chromosomes are discussed. 33 refs., 4 figs.

  4. qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

    SciTech Connect

    Jackson, Christopher B.; Gallati, Sabina; Schaller, Andre

    2012-07-06

    Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in

  5. 59 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    1994-10-25

    ... From the Federal Register Online via the Government Printing Office ] CONTENTS Vol. 59, No. 205 Tuesday, October 25, 1994 Agricultural Marketing Service RULES Kiwifruit grown in California, 53563-53565... carbon monoxide content; report availability, 53650 Premerger notification waiting periods;...

  6. Plasticity and ab initio characterizations on Fe 4N produced on the surface of nanocrystallized 18Ni-maraging steel plasma nitrided at lower temperature

    NASA Astrophysics Data System (ADS)

    Yan, M. F.; Wu, Y. Q.; Liu, R. L.

    2009-08-01

    18Ni-maraging steel has been entirely nanocrystallized by a series of processes including solution treatment, hot-rolling deformation, cold-drawn deformation and direct electric heating. The plasma nitriding of nanocrystallized 18Ni-maraging steel was carried out at 410 °C for 3 h and 6 h in a mixture gas of 20% N 2 + 80% H 2 with a pressure of 400 Pa. The surface phase constructions and nitrogen concentration profile in surface layer were analyzed using an X-ray diffractometer (XRD) and the glow discharge spectrometry (GDS), respectively. The results show that an about 2 μm thick compound layer (mono-phase γ'-Fe 4N) can be produced on the top of the surface layer of nanocrystallized 18Ni-maraging steel plasma nitrided at 410 °C for 6 h. The measured hardness value of the nitrided surface is 11.6 GPa. More importantly, the γ'-Fe 4N phase has better plasticity, i.e., its plastic deformation energy calculated from the load-displacement curve obtained by nano-indentation tester is close to that of nanocrystallized 18Ni-maraging steel. Additionally, the mechanical properties of γ'-Fe 4N phase were also characterized by first-principles calculations. The calculated results indicate that the hardness value and the ratio of bulk to shear modulus ( B/ G) of the γ'-Fe 4N phase are 10.15 GPa and 3.12 (>1.75), respectively. This demonstrates that the γ'-Fe 4N phase has higher hardness and better ductility.

  7. Presequence-Independent Mitochondrial Import of DNA Ligase Facilitates Establishment of Cell Lines with Reduced mtDNA Copy Number

    PubMed Central

    Spadafora, Domenico; Kozhukhar, Natalia; Alexeyev, Mikhail F.

    2016-01-01

    Due to the essential role played by mitochondrial DNA (mtDNA) in cellular physiology and bioenergetics, methods for establishing cell lines with altered mtDNA content are of considerable interest. Here, we report evidence for the existence in mammalian cells of a novel, low- efficiency, presequence-independent pathway for mitochondrial protein import, which facilitates mitochondrial uptake of such proteins as Chlorella virus ligase (ChVlig) and Escherichia coli LigA. Mouse cells engineered to depend on this pathway for mitochondrial import of the LigA protein for mtDNA maintenance had severely (up to >90%) reduced mtDNA content. These observations were used to establish a method for the generation of mouse cell lines with reduced mtDNA copy number by, first, transducing them with a retrovirus encoding LigA, and then inactivating in these transductants endogenous Lig3 with CRISPR-Cas9. Interestingly, mtDNA depletion to an average level of one copy per cell proceeds faster in cells engineered to maintain mtDNA at low copy number. This makes a low-mtDNA copy number phenotype resulting from dependence on mitochondrial import of DNA ligase through presequence-independent pathway potentially useful for rapidly shifting mtDNA heteroplasmy through partial mtDNA depletion. PMID:27031233

  8. Detecting DNA regulatory motifs by incorporating positional trendsin information content

    SciTech Connect

    Kechris, Katherina J.; van Zwet, Erik; Bickel, Peter J.; Eisen,Michael B.

    2004-05-04

    On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

  9. Content-Based Instruction.

    ERIC Educational Resources Information Center

    CATESOL Journal, 1992

    1992-01-01

    This English-as-a-Second Language (ESL) journal periodical devotes entire issues to specific issues. The theme of this issue is "Content-Base Instruction." Articles include: "Syllabus Design in Content-Based Instruction" (David E. Eskey); "How Relevant Is Relevance?: An Examination of Student Needs, Interests, and Motivation in the Content-Based…

  10. 67 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    2002-05-31

    ... From the Federal Register Online via the Government Publishing Office #0; #0; #0; CONTENTS #0; #0...;/&thnsp;Contents#0;#0; ] Agency for International Development NOTICES Agency information collection... subscribe to the Federal Register Table of Contents LISTSERV electronic mailing list, go to...

  11. Raman spectroscopy for DNA quantification in cell nucleus.

    PubMed

    Okotrub, K A; Surovtsev, N V; Semeshin, V F; Omelyanchuk, L V

    2015-01-01

    Here we demonstrate the feasibility of a novel approach to quantify DNA in cell nuclei. This approach is based on spectroscopy analysis of Raman light scattering, and avoids the problem of nonstoichiometric binding of dyes to DNA, as it directly measures the signal from DNA. Quantitative analysis of nuclear DNA contribution to Raman spectrum could be reliably performed using intensity of a phosphate mode at 1096 cm(-1) . When compared to the known DNA standards from cells of different animals, our results matched those values at error of 10%. We therefore suggest that this approach will be useful to expand the list of DNA standards, to properly adjust the duration of hydrolysis in Feulgen staining, to assay the applicability of fuchsines for DNA quantification, as well as to measure DNA content in cells with complex hydrolysis patterns, when Feulgen densitometry is inappropriate.

  12. Mitochondrial DNA mutations in ageing and disease: implications for HIV?

    PubMed

    Payne, Brendan A I; Gardner, Kristian; Chinnery, Patrick F

    2015-01-01

    Mitochondrial DNA (mtDNA) mutations cause neurological and multisystem disease. Somatic (acquired) mtDNA mutations are also associated with degenerative diseases and with normal human ageing. It is well established that certain nucleoside reverse transcriptase inhibitor (NRTI) antiretroviral drugs cause inhibition of the mtDNA polymerase, pol γ, leading to a reduction in mtDNA content (depletion). Given this effect of NRTI therapy on mtDNA replication, it is plausible that NRTI treatment may also lead to increased mtDNA mutations. Here we review recent evidence for an effect of HIV infection or NRTI therapy on mtDNA mutations, as well as discussing the methodological challenges in addressing this question. Finally, we discuss the possible implications for HIV-infected persons, with particular reference to ageing.

  13. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOEpatents

    Dolbeare, F.A.; Gray, J.W.

    1983-10-18

    A method for the simultaneous flow cylometric measurement of total cellular DNA content and of the uptake of DNA precursors as a measure of DNA synthesis during various phases of the cell cycle in normal and malignant cells in vitro and in vivo is described. The method comprises reacting cells with labelled halodeoxyuridine (HdU), partially denaturing cellular DNA, adding to the reaction medium monoclonal antibodies (mabs) reactive with HdU, reacting the bound mabs with a second labelled antibody, incubating the mixture with a DNA stain, and measuring simultaneously the intensity of the DNA stain as a measure of the total cellular DNA and the HdU incorporated as a measure of DNA synthesis. (ACR)

  14. DNA Nanotechnology-- Architectures Designed with DNA

    NASA Astrophysics Data System (ADS)

    Han, Dongran

    As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.

  15. DNA vaccines: a simple DNA sensing matter?

    PubMed

    Coban, Cevayir; Kobiyama, Kouji; Jounai, Nao; Tozuka, Miyuki; Ishii, Ken J

    2013-10-01

    Since the introduction of DNA vaccines two decades ago, this attractive strategy has been hampered by its low immunogenicity in humans. Studies conducted to improve the immunogenicity of DNA vaccines have shown that understanding the mechanism of action of DNA vaccines might be the key to successfully improving their immunogenicity. Our current understanding is that DNA vaccines induce innate and adaptive immune responses in two ways: (1) encoded protein (or polypeptide) antigen(s) by the DNA plasmid can be expressed in stromal cells (i.e., muscle cells) as well as DCs, where these antigens are processed and presented to naïve CD4 or CD8 T cells either by direct or cross presentation, respectively; and (2) the transfected DNA plasmid itself may bind to an un-identified cytosolic DNA sensor and activate the TBK1-STING pathway and the production of type I interferons (IFNs) which function as an adjuvant. Recent studies investigating double-stranded cytosolic DNA sensor(s) have highlighted new mechanisms in which cytosolic DNA may release secondary metabolites, which are in turn recognized by a novel DNA sensing machinery. Here, we discuss these new metabolites and the possibilities of translating this knowledge into improved immunogenicity for DNA vaccines.

  16. Photoprotection by topical DNA repair enzymes: molecular correlates of clinical studies.

    PubMed

    Yarosh, D B; O'Connor, A; Alas, L; Potten, C; Wolf, P

    1999-02-01

    A new approach to photoprotection is to repair DNA damage after UV exposure. This can be accomplished by delivery of a DNA repair enzyme with specificity to UV-induced cyclobutane pyrimidine dimers into skin by means of specially engineered liposomes. Treatment of DNA-repair-deficient xeroderma pigmentosum patients or skin cancer patients with T4N5 liposome lotion containing such DNA repair liposomes increases the removal of DNA damage in the first few hours after treatment. In these studies, a DNA repair effect was observed in some patients treated with heat-inactivated enzyme. Unexpectedly, it was discovered that the heat-inactivated T4 endonuclease V enzyme refolds and recovers enzymatic activity. These studies demonstrate that measurements of molecular changes induced by biological drugs are useful adjuvants to clinical studies.

  17. Naturalising Representational Content

    PubMed Central

    Shea, Nicholas

    2014-01-01

    This paper sets out a view about the explanatory role of representational content and advocates one approach to naturalising content – to giving a naturalistic account of what makes an entity a representation and in virtue of what it has the content it does. It argues for pluralism about the metaphysics of content and suggests that a good strategy is to ask the content question with respect to a variety of predictively successful information processing models in experimental psychology and cognitive neuroscience; and hence that data from psychology and cognitive neuroscience should play a greater role in theorising about the nature of content. Finally, the contours of the view are illustrated by drawing out and defending a surprising consequence: that individuation of vehicles of content is partly externalist. PMID:24563661

  18. Quantitative DNA fiber mapping

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich G.

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  19. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOEpatents

    Dolbeare, Frank A.; Gray, Joe W.

    1988-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide or Hoechst 33258 is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as halodeoxy-uridine (HdU), more specifically bromodeoxyuridine (BrdU) is used as a probe for the measurement of HdU or BrdU uptake by the cells as a measure of DNA synthesis.

  20. Greenhouse gas (CO2, CH4, N2O) emissions from soils following afforestation in central China

    NASA Astrophysics Data System (ADS)

    Dou, Xiaolin; Zhou, Wei; Zhang, Quanfa; Cheng, Xiaoli

    2016-02-01

    The effects of afforestation are of great importance for terrestrial carbon sequestration. However, the consequences of afforestation for greenhouse gas (GHG, CO2, CH4 and N2O) fluxes remain poorly quantified. We investigate the temporal variations in CO2, CH4 and N2O fluxes in afforested soils (implementing woodland and shrubland) and the adjacent uncultivated area in the Danjiangkou Reservoir area of central China. We examined the effects of soil factors [e.g. soil temperature, soil moisture, soil pH, soil organic carbon (SOC), soil organic nitrogen (SON)], litter exclusion and vegetation types on GHG fluxes. Our results revealed that afforestation lead to a higher average CO2 flux from soils by 63.96% and a higher N2O flux by 54.53% in the observed year. The peak CO2 and CH4 fluxes from afforested soils occurred in summer, while the peak N2O flux occurred in winter. Afforestation also enhanced CH4 flux from soil with the largest increase by 247.94% in woodland and by 188.18% in shrubland in spring compared with the open area. On average, surface litter exclusion reduced soil CO2 fluxes by 18.84% and N2O fluxes by 27.93% in the woodland. The surface litter exclusion did not significantly affect CH4 flux from the afforested soils. The CO2, CH4 and N2O fluxes from soils were strongly influenced by soil temperature, moisture and SOC content across seasons. The N2O flux was also strongly affected by SON content in our experimental field. Our results suggested that afforestation enhanced GHG fluxes from soils; however, the magnitude of the GHG fluxes should also be considered from various environmental conditions and vegetation types.

  1. Assessment of efficacy, safety, and tolerability of 4-n-butylresorcinol 0.3% cream: an Indian multicentric study on melasma

    PubMed Central

    Madan Mohan, NT; Gowda, Adarsh; Jaiswal, Ashok Kumar; Sharath Kumar, BC; Shilpashree, P; Gangaboraiah, Bilugumba; Shamanna, Manjula

    2016-01-01

    Introduction Melasma is one of the commonly reported pigmentory disorders in the Indian population. Numerous therapeutic modalities are available. However, very few have produced complete satisfactory response. 4-n-Butylresorcinol 0.3% cream has recently been introduced in India as a new hypopigmenting agent. It is a resorcinol derivative and acts by inhibiting both tyrosinase and tyrosinase-related protein-1. Objective The available published literatures are with 4-n-butylresorcinol 0.1% cream, and there is paucity of clinical studies with 4-n-butylresorcinol 0.3% cream. Furthermore, considering the fact that Indian skin is more prone to irritation with hypopigmenting agents, our study explores the efficacy, safety, and tolerability of 4-n-butylresorcinol 0.3% cream in Indian subjects with melasma. Methods Fifty-two subjects with melasma participated in this open-label, single arm, observational study. All the patients were advised twice daily application of 4-n-butylresorcinol 0.3% cream for 8 weeks over the areas of melasma. Assessment parameters included modified Melasma Area Severity Index (mMASI) score. Digital photographs of all the patients at baseline, week 4, and week 8 were taken. During this 8-week study period, all the adverse events were observed and recorded. Results All the 52 subjects completed the study. Out of 52 subjects, 90.38% were females. The mean age of patients was 38.5±7.8 years. Mean ± standard error of MASI score measurements showed a significant decrease from baseline score of 14.73±0.59 to 11.09±0.53 after week 4 (P<0.001) and 6.48±0.43 at week 8 (P<0.001). The digital photographs of the study subjects taken at week 4 and week 8 also showed decrease in melasma pigmentation compared to baseline photograph and correlated with the changes in the mMASI score. The treatment was well tolerated by all the study subjects. No adverse reactions were reported throughout the study period. Conclusion Our data suggest that the 4-n

  2. Heterogeneous base distribution in mitochondrial DNA of Neurospora crassa.

    PubMed Central

    Terpstra, P; Holtrop, M; Kroon, A

    1977-01-01

    The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+C rich, part of the genome. PMID:141040

  3. Variable DNA methylation changes during differentiation of human melanoma cells.

    PubMed

    Steigerwald, S D; Pfeifer, G P

    1988-09-01

    The DNA 5-methylcytosine content has been analyzed in the human melanoma cell line M21 at several time points after induction of differentiation by a variety of inducers. 5-Aza-2'-deoxycytidine reduces DNA methylation to about 50% of the control level and this demethylation occurs prior to the establishment of the differentiated phenotype. The DNA synthesis inhibitors cytosine arabinoside, aphidicolin, and hydroxyurea exert different effects on DNA methylation in these cells. Cytosine arabinoside induces an early DNA hypermethylation, which is however reversible and drops to the original level after 24 h. Hydroxyurea induces DNA hypermethylation after a lag period of more than 48 h and the DNA polymerase alpha inhibitor aphidicolin has no effect on the DNA methylation level. Treatment of cells with phorbol 12-myristate 13-acetate, another potent inducer of melanoma cell differentiation, does not result in a change of total DNA methylation over a period of 96 h. These results indicate that differentiation of human melanoma cells can be accompanied by variable changes of the DNA methylation pattern. These changes can be neither generally related to the differentiation process itself nor related to the effects of DNA synthesis inhibition on DNA methylation, but may more likely reflect a direct or indirect particular effect of the inducer on the DNA methylation process.

  4. Perpendicular magnetic anisotropy of Mn{sub 4}N films on MgO(001) and SrTiO{sub 3}(001) substrates

    SciTech Connect

    Yasutomi, Yoko; Ito, Keita; Sanai, Tatsunori; Toko, Kaoru; Suemasu, Takashi

    2014-05-07

    We grew Mn{sub 4}N epitaxial thin films capped with Au layers on MgO(001) and SrTiO{sub 3}(001) substrates by molecular beam epitaxy. Perpendicular magnetic anisotropy (PMA) was confirmed in all the samples at room temperature from the magnetization versus magnetic field curves using superconducting quantum interference device magnetometer. From the ω-2θ x-ray diffraction (XRD) and ϕ-2θ{sub χ} XRD patterns, the ratios of perpendicular lattice constant c to in-plane lattice constant a, c/a, were found to be about 0.99 for all the samples. These results imply that PMA is attributed to the in-plane tensile strain in the Mn{sub 4}N films.

  5. Synthesis, characterization and electrochemical performance of graphene decorated with 1D NiMoO4.nH2O nanorods

    NASA Astrophysics Data System (ADS)

    Ghosh, Debasis; Giri, Soumen; Das, Chapal Kumar

    2013-10-01

    One-dimensional NiMoO4.nH2O nanorods and their graphene based hybrid composite with good electrochemical properties have been synthesized by a cost effective hydrothermal procedure. The formation of the mixed metal oxide and the composite was confirmed by XRD, XPS and Raman analyses. The morphological characterizations were carried out using FESEM and TEM analyses. The materials were subjected to electrochemical characterization through cyclic voltammetry (CV), galvanostatic charge-discharge (GCD) and electrochemical impedance spectroscopy (EIS) studies with 6 M KOH as the supporting electrolyte. For NiMoO4.nH2O, a maximum specific capacitance of 161 F g-1 was obtained at 5 A g-1 current density, accompanied with an energy density of 4.53 W h kg-1 at a steady power delivery rate of 1125 W kg-1. The high utility of the pseudocapacitive NiMoO4.nH2O was achieved in its graphene based composite, which exhibited a high specific capacitance of 367 F g-1 at 5 A g-1 current density and a high energy density of 10.32 W h kg-1 at a power density of 1125 W kg-1 accompanied with long term cyclic stability.One-dimensional NiMoO4.nH2O nanorods and their graphene based hybrid composite with good electrochemical properties have been synthesized by a cost effective hydrothermal procedure. The formation of the mixed metal oxide and the composite was confirmed by XRD, XPS and Raman analyses. The morphological characterizations were carried out using FESEM and TEM analyses. The materials were subjected to electrochemical characterization through cyclic voltammetry (CV), galvanostatic charge-discharge (GCD) and electrochemical impedance spectroscopy (EIS) studies with 6 M KOH as the supporting electrolyte. For NiMoO4.nH2O, a maximum specific capacitance of 161 F g-1 was obtained at 5 A g-1 current density, accompanied with an energy density of 4.53 W h kg-1 at a steady power delivery rate of 1125 W kg-1. The high utility of the pseudocapacitive NiMoO4.nH2O was achieved in its graphene

  6. Mechanism of extraordinary DNA digestion by pepsin.

    PubMed

    Zhang, Yanfang; Li, Chunchuan; Liu, Yu; Wang, Xiaoqian; Dong, Ping; Liang, Xingguo

    2016-03-25

    Recently, the protein-specific enzyme pepsin was found be capable of digesting nucleic acids unexpectedly. In this study, the effects of DNA sequence specificity, purine content (AG content), depurination and length on the nucleic acid (NA) digestion by pepsin were investigated. The results showed that pepsin functioned similar as endonuclease, and presented a moderate sequence preference compared with restriction enzymes and non-specific nuclease. The digestion was specific (sequence dependent to some extent), and pepsin preferred to cleave purine-rich sequences. The digestion of favorable sequence was dramatically accelerated when the purine base at the cleavage site was removed (created an apurinic (AP) site). However, the AP site did not help to cleave the sequence that pepsin could not cleave originally. Moreover, the results indicated that pepsin preferred to digest longer DNA (e.g. > 59 bases) than shorter one, and sequence shorter than 30 bases was barely digested. The mechanism of DNA digestion by pepsin was also discussed.

  7. The first quaternary lanthanide(III) nitride iodides: NaM{sub 4}N{sub 2}I{sub 7} (M=La-Nd)

    SciTech Connect

    Schurz, Christian M.; Schleid, Thomas

    2010-10-15

    In attempts to synthesize lanthanide(III) nitride iodides with the formula M{sub 2}NI{sub 3} (M=La-Nd), moisture-sensitive single crystals of the first quaternary sodium lanthanide(III) nitride iodides NaM{sub 4}N{sub 2}I{sub 7} (orthorhombic, Pna2{sub 1}; Z=4; a=1391-1401, b=1086-1094, c=1186-1211 pm) could be obtained. The dominating structural features are {sup 1}{sub {infinity}}{l_brace}[NM{sub 4/2}{sup e}]{sup 3+}{r_brace} chains of trans-edge linked [NM{sub 4}]{sup 9+} tetrahedra, which run parallel to the polar 2{sub 1}-axis [001]. Between the chains, direct bonding via special iodide anions generates cages, in which isolated [NaI{sub 6}]{sup 5-} octahedra are embedded. The IR spectrum of NaLa{sub 4}N{sub 2}I{sub 7} recorded from 100 to 1000 cm{sup -1} shows main bands at {upsilon}=337, 373 and 489 cm{sup -1}. With decreasing radii of the lanthanide trications these bands, which can be assigned as an influence of the vibrations of the condensed [NM{sub 4}]{sup 9+} tetrahedra, are shifted toward higher frequencies for the NaM{sub 4}N{sub 2}I{sub 7} series (M=La-Nd), following the lanthanide contraction. - Abstract: View at the main structural features of the NaM{sub 4}N{sub 2}I{sub 7} series (M=La-Nd): The {sup 1}{sub {infinity}}{l_brace}[NM{sub 4/2}{sup e}]{sup 3+}{r_brace} chains, consisting of trans-edge connected [NM{sub 4}]{sup 9+} tetrahedra, and the special kind of iodide anions, namely (I7){sup -}, form cages, in which isolated [NaI{sub 6}]{sup 5-} octahedra are embedded.

  8. [Seasonal variation patterns of NH4(+) -N/NO3(-) -N ratio and delta 15 NH4(+) value in rainwater in Yangtze River Delta].

    PubMed

    Xie, Ying-Xin; Zhang, Shu-Li; Zhao, Xu; Xiong, Zheng-Qin; Xing, Guang-Xi

    2008-09-01

    By using a customized manual rainwater sampler made of polyvinyl chloride plastic, the molar ratio of NH4(+) -N/NO3(-) -N and the natural 15N abundance of NH4(+) (delta 15 NH4(+) in rainwater was monitored all year round from June 2003 to July 2005 at three observation sites (Changshu, Nanjing, and Hangzhou) in the Yangtze River Delta. The results indicated that at the three sites, the NH4(+) -N/NO3(-) -N ratio and the delta 15 NH4(+) value in rainwater had the similar seasonal variation trend, being more obvious in Changshu (rural monitoring type) site than in Nanjing (urban monitoring type) and Hangzhou (urban-rural monitoring type) sites. The NH4(+) -N/NO3(-) -N ratio peaked from early June to early August, declined gradually afterwards, and reached the bottom in winter; while the delta 15 NH4(+) value was negative from late June to mid-August, turned positive from late August to mid or late November, became negative again when winter dominated from December to March, but turned positive again in next May and negative again in next July. These seasonal variation patterns of NH4(+) -N/NO3(-) -N ratio and delta 15 NH4(+) value were found in relation to the application of chemical nitrogen fertilizers during different crop growth periods, and also, the alternation of seasons and the NH3 volatilization from other NH3 emission sources (including excrements of human and animals, nitrogen- polluted water bodies, and organic nitrogen sources, etc.), which could be taken as an indicator of defining the sources and form composition of NH4(+) in atmospheric wet deposition and the intensity of various terrestrial NH3 emission sources.

  9. Synthesis and characterization of a cadmium bipyridinium compound (CdCl{sub 4})(N,N'-dimethyl-2,2'-bipyridinium)

    SciTech Connect

    Luo, Hui; Zhu, Li-Cheng; Wang, Qi

    2015-12-15

    A cadmium bipyridinium compound (CdCl{sub 4})(N,N'-dimethyl-2,2'-bipyridinium), in which the (N,N'-dimethyl-2,2'-bipyridinium){sup 2+} moieties were generated in situ, has been prepared via solvothermal reactions and structurally characterized with single crystal X-ray diffraction method. Fluorescence measurement revealed a broad and strong emission band in the blue region.

  10. Synthesis and evaluation of substituted 4-(N-benzylamino)cinnamate esters as potential anti-cancer agents and HIV-1 integrase inhibitors.

    PubMed

    Faridoon; Edkins, Adrienne L; Isaacs, Michelle; Mnkandhla, Dumisani; Hoppe, Heinrich C; Kaye, Perry T

    2016-08-01

    Encouraging selectivity and low micromolar activity against HeLa cervical carcinoma (IC50⩾3.0μM) and the aggressive MDA-MB-231 triple negative breast carcinoma (IC50⩾9.6μM) cell lines has been exhibited by a number of readily accessible 4-(N-benzylamino)cinnamate esters. The potential of the ligands as HIV-1 integrase inhibitors has also been examined. PMID:27317645

  11. Pharmacological stress is required for the anti-alcohol effect of the α3β4* nAChR partial agonist AT-1001.

    PubMed

    Cippitelli, Andrea; Brunori, Gloria; Gaiolini, Kelly A; Zaveri, Nurulain T; Toll, Lawrence

    2015-06-01

    Alcohol and nicotine are often taken together. The mechanisms underlying this frequent co-abuse are not well known. Genetic and pharmacological evidence suggests that the nicotinic acetylcholine receptors (nAChRs) containing the α3 and β4 subunits play a role in alcohol as well as nicotine addiction. AT-1001 is a high affinity α3β4 nAChR partial agonist recently found to block nicotine self-administration and relapse-like behavior in rats. Here, to study the involvement of α3β4 nAChRs in the mechanisms that regulate alcohol abuse we evaluated the effects of AT-1001 on alcohol taking and seeking in Sprague-Dawley rats. AT-1001 reduced operant alcohol self-administration at the highest dose examined (3.0 mg/kg), an effect also observed for food self-administration. A dose of 1.5 mg/kg AT-1001, which had no effect on alcohol or food self-administration, essentially eliminated reinstatement of alcohol seeking induced by yohimbine (0.625 mg/kg) whereas, reinstatement induced by alcohol-associated cues was not altered, nor did AT-1001 induce reinstatement of extinguished self-administration on its own. Finally, AT-1001 showed an anxiolytic activity when measured in the presence or absence of yohimbine stress in the elevated plus maze paradigm. Together, these observations do not support a specific involvement of the α3β4 nAChR in mediating alcohol reward or cue-induced relapse to alcohol seeking but rather indicate that the α3β4 nAChR partial agonism may constitute an attractive approach for treating alcohol use disorders exacerbated by elevated stress response.

  12. DNA Damage, DNA Repair, Aging, and Neurodegeneration.

    PubMed

    Maynard, Scott; Fang, Evandro Fei; Scheibye-Knudsen, Morten; Croteau, Deborah L; Bohr, Vilhelm A

    2015-09-18

    Aging in mammals is accompanied by a progressive atrophy of tissues and organs, and stochastic damage accumulation to the macromolecules DNA, RNA, proteins, and lipids. The sequence of the human genome represents our genetic blueprint, and accumulating evidence suggests that loss of genomic maintenance may causally contribute to aging. Distinct evidence for a role of imperfect DNA repair in aging is that several premature aging syndromes have underlying genetic DNA repair defects. Accumulation of DNA damage may be particularly prevalent in the central nervous system owing to the low DNA repair capacity in postmitotic brain tissue. It is generally believed that the cumulative effects of the deleterious changes that occur in aging, mostly after the reproductive phase, contribute to species-specific rates of aging. In addition to nuclear DNA damage contributions to aging, there is also abundant evidence for a causative link between mitochondrial DNA damage and the major phenotypes associated with aging. Understanding the mechanistic basis for the association of DNA damage and DNA repair with aging and age-related diseases, such as neurodegeneration, would give insight into contravening age-related diseases and promoting a healthy life span.

  13. High capacity and superlong cycle life of Li3VO4/N-C hybrids as anode for high performance Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Zhang, Jicheng; Ni, Shibing; Ma, Jianjun; Yang, Xuelin; Zhang, Lulu

    2016-01-01

    High capacity and superlong cycle life of Li3VO4 have been actualized via carbon hybridization and N doping. The Li3VO4/N doped C (Li3VO4/N-C) that fabricated via an in situ carbonization method based on an intermedial solution phase delivers initial discharge and charge capacities of 686 and 540 mAh g-1 at a specific current of 0.15 A g-1, which maintain of 538 and 536 mAh g-1 after 800 cycles, showing excellent cycle stability. Meanwhile, the Li3VO4/N-C exhibits superior rate performance and long life performance. After 150 cycles at various specific currents from 0.1 to 2.0 A g-1, the discharge and charge capacities can restore 100% when reverting the specific current to 0.1 A g-1. After 1100 cycles at a specific current of 2.0 A g-1, the discharge and charge capacities can maintain of 340 and 337 mAh g-1, showing no capacity attenuation in cycling.

  14. Coexistence of Three Ferroic Orders in the Multiferroic Compound [(CH3 )4 N][Mn(N3 )3 ] with Perovskite-Like Structure.

    PubMed

    Gómez-Aguirre, L Claudia; Pato-Doldán, Breogán; Stroppa, Alessandro; Yang, Li-Ming; Frauenheim, Thomas; Mira, Jorge; Yáñez-Vilar, Susana; Artiaga, Ramón; Castro-García, Socorro; Sánchez-Andújar, Manuel; Señarís-Rodríguez, María Antonia

    2016-06-01

    The perovskite azido compound [(CH3 )4 N][Mn(N3 )3 ], which undergoes a first-order phase change at Tt =310 K with an associated magnetic bistability, was revisited in the search for additional ferroic orders. The driving force for such structural transition is multifold and involves a peculiar cooperative rotation of the [MnN6 ] octahedral as well as order/disorder and off-center shifts of the [(CH3 )4 N](+) cations and bridging azide ligands, which also bend and change their coordination mode. According to DFT calculations the latter two give rise to the appearance of electric dipoles in the low-temperature (LT) polymorph, the polarization of which nevertheless cancels out due to their antiparallel alignment in the crystal. The conversion of this antiferroelectric phase to the paraelectric phase could be responsible for the experimental dielectric anomaly detected at 310 K. Additionally, the structural change involves a ferroelastic phase transition, whereby the LT polymorph exhibits an unusual and anisotropic thermal behavior. Hence, [(CH3 )4 N][Mn(N3 )3 ] is a singular material in which three ferroic orders coexist even above room temperature. PMID:27072487

  15. Spectroscopic studies of non-volatile residue formed by photochemistry of solid C4N2: A model of condensed aerosol formation on Titan

    NASA Astrophysics Data System (ADS)

    Couturier-Tamburelli, Isabelle; Gudipati, Murthy S.; Lignell, Antti; Jacovi, Ronen; Piétri, Nathalie

    2014-05-01

    Following our recent communication (Gudipati, M.S. et al. [2013]. Nat. Commun. 4, 1648. http://dx.doi.org/10.1038/ncomms2649) on the discovery of condensed-phase non-volatile polymeric material with similar spectral features as tholins, we present here a comprehensive spectroscopic study of photochemical formation of polymeric material from condensed dicyanoacetylene (C4N2) ice films. C4N2 is chosen as starting material for the laboratory simulations because of the detection of this and similar molecules (nitriles and cyanoacetylenes) in Titan’s atmosphere. UV-Vis and infrared spectra obtained during long-wavelength (>300 nm) photon irradiation and subsequent warming of the ice films are used to analyze changes in C4N2 ice, evolution of tholins, and derive photopolymerization mechanisms. Our data analysis revealed that many processes occur during the photolysis of condensed Titan’s aerosol analogs, including isomerization and polymerization leading to the formation of long-chain as well as aromatic cyclic polymer molecules. In the light of tremendous new data from the Cassini mission on the seasonal variations in Titan’s atmosphere, our laboratory study and its results provide fresh insight into the formation and evolution of aerosols and haze in Titan’s atmosphere.

  16. Calculation of the thermal conductivity of low-density CH4-N2 gas mixtures using an improved kinetic theory approach.

    PubMed

    Hellmann, Robert; Bich, Eckard; Vesovic, Velisa

    2016-04-01

    The thermal conductivity of low-density CH4-N2 gas mixtures has been calculated by means of the classical trajectory method using state-of-the-art intermolecular potential energy surfaces for the CH4-CH4, N2-N2, and CH4-N2 interactions. Results are reported in the temperature range from 70 K to 1200 K. Since the thermal conductivity is influenced by the vibrational degrees of freedom of the molecules, which are not included in the rigid-rotor classical trajectory computations, a new correction scheme to account for vibrational degrees of freedom in a dilute gas mixture is presented. The calculations show that the vibrational contribution at the highest temperature studied amounts to 46% of the total thermal conductivity of an equimolar mixture compared to 13% for pure nitrogen and 58% for pure methane. The agreement with the available experimental thermal conductivity data at room temperature is good, within ±1.4%, whereas at higher temperatures, larger deviations up to 4.5% are observed, which can be tentatively attributed to deteriorating performance of the measuring technique employed. Results are also reported for the magnitude and temperature dependence of the rotational collision number, Z(rot), for CH4 relaxing in collisions with N2 and for N2 relaxing in collisions with CH4. Both collision numbers increase with temperature, with the former being consistently about twice the value of the latter. PMID:27059564

  17. Local electronic states of Fe{sub 4}N films revealed by x-ray absorption spectroscopy and x-ray magnetic circular dichroism

    SciTech Connect

    Ito, Keita; Toko, Kaoru; Suemasu, Takashi; Takeda, Yukiharu; Saitoh, Yuji; Oguchi, Tamio; Kimura, Akio

    2015-05-21

    We performed x-ray absorption spectroscopy (XAS) and x-ray magnetic circular dichroism (XMCD) measurements at Fe L{sub 2,3} and N K-edges for Fe{sub 4}N epitaxial films grown by molecular beam epitaxy. In order to clarify the element specific local electronic structure of Fe{sub 4}N, we compared experimentally obtained XAS and XMCD spectra with those simulated by a combination of a first-principles calculation and Fermi's golden rule. We revealed that the shoulders observed at Fe L{sub 2,3}-edges in the XAS and XMCD spectra were due to the electric dipole transition from the Fe 2p core-level to the hybridization state generated by σ* anti-bonding between the orbitals of N 2p at the body-centered site and Fe 3d on the face-centered (II) sites. Thus, the observed shoulders were attributed to the local electronic structure of Fe atoms at II sites. As to the N K-edge, the line shape of the obtained spectra was explained by the dipole transition from the N 1s core-level to the hybridization state formed by π* and σ* anti-bondings between the Fe 3d and N 2p orbitals. This hybridization plays an important role in featuring the electronic structures and physical properties of Fe{sub 4}N.

  18. Calculation of the thermal conductivity of low-density CH4-N2 gas mixtures using an improved kinetic theory approach.

    PubMed

    Hellmann, Robert; Bich, Eckard; Vesovic, Velisa

    2016-04-01

    The thermal conductivity of low-density CH4-N2 gas mixtures has been calculated by means of the classical trajectory method using state-of-the-art intermolecular potential energy surfaces for the CH4-CH4, N2-N2, and CH4-N2 interactions. Results are reported in the temperature range from 70 K to 1200 K. Since the thermal conductivity is influenced by the vibrational degrees of freedom of the molecules, which are not included in the rigid-rotor classical trajectory computations, a new correction scheme to account for vibrational degrees of freedom in a dilute gas mixture is presented. The calculations show that the vibrational contribution at the highest temperature studied amounts to 46% of the total thermal conductivity of an equimolar mixture compared to 13% for pure nitrogen and 58% for pure methane. The agreement with the available experimental thermal conductivity data at room temperature is good, within ±1.4%, whereas at higher temperatures, larger deviations up to 4.5% are observed, which can be tentatively attributed to deteriorating performance of the measuring technique employed. Results are also reported for the magnitude and temperature dependence of the rotational collision number, Z(rot), for CH4 relaxing in collisions with N2 and for N2 relaxing in collisions with CH4. Both collision numbers increase with temperature, with the former being consistently about twice the value of the latter.

  19. Calculation of the thermal conductivity of low-density CH4-N2 gas mixtures using an improved kinetic theory approach

    NASA Astrophysics Data System (ADS)

    Hellmann, Robert; Bich, Eckard; Vesovic, Velisa

    2016-04-01

    The thermal conductivity of low-density CH4-N2 gas mixtures has been calculated by means of the classical trajectory method using state-of-the-art intermolecular potential energy surfaces for the CH4-CH4, N2-N2, and CH4-N2 interactions. Results are reported in the temperature range from 70 K to 1200 K. Since the thermal conductivity is influenced by the vibrational degrees of freedom of the molecules, which are not included in the rigid-rotor classical trajectory computations, a new correction scheme to account for vibrational degrees of freedom in a dilute gas mixture is presented. The calculations show that the vibrational contribution at the highest temperature studied amounts to 46% of the total thermal conductivity of an equimolar mixture compared to 13% for pure nitrogen and 58% for pure methane. The agreement with the available experimental thermal conductivity data at room temperature is good, within ±1.4%, whereas at higher temperatures, larger deviations up to 4.5% are observed, which can be tentatively attributed to deteriorating performance of the measuring technique employed. Results are also reported for the magnitude and temperature dependence of the rotational collision number, Zrot, for CH4 relaxing in collisions with N2 and for N2 relaxing in collisions with CH4. Both collision numbers increase with temperature, with the former being consistently about twice the value of the latter.

  20. Synthetic precursors for TCNQF4(2-) compounds: synthesis, characterization, and electrochemical studies of (Pr4N)2TCNQF4 and Li2TCNQF4.

    PubMed

    Lu, Jinzhen; Le, Thanh Hai; Traore, Daouda A K; Wilce, Matthew; Bond, Alan M; Martin, Lisandra L

    2012-12-01

    Careful control of the reaction stoichiometry and conditions enables the synthesis of both LiTCNQF(4) and Li(2)TCNQF(4) to be achieved. Reaction of LiI with TCNQF(4), in a 4:1 molar ratio, in boiling acetonitrile yields Li(2)TCNQF(4). However, deviation from this ratio or the reaction temperature gives either LiTCNQF(4) or a mixture of Li(2)TCNQF(4) and LiTCNQF(4). This is the first report of the large-scale chemical synthesis of Li(2)TCNQF(4). Attempts to prepare a single crystal of Li(2)TCNQF(4) have been unsuccessful, although air-stable (Pr(4)N)(2)TCNQF(4) was obtained by mixing Pr(4)NBr with Li(2)TCNQF(4) in aqueous solution. Pr(4)NTCNQF(4) was also obtained by reaction of LiTCNQF(4) with Pr(4)NBr in water. Li(2)TCNQF(4), (Pr(4)N)(2)TCNQF(4), and Pr(4)NTCNQF(4) have been characterized by UV-vis, FT-IR, Raman, and NMR spectroscopy, high resolution electrospray ionization mass spectrometry, and electrochemistry. The structures of single crystals of (Pr(4)N)(2)TCNQF(4) and Pr(4)NTCNQF(4) have been determined by X-ray crystallography. These TCNQF(4)(2-) salts will provide useful precursors for the synthesis of derivatives of the dianions. PMID:23153174

  1. Multimedia content description framework

    NASA Technical Reports Server (NTRS)

    Bergman, Lawrence David (Inventor); Kim, Michelle Yoonk Yung (Inventor); Li, Chung-Sheng (Inventor); Mohan, Rakesh (Inventor); Smith, John Richard (Inventor)

    2003-01-01

    A framework is provided for describing multimedia content and a system in which a plurality of multimedia storage devices employing the content description methods of the present invention can interoperate. In accordance with one form of the present invention, the content description framework is a description scheme (DS) for describing streams or aggregations of multimedia objects, which may comprise audio, images, video, text, time series, and various other modalities. This description scheme can accommodate an essentially limitless number of descriptors in terms of features, semantics or metadata, and facilitate content-based search, index, and retrieval, among other capabilities, for both streamed or aggregated multimedia objects.

  2. DNA from plant mitochondria.

    PubMed

    Suyama, Y; Bonner, W D

    1966-03-01

    DNA WAS ISOLATED FROM A MITOCHONDRIAL FRACTION OF EACH OF THE FOLLOWING PLANT MATERIALS: Mung bean (Phaseolus aureus) etiolated hypocotyl; turnip (Brassica rapa) root; sweet potato (Ipomoea batatas) root; and onion (Allium cepa) bulb. It was found that all of these mitochondrial fractions contained DNA, the densities of which were identical (rho=1.706 g.cm(-3)). An additional DNA (rho=1.695) band found in the mitochondrial fraction of Brassica rapa, was identical to DNA separately isolated from the chloroplast-rich fraction. The origin of the second DNA from Allium mitochondrial fraction was not identified.Contrary to the identity of the mitochondrial DNA, DNA from nuclear fractions differed not only with each other but from the corresponding mitochondrial DNA.DNA from Phaseolus and Brassica mitochondria showed the hyperchromicity characteristic of double stranded, native DNA upon heating; Tm's in 0.0195 Na(+) were the same; 72.0 degrees . The amount of DNA within the mitochondrion of Phaseolus was estimated to be 5.0 x 10(-10) mug; this estimate was made by isolating the mitochondrial DNA concomitantly with the known amount of added (15)N(2)H B. subtilis DNA (rho=1.740). Approximately the same amount of DNA was present in the mitochondrion of Brassica or Ipomoea.

  3. An improved electroelution method for separation of DNA from humic substances in marine sediment DNA extracts.

    PubMed

    Kallmeyer, Jens; Smith, David C

    2009-07-01

    We present a method for the rapid and simple extraction of DNA from marine sediments using electroelution. It effectively separates DNA from compounds, including humic substances, that interfere with subsequent DNA quantification and amplification. After extraction of the DNA from the sediment into an aqueous solution, the crude sample is encased in 2% agarose gel and exposed to an electrical current, which draws the DNA out of the gel into a centrifugal filter vial. After electroelution, the sample is centrifuged to remove contaminants DNA using this method is quantitative and does not discriminate on the basis of size, as determined using DNA standards and DNA extracts from environmental samples. Amplification of DNA is considerably improved due to removal of PCR inhibitors. For Archaea, only these purified extracts yielded PCR products. This method allows for the use of relatively large volumes of sediment and is particularly useful for sediments containing low biomass such as deeply buried marine sediments. It works with both organic-rich and -poor sediment, as well as with sediment where calcium carbonate is abundant and sediment where it is limited; consequently, adjustment of protocols is unnecessary for samples with very different organic and mineral contents.

  4. Mitochondrial DNA Copy Number in Spermatozoa of Fertile Stallions.

    PubMed

    Orsztynowicz, M; Pawlak, P; Podstawski, Z; Nizanski, W; Partyka, A; Gotowiecka, M; Kosiniak-Kamysz, K; Lechniak, D

    2016-06-01

    Predicting male fertility on non-invasive sperm traits is of big importance to human and animal reproduction strategies. Combining the wide range of parameters monitored by computer-assisted sperm analysis (CASA) with some molecular traits (e.g. mtDNA content) may help to identify markers of the male fertility. The aim of this study was to characterize variation in the mtDNA copy number in equine sperm and to investigate whether mtDNA content is correlated with quality traits of stallion spermatozoa and the age of the male. Ejaculates collected from 53 fertile stallions were divided into four age groups (3-5, 6-10, 11-14 and >15 years) and were subjected to a complex investigation including conventional analysis, CASA, flow cytometry and mtDNA content (real-time PCR). The mean (±SD) number of mtDNA copies equalled 14 ± 9 and varied from 3 to 64. Considering the great number of sperm parameters monitored in this study, only few of them were correlated with the mtDNA content: ejaculate volume (a positive correlation), the amplitude of lateral head displacement (ALH; a negative correlation) and the high mitochondrial activity index (a negative correlation). The stallion age was not correlated with the mtDNA copy number. This study provides the first set of data on mtDNA content in equine sperm and confirms phenomena previously described for humans and dog on associations between sperm mtDNA content and selected motility parameters monitored by the CASA. Basing our study on spermatozoa from fertile stallions could however limit the extent of detected associations. PMID:27037507

  5. The disposition of DNA in Prochloron (Prochlorophyta)

    NASA Technical Reports Server (NTRS)

    Coleman, A. W.; Lewin, R. A.

    1983-01-01

    The discovery of both chlorophyll a and b in the prokaryote Prochloron Lewin, a trait otherwise unique to eukaryotic photosynthetic organisms, has stimulated speculation on the possible endosymbiont origins of the plastids of eukaryotic cells. The arrangement of DNA in Prochloron was therefore dyed in situ with the fluorochrome dye DAPI and compared with the plastid DNA of various eukaryote cells. The DNA of Prochloron is found to be clearly different in arrangement and locale from that of blue-green algae. In the great size of its nucleoids and their apparently high DNA content, Prochloron also differs from the plastids of any eukaryotes, with the possible exception of dinoflagellates. Prochloron remains an evolutionary puzzle.

  6. Purification of mitochondrial and plastid DNA.

    PubMed

    Lang, B Franz; Burger, Gertraud

    2007-01-01

    The size, structure and conformation of mitochondrial and plastid genomes differ dramatically among eukaryotes. Similarly, the yield and purity of extracted organelle DNA also vary, and are crucial factors for the success of restriction mapping and sequencing experiments. We describe here procedures for the purification of organelle DNA from a broad range of eukaryotes. By emphasizing the underlying principles, these procedures will facilitate the development of new species-specific protocols. The presented purification schemes involve either isolation of organelles and subsequent extraction of DNA from this subcellular fraction, or processing of whole-cell lysates followed by CsCl gradient centrifugation to separate nuclear and organelle DNAs according to their A + T content. We have successfully used the described procedures for organelle genome sequencing from diverse eukaryotes, including non-axenic protists. Procedures can be completed in 3-5 days, typically yielding a few micrograms of DNA-ample for sequencing complete genomes.

  7. LCAT DNA shearing.

    PubMed

    Okabe, Yuka; Lee, Abraham P

    2014-04-01

    We present a novel method to fragment DNA by using lateral cavity acoustic transducers (LCATs). DNA solution is placed within a microfluidic device containing LCATs. The LCATs cause microstreaming, which fragments DNA within the solution without any need for purification or downstream processing. The LCAT-based DNA fragmentation method offers an easy-to-use, low-cost, low-energy way to fragment DNA that is amenable to integration on microfluidic platforms to further automate DNA processing. Furthermore, the LCAT microdevice requires less than 10 µL of sample, and no external equipment is needed besides a piezoelectric transducer. PMID:23850863

  8. Hydroponics: Content and Rationale

    ERIC Educational Resources Information Center

    Ernst, Jeremy V.; Busby, Joe R.

    2009-01-01

    Technology education has the means of becoming the catalyst for integrated content and curricula, especially in core academic areas, such as science and mathematics, where it has been found difficult to incorporate other subject matter. Technology is diverse enough in nature that it can be addressed by a variety of content areas, serving as a true…

  9. Content Analysis: Television.

    ERIC Educational Resources Information Center

    Williams, Tannis MacBeth; And Others

    Content analyses of the depiction of aggression and images of reality on Canadian television were performed on 109 program tapes of top-rated Toronto programs. Content was coded in terms of global messages communicated, character portrayals, context and setting of the program, amount and nature of conflict portrayed, and detailed information on…

  10. Content-Based Instruction

    ERIC Educational Resources Information Center

    DelliCarpini, M.; Alonso, O.

    2013-01-01

    DelliCarpini and Alonso's book "Content-Based Instruction" explores different approaches to teaching content-based instruction (CBI) in the English language classroom. They provide a comprehensive overview of how to teach CBI in an easy-to-follow guide that language teachers will find very practical for their own contexts. Topics…

  11. 'Junk' DNA and long-term phenotypic evolution in Silene section Elisanthe (Caryophyllaceae).

    PubMed Central

    Meagher, Thomas R; Costich, Denise E

    2004-01-01

    Nuclear DNA content variation over orders of magnitude across species has been attributed to 'junk' repetitive DNA with limited adaptive significance. By contrast, our previous work on Silene latifolia showed that DNA content is negatively correlated with flower size, a character of clear adaptive relevance. The present paper explores this relationship in a broader phylogenetic context to investigate the long-term evolutionary impacts of DNA content variation. The relationship between nuclear DNA content and phenotype variation was determined for four closely related species of Silene section Elisanthe (Caryophyllaceae). In addition to a consistent sexual dimorphism in DNA content across all of the species, we found DNA content variation among populations within, as well as among, species. We also found a general trend towards a negative correlation between DNA content and flower and leaf size over all four species, within males and females as well as overall. These results indicate that repetitive DNA may play a role in long-term phenotypic evolution. PMID:15801614

  12. [Uracil-DNA glycosylases].

    PubMed

    Pytel, Dariusz; Słupianek, Artur; Ksiazek, Dominika; Skórski, Tomasz; Błasiak, Janusz

    2008-01-01

    Uracil is one of four nitrogen bases, most frequently found in normal RNA. Uracyl can be found also in DNA as a result of enzymatic or non-enzymatic deamination of cytosine as well as misincorporation of dUMP instead of dTMP during DNA replication. Uracil from DNA can be removed by DNA repair enzymes with apirymidine site as an intermediate. However, if uracil is not removed from DNA a pair C:G in parental DNA can be changed into a T:A pair in the daughter DNA molecule. Therefore, uracil in DNA may lead to a mutation. Uracil in DNA, similarly to thymine, forms energetically most favorable hydrogen bonds with adenine, therefore uracil does not change the coding properties of DNA. Uracil in DNA is recognized by uracil DNA glycosylase (UDGs), which initiates DNA base excision repair, leading to removing of uracil from DNA and replacing it by thymine or cytosine, when arose as a result of cytosine deamination. Eukaryotes have at least four nuclear UDGs: UNG2, SMUG1, TDG i MBD4, while UNG1 operates in the mitochondrium. UNG2 is involved in DNA repair associated with DNA replication and interacts with PCNA and RPA proteins. Uracil can also be an intermediate product in the process of antigen-dependent antibody diversification in B lymphocytes. Enzymatic deamination of viral DNA by host cells can be a defense mechanism against viral infection, including HIV-1. UNG2, MBD4 and TDG glycosylases may cooperate with mismatch repair proteins and TDG can be involved in nucleotide excision repair system.

  13. The unholy trinity: taxonomy, species delimitation and DNA barcoding.

    PubMed

    DeSalle, Rob; Egan, Mary G; Siddall, Mark

    2005-10-29

    Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings--Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.

  14. DNA double-strand-break sensitivity, DNA replication, and cell cycle arrest phenotypes of Ku-deficient Saccharomyces cerevisiae

    PubMed Central

    Barnes, Georjana; Rio, Donald

    1997-01-01

    In mammalian cells, the Ku heterodimer is involved in DNA double-strand-break recognition and repair. We have established in yeast a connection between Ku activity and DNA double-strand-break damage repair, and a connection between Ku activity and commitment to DNA replication. We generated double-stranded DNA breaks in yeast cells in vivo by expressing a restriction endonuclease and have shown that yeast mutants lacking Ku p70 activity died while isogenic wild-type cells did not. Moreover, we have discovered that DNA damage occurs spontaneously during normal yeast mitotic growth, and that Ku functions in repair of this damage. We also observed that mitotically growing Ku p70 mutants have an anomalously high DNA content, suggesting a role for Ku in regulation of DNA synthesis. Finally, we present evidence that Ku p70 function is conserved between yeast, Drosophila, and humans. PMID:9023348

  15. Large-scale purification of pharmaceutical-grade plasmid DNA using tangential flow filtration and multi-step chromatography.

    PubMed

    Sun, Bo; Yu, XiangHui; Yin, Yuhe; Liu, Xintao; Wu, Yongge; Chen, Yan; Zhang, Xizhen; Jiang, Chunlai; Kong, Wei

    2013-09-01

    The demand for pharmaceutical-grade plasmid DNA in vaccine applications and gene therapy has been increasing in recent years. In the present study, a process consisting of alkaline lysis, tangential flow filtration, purification by anion exchange chromatography, hydrophobic interaction chromatography and size exclusion chromatography was developed. The final product met the requirements for pharmaceutical-grade plasmid DNA. The chromosomal DNA content was <1 μg/mg plasmid DNA, and RNA was not detectable by agarose gel electrophoresis. Moreover, the protein content was <2 μg/mg plasmid DNA, and the endotoxin content was <10 EU/mg plasmid DNA. The process was scaled up to yield 800 mg of pharmaceutical-grade plasmid DNA from approximately 2 kg of bacterial cell paste. The overall yield of the final plasmid DNA reached 48%. Therefore, we have established a rapid and efficient production process for pharmaceutical-grade plasmid DNA.

  16. Structural Organization of DNA.

    ERIC Educational Resources Information Center

    Banfalvi, Gaspar

    1986-01-01

    Explains the structural organization of DNA by providing information on the primary, secondary, tertiary, and higher organization levels of the molecule. Also includes illustrations and descriptions of sign-inversion and rotating models for supercoiling of DNA. (ML)

  17. DNA tagged microparticles

    DOEpatents

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  18. Modeling DNA Replication.

    ERIC Educational Resources Information Center

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  19. Simple determination of o-phenylphenol in skin lotion by high-performance liquid chromatography coupled with fluorescence detection after pre-column derivatization with 4-(N-chloroformylmethyl-N-methylamino)-7-nitro-2,1,3-benzoxadiazole.

    PubMed

    Higashi, Yasuhiko; Konno, Kazunori

    2015-01-01

    o-Phenylphenol (OPP) in skin lotion was quantitated by high-performance liquid chromatography coupled with fluorescence detection after pre-column derivatization with 4-(N-chloroformylmethyl-N-methylamino)-7-nitro-2,1,3-benzoxadiazole (NBD-COCl) in borate buffer (pH 8.5) at room temperature for 2 min. The column [150 mm x 3.0 mm internal diameter (i.d.)], which contained 5 μm particles of C18 packing material, was eluted at room temperature (flow rate: 0.5 ml/min) with mobile phase prepared by addition of acetonitrile (550 ml) to 450 ml of Milli-Q water containing trifluoroacetic acid (0.1 v/v%). 2-Hydroxyfluorene was used as an internal standard. The retention times of NBD-CO-OPP and NBD-CO-IS derivatives were 16.2 and 22.2 min, respectively. The calibration plot was linear in the range of 0.01-0.2 μg/ml with an r2 value of 0.9960, and the lower limit of detection was 0.003 μg/ml (at a signal-to-noise ratio of 3:1; absolute amount of 12 pg/20 μl injection). The coefficient of variation was less than 8.8%. Contents of OPP in three skin lotions were determined with the present system, and the recovery from spiked samples was satisfactory. PMID:26454976

  20. Simple determination of o-phenylphenol in skin lotion by high-performance liquid chromatography coupled with fluorescence detection after pre-column derivatization with 4-(N-chloroformylmethyl-N-methylamino)-7-nitro-2,1,3-benzoxadiazole.

    PubMed

    Higashi, Yasuhiko; Konno, Kazunori

    2015-01-01

    o-Phenylphenol (OPP) in skin lotion was quantitated by high-performance liquid chromatography coupled with fluorescence detection after pre-column derivatization with 4-(N-chloroformylmethyl-N-methylamino)-7-nitro-2,1,3-benzoxadiazole (NBD-COCl) in borate buffer (pH 8.5) at room temperature for 2 min. The column [150 mm x 3.0 mm internal diameter (i.d.)], which contained 5 μm particles of C18 packing material, was eluted at room temperature (flow rate: 0.5 ml/min) with mobile phase prepared by addition of acetonitrile (550 ml) to 450 ml of Milli-Q water containing trifluoroacetic acid (0.1 v/v%). 2-Hydroxyfluorene was used as an internal standard. The retention times of NBD-CO-OPP and NBD-CO-IS derivatives were 16.2 and 22.2 min, respectively. The calibration plot was linear in the range of 0.01-0.2 μg/ml with an r2 value of 0.9960, and the lower limit of detection was 0.003 μg/ml (at a signal-to-noise ratio of 3:1; absolute amount of 12 pg/20 μl injection). The coefficient of variation was less than 8.8%. Contents of OPP in three skin lotions were determined with the present system, and the recovery from spiked samples was satisfactory.

  1. Design of polyelectrolyte core-shells with DNA to control TMPyP binding.

    PubMed

    Serra, Vanda Vaz; Teixeira, Raquel; Andrade, Suzana M; Costa, Sílvia M B

    2016-10-01

    The interaction of DNA with 5,10,15,20-tetrakis(4-N-methylpyridiniumyl)porphyrin (TMPyP) in polyelectrolyte core-shells obtained via layer by layer adsorption of poly(sodium 4-styrenesulfonate), PSS, and poly(allylamine hydrochloride), PAH, polyelectrolytes was followed by steady state, time resolved fluorescence and by Fluorescence Lifetime Imaging Microscopy (FLIM). Our results show that DNA adsorption onto polyelectrolyte core-shell changes the TMPyP interaction within PSS/PAH core-shells structure and increase significantly the TMPyP uptake. Specific DNA/TMPyP interactions are also altered by DNA adsorption favouring porphyrin intercalation onto GC pair rich regions. Circular dichroism (CD) spectra reveal that DNA undergoes important conformational changes upon adsorption onto the core-shell surface, which are reverted upon TMPyP encapsulation.

  2. Gibberellic Acid enhancement of DNA turnover in barley aleurone cells.

    PubMed

    Taiz, L; Starks, J E

    1977-08-01

    When imbibed, deembryonated halfseeds from barley (Hordeum vulgare L., var. Himalaya) are incubated in buffer, the DNA content of the aleurone layer increases 25 to 40% over a 24-hour period. In contrast, the DNA of isolated aleurone layers declines by 20% over the same time period. Gibberellic acid (GA) causes a reduction in DNA levels in both halfseed aleurone layers and isolated aleurone layers. GA also increases the specific radioactivity of [(3)H]thymidine-labeled halfseed aleurone layer DNA during the first 12 hours of treatment. Pulse-chase studies demonstrated that the newly synthesized DNA is metabolically labile.The buoyant density on CsCl density gradients of hormone-treated aleurone DNA is identical with that of DNA extracted from whole seedlings. After density-labeling halfseed DNA with 5-bromodeoxyuridine, a bimodal absorption profile is obtained in neutral CsCl. The light band (1.70 g/ml) corresponds to unsubstituted DNA, while the heavy band (1.725-1.74 g/ml) corresponds to a hybrid density-labeled species. GA increases the relative amount of the heavy (hybrid) peak in halfseed aleurone layer DNA, further suggesting that the hormone enhances semiconservative replication in halfseeds.DNA methylation was also demonstrated. Over 60% of the radioactivity from [(3)H-Me]methionine is incorporated into 5-methylcytosine. GA has no effect on the percentage distribution of label among the bases.It was concluded that GA enhances the rate of DNA degradation and DNA synthesis (turnover) in halfseeds, but primarily DNA degradation in isolated aleurone layers. Incorporation by isolated aleurone layers is due to DNA repair. Semiconservative replication apparently plays no physiological role in the hormone response, since both isolated aleurone layers and gamma-irradiated halfseeds respond normally. The hypothesis was advanced that endoreduplication and DNA degradation are means by which the seed stores and mobilizes deoxyribonucleotides for the embryo during

  3. DNA quantification of basidiomycetous fungi during storage of logging residues

    PubMed Central

    Alfredsen, Gry; Filbakk, Tore; Fossdal, Carl Gunnar

    2015-01-01

    The demand for bioenergy caused an increased use of logging residues, branches and treetops that were previously left on the ground after harvesting. Residues are stored outdoors in piles and it is unclear to what extent fungi transform this material. Our objective was to quantify the amount of wood degrading fungi during storage using quantitative real-time PCR (qPCR) to detect basidiomycetous DNA in logging residues, a novel approach in this field. We found that the qPCR method was accurate in quantifying the fungal DNA during storage. As the moisture content of the piled logging residues decreased during the storage period, the fungal DNA content also decreased. Scots pine residues contained more fungal DNA than residues from Norway spruce. Loose piles had generally more fungal DNA than bundled ones. PMID:25870777

  4. DNA quantification of basidiomycetous fungi during storage of logging residues.

    PubMed

    Børja, Isabella; Alfredsen, Gry; Filbakk, Tore; Fossdal, Carl Gunnar

    2015-01-01

    The demand for bioenergy caused an increased use of logging residues, branches and treetops that were previously left on the ground after harvesting. Residues are stored outdoors in piles and it is unclear to what extent fungi transform this material. Our objective was to quantify the amount of wood degrading fungi during storage using quantitative real-time PCR (qPCR) to detect basidiomycetous DNA in logging residues, a novel approach in this field. We found that the qPCR method was accurate in quantifying the fungal DNA during storage. As the moisture content of the piled logging residues decreased during the storage period, the fungal DNA content also decreased. Scots pine residues contained more fungal DNA than residues from Norway spruce. Loose piles had generally more fungal DNA than bundled ones.

  5. Role of hydrogen on the deposition and properties of fluorinated silicon-nitride films prepared by inductively coupled plasma enhanced chemical vapor deposition using SiF{sub 4}/N{sub 2}/H{sub 2} mixtures

    SciTech Connect

    Fandino, J.; Santana, G.; Rodriguez-Fernandez, L.; Cheang-Wong, J.C.; Ortiz, A.; Alonso, J.C.

    2005-03-01

    Fluorinated silicon-nitride films have been prepared at low temperature (250 deg. C) by remote plasma enhanced chemical vapor deposition using mixtures of SiF{sub 4}, N{sub 2}, Ar, and various H{sub 2} flow rates. The deposited films were characterized by means of single wavelength ellipsometry, infrared transmission, resonant nuclear reactions, Rutherford backscattering analysis, and current-voltage measurements. It was found that films deposited without hydrogen grow with the highest deposition rate, however, they result with the highest fluorine content ({approx}27 at. %) and excess of silicon (Si/N ratio{approx_equal}1.75). These films also have the lowest refractive index and the highest etch rate, and exhibit very poor dielectric properties. As a consequence of the high fluorine content, these films hydrolize rapidly upon exposure to the ambient moisture, forming Si-H and N-H bonds, however, they do not oxidize completely. The addition of hydrogen to the deposition process reduces the deposition rate but improves systematically the stability and insulating properties of the films by reducing the amount of both silicon and fluorine incorporated during growth. All the fluorinated silicon-nitride films deposited at hydrogen flow rates higher than 3.5 sccm resulted free of Si-H bonds. In spite of the fact that films obtained at the highest hydrogen flow rate used in this work are still silicon rich (Si/N ratio{approx_equal}1.0) and contain a considerable amount of fluorine ({approx}16 at. %), they are chemically stable and show acceptable dielectric properties.

  6. An Altered Immune Response, but Not Individual Cationic Antimicrobial Peptides, Is Associated with the Oral Attenuation of Ara4N-Deficient Salmonella enterica Serovar Typhimurium in Mice

    PubMed Central

    Tamayo, Rita; Reeves, Linh T.; Gunn, John S.

    2012-01-01

    Salmonella enterica serovar Typhimurium (S. Typhimurium) uses two-component regulatory systems (TCRS) to respond to stimuli in the local microenvironment. Upon infection, the Salmonella TCRSs PhoP-PhoQ (PhoPQ) and PmrA-PmrB (PmrAB) are activated by environmental signals in the intestinal lumen and within host cells. TCRS-mediated gene expression results in lipopolysaccharide (LPS) modification and cationic antimicrobial peptide resistance. The PmrA-regulated pmrHFIJKLM operon mediates 4-amino-4-deoxy-L-arabinose (Ara4N) production and attachment to the lipid A of LPS. A ΔpmrF S. Typhimurium strain cannot produce Ara4N, exhibits increased sensitivity to cationic antimicrobial peptide (CAMP)-mediated killing, and attenuated virulence in mice upon oral infection. CAMPs are predicted to play a role in elimination of Salmonella, and may activate PhoPQ and PmrAB in vivo, which could increase bacterial resistance to host defenses. Competition experiments between wild type (WT) and ΔpmrF mutant strains of S. Typhimurium indicated that selection against this mutant first occurs within the intestinal lumen early during infection. However, CRAMP and active cryptdins alone are not responsible for elimination of Ara4N-deficient bacteria in vivo. Investigation into the early immune response to ΔpmrF showed that it differed slightly from the early immune response to WT S. Typhimurium. Further investigation into the early immune response to infection of Peyer’s patches suggests a role for IL-13 in the attenution of the ΔpmrF mutant strain. Thus, prominent CAMPs present in the mouse intestine are not responsible for the selection against the ΔpmrF strain in this location, but limited alterations in innate immune induction were observed that affect bacterial survival and virulence. PMID:23166721

  7. Development of a Vero cell DNA reference standard for residual DNA measurement in China

    PubMed Central

    Cao, Shouchun; Dong, Guanmu; Tang, Jianrong; Li, Jia; Liu, Jinghua; Shi, Leitai; Li, Changgui; Wang, Junzhi

    2013-01-01

    This collaborative study developed a Vero cell DNA reference for standardizing dot blot hybridization, an assay widely employed to measure residual DNA contents of viral vaccines prepared with Vero cells. High purity of Vero cell DNA was extracted and characterized by Hind III enzyme digestion and DNA sequencing. Then, with a cooperative calibration, the concentration of Vero cell DNA reference bulk solution was determined (64.0 ± 1.9 μg/mL, OD260/OD280 = 1.87) and diluted (40 ng/mL) with Tris-EDTA buffer containing bovine serum albumin as freeze-dried excipients. With industrial filling apparatus, the diluted bulk was loaded into ampoules (0.5 mL each) which were heat sealed after nitrogen filling. Finally, a collaborative study showed that the Vero cell DNA reference could reach a sensitivity of 1 to 5 pg/dot and maintained good stability after accelerated destruction test. The successful establishment of the Vero cell DNA quantitative reference will facilitate the standardization of dot blot hybridization for testing residual host cell DNA. PMID:23291952

  8. DNA nanoarchitectonics: assembled DNA at interfaces.

    PubMed

    Howorka, Stefan

    2013-06-18

    DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.

  9. 59 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    1994-11-08

    ... From the Federal Register Online via the Government Printing Office ] CONTENTS Vol. 59, No. 215 Tuesday, November 8, 1994 Agricultural Marketing Service RULES Oranges, grapefruit, tangerines, and tangelos grown in Florida and imported grapefruit, 55571-55573 Agriculture Department See...

  10. Two-photon fluorescence and fluorescence imaging of two styryl heterocyclic dyes combined with DNA

    NASA Astrophysics Data System (ADS)

    Gao, Chao; Liu, Shu-yao; Zhang, Xian; Liu, Ying-kai; Qiao, Cong-de; Liu, Zhao-e.

    2016-03-01

    Two new styryl heterocyclic two-photon (TP) materials, 4-[4-(N-methyl)styrene]-imidazo [4,5-f][1,10] phenanthroline-benzene iodated salt (probe-1) and 4,4- [4-(N-methyl)styrene] -benzene iodated salt (probe-2) were successfully synthesized and studied as potential fluorescent probes of DNA detection. The linear and nonlinear photophysical properties of two compounds in different solvents were investigated. The absorption, one- and two-photon fluorescent spectra of the free dye and dye-DNA complex were also examined to evaluate their photophysical properties. The binding constants of dye-DNA were obtained according to Scatchard equation with good values. The results showed that two probes could be used as fluorescent DNA probes by two-photon excitation, and TP fluorescent properties of probe-1 are superior to that of probe-2. The fluorescent method date indicated that the mechanisms of dye-DNA complex interaction may be groove binding for probe-1 and electrostatic interaction for probe-2, respectively. The MTT assay experiments showed two probes are low toxicity. Moreover, the TP fluorescence imaging of DNA detection in living cells at 800 nm indicated that the ability to locate in cell nuclei of probe-1 is better than that of probe-2.

  11. Two-photon fluorescence and fluorescence imaging of two styryl heterocyclic dyes combined with DNA.

    PubMed

    Gao, Chao; Liu, Shu-yao; Zhang, Xian; Liu, Ying-kai; Qiao, Cong-de; Liu, Zhao-e

    2016-03-01

    Two new styryl heterocyclic two-photon (TP) materials, 4-[4-(N-methyl)styrene]-imidazo [4,5-f][1,10] phenanthroline-benzene iodated salt (probe-1) and 4,4-[4-(N-methyl)styrene]-benzene iodated salt (probe-2) were successfully synthesized and studied as potential fluorescent probes of DNA detection. The linear and nonlinear photophysical properties of two compounds in different solvents were investigated. The absorption, one- and two-photon fluorescent spectra of the free dye and dye-DNA complex were also examined to evaluate their photophysical properties. The binding constants of dye-DNA were obtained according to Scatchard equation with good values. The results showed that two probes could be used as fluorescent DNA probes by two-photon excitation, and TP fluorescent properties of probe-1 are superior to that of probe-2. The fluorescent method date indicated that the mechanisms of dye-DNA complex interaction may be groove binding for probe-1 and electrostatic interaction for probe-2, respectively. The MTT assay experiments showed two probes are low toxicity. Moreover, the TP fluorescence imaging of DNA detection in living cells at 800 nm indicated that the ability to locate in cell nuclei of probe-1 is better than that of probe-2.

  12. Spectral detectability of CH4-N2 clathrates for in-situ and remote observation of Titan and other icy moons

    NASA Astrophysics Data System (ADS)

    Nna-Mvondo, D.; Tobie, G.; Le Menn, E.; Grasset, O.

    2015-10-01

    Multicomponent clathrates may be present at the surface of several icy moons, although they have not been detected yet, possibly due to the absence of reliable spectral data. In this work, w e present infrared (IR) and Raman spectral studies of CH4-N2 clathrates at low temperature and pressure, in order to identify discriminating criteria for their possible detection. These clathrates are particularly interesting for Titan and Pluto. Our experimental results indicate that identification of mixed clathrate from remote sensing is very challenging, and that only in- situ Raman spectroscopy may provide a clear identification of clathrate and co nstraints on their composition.

  13. Absorption intensities and complex refractive indices of crystalline HCN, HC3N, and C4N2 in the infrared region

    NASA Technical Reports Server (NTRS)

    Masterson, C. M.; Khanna, R. K.

    1990-01-01

    IR absorption intensities are presented for thin crystalline films of HCN, HC3N, and C4N2, together with n and k complex refractive indices determined on the basis of an iterative program for the Kramers-Konig integral via a least-squares, point-by-point fitting of the experimental transmission data. It is established that the transmission spectra generated by means of these n and k values can reproduce the experimental transmission observation values to within + or - 2 percent.

  14. Second hyperpolarizability of the calcium-doped lithium salt of pyridazine Li-H3C4N2 ⋯ Ca

    NASA Astrophysics Data System (ADS)

    Marques, Suélio; Castro, Marcos A.; Leão, Salviano A.; Fonseca, Tertius L.

    2016-08-01

    In this work we report results of coupled cluster calculations for the second hyperpolarizability of the calcium-doped lithium salt of pyridazine (Li-H3C4N2 ⋯ Ca) molecule. In the static limit an unusual value of 4.34 ×106 au was obtained at the CCSD level of calculation. Results obtained for the dc-Kerr effect through SCF, CCS and CCSD methods show that γ (- ω; ω, 0, 0) is strongly dependent of the electron correlation treatment. Dynamic results obtained at the CCSD level are also reported for the IDRI, dc-SHG and THG nonlinear optical processes.

  15. Synthesis, spectral characteristics, and the crystal and molecular structures of 2,3-dimethyl-1-phenyl-4-(N-phthalimido)pyrazolone-5

    SciTech Connect

    Sokol, V. I.; Strashnova, S. B. Kovalchukova, O. V.; Sergienko, V. S.; Davydov, V. V.; Zaitsev, B. E.; Evtushenko, Yu. M.

    2008-11-15

    2,3-Dimethyl-1-phenyl-4-(N-phthalimido)pyrazolone-5 (I) is synthesized and isolated in the form of single crystals. The crystal structure of compound I is determined using X-ray diffraction. The phthalimide and pyrazolone rings in the molecule are not coplanar: the angle between their median planes is 56.4{sup o}. The bond lengths in the rings level off, which indicates the delocalization of the electron density. The spectral characteristics (IR and electronic spectra) of molecule I are determined.

  16. meso-(4-(N,N-dialkylamino)phenyl)-substituted subporphyrins: remarkably perturbed absorption spectra and enhanced fluorescence by intramolecular charge transfer interactions.

    PubMed

    Inokuma, Yasuhide; Easwaramoorthi, Shanmugam; Yoon, Zin Seok; Kim, Dongho; Osuka, Atsuhiro

    2008-09-17

    A series of meso-(4-(N,N-dibenzylamino)phenyl)-substituted subporphyrins was synthesized by means of Buchwald-Hartwig amination protocol. Substitution of the amino group at the 4-position of the meso-phenyl substituent resulted in a remarkable red shift in the absorption spectra and drastic enhancement of fluorescence intensity probably as a consequence of intramolecular CT interaction. These characteristics have been utilized to construct a cation-sensing system by appending a 1-aza-15-crown-5 unit to subporphyrin that displays large spectral changes upon cation binding.

  17. Nonlinear Aspects of Coding and Noncoding DNA Sequences

    NASA Astrophysics Data System (ADS)

    Stanley, H. Eugene

    2001-03-01

    One of the most remarkable features of human DNA is that 97 percent is not coding for proteins. Studying this noncoding DNA is important both for practical reasons (to distinguish it from the coding DNA as the human genome is sequenced), and for scientific reasons (why is the noncoding DNA present at all, if it appears to have little if any purpose?). In this talk we discuss new methods of analyzing coding and noncoding DNA in parallel, with a view to uncovering different statistical properties of the two kinds of DNA. We also speculate on possible roles of noncoding DNA. The work reported here was carried out primarily by P. Bernaola-Galvan, S. V. Buldyrev, P. Carpena, N. Dokholyan, A. L. Goldberger, I. Grosse, S. Havlin, H. Herzel, J. L. Oliver, C.-K. Peng, M. Simons, H. E. Stanley, R. H. R. Stanley, and G. M. Viswanathan. [1] For a brief overview in language that physicists can understand, see H. E. Stanley, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, and M. Simons, "Scaling Features of Noncoding DNA" [Proc. XII Max Born Symposium, Wroclaw], Physica A 273, 1-18 (1999). [2] I. Grosse, H. Herzel, S. V. Buldyrev, and H. E. Stanley, "Species Independence of Mutual Information in Coding and Noncoding DNA," Phys. Rev. E 61, 5624-5629 (2000). [3] P. Bernaola-Galvan, I. Grosse, P. Carpena, J. L. Oliver, and H. E. Stanley, "Identification of DNA Coding Regions Using an Entropic Segmentation Method," Phys. Rev. Lett. 84, 1342-1345 (2000). [4] N. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Distributions of Dimeric Tandem Repeats in Non-coding and Coding DNA Sequences," J. Theor. Biol. 202, 273-282 (2000). [5] R. H. R. Stanley, N. V. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Clumping of Identical Oligonucleotides in Coding and Noncoding DNA Sequences," J. Biomol. Structure and Design 17, 79-87 (1999). [6] N. Dokholyan, S. V. Buldyrev, S. Havlin, and H. E. Stanley, "Distribution of Base Pair Repeats in Coding and Noncoding DNA

  18. The Many Sides of DNA.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    1997-01-01

    Explores the meaning of DNA. Discusses histories of DNA, literature on DNA, the contributions of Max Delbruck and Barbara McClintock, life, views of control, current research, and the language of DNA. Contains 24 references. (JRH)

  19. DNA profiling from heroin street dose packages.

    PubMed

    Zamir, Ashira; Cohen, Yaron; Azoury, Myriam

    2007-03-01

    A large amount of heroin street doses are seized and examined for drug content by the Israel police. These are generally wrapped in heat-sealed plastic. Occasionally it is possible to visualize latent fingerprints on the plastic wrap itself, but the small size of the plastic item and the sealing process makes the success rate very low. In this study, the possibility of extracting and profiling DNA from the burnt edge of the plastic wrap was investigated. The idea was based on the assumption that epithelial cells might be trapped during the sealing process. The results show that there are sufficient quantities of DNA deposited at the "amorphic" burnt edges of sealed street doses for DNA profiling to be carried out. A controlled experiment using a known donor was performed. This subject carried out sealing of "street drug" packages and consequent DNA extractions were performed to show that known DNA profiles could be recovered from such packages, as a result of handling by the "packer." "Square-like" burnt edges did not yield DNA profiles, probably because of differences in the sealing process. It was also shown that DNA could be recovered from the plastic wrap itself and not only from the amorphic burnt edges. As heroin dealers and drug users are often involved in other crimes and run-ins with the law, the effective extraction and addition of their DNA profiles from such items of evidence to the newly established DNA database in Israel provides new avenues in the continued fight against crime and drug traffickers.

  20. DNA Sequencing apparatus

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  1. Racemic DNA crystallography.

    PubMed

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.

  2. Gold nanoparticles immobilized on metal-organic frameworks with enhanced catalytic performance for DNA detection.

    PubMed

    Liu, Ya Li; Fu, Wen Liang; Li, Chun Mei; Huang, Cheng Zhi; Li, Yuan Fang

    2015-02-25

    In this work, gold nanoparticles (AuNPs) assembled on the surface of iron based metal-organic frameworks (MOFs), Fe-MIL-88, are facilely prepared through electrostatic interactions using polyethyleneimine (PEI) molecules as linker. The resulting hybrid materials possess synergetic peroxidase-like activity. Because iron based metal-organic frameworks, Fe-MIL-88, exhibits highly peroxidase-like activity, and AuNPs has the distinct adsorption property to single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). The peroxidase-like activity of Au@Fe-MIL-88 exhibit excellent switchable in response to specific DNA, ssDNA is easily adsorbed on the surface of the Au@Fe-MIL-88 hybrids, resulting in the reduce of the peroxidase-like activity of the hybrids. While it is recovered by the addition of target DNA, and the recovery degree is proportional to the target DNA concentration over the range of 30-150 nM with a detection limit of 11.4 nM. Based on these unique properties, we develop a label-free colorimetric method for DNA hybridization detection. In control experiment, base-mismatched DNA cannot induce recovery of the peroxidase-like activity. This detection method is simple, cheap, rapid and colorimetric.

  3. Gold nanoparticles immobilized on metal-organic frameworks with enhanced catalytic performance for DNA detection.

    PubMed

    Liu, Ya Li; Fu, Wen Liang; Li, Chun Mei; Huang, Cheng Zhi; Li, Yuan Fang

    2015-02-25

    In this work, gold nanoparticles (AuNPs) assembled on the surface of iron based metal-organic frameworks (MOFs), Fe-MIL-88, are facilely prepared through electrostatic interactions using polyethyleneimine (PEI) molecules as linker. The resulting hybrid materials possess synergetic peroxidase-like activity. Because iron based metal-organic frameworks, Fe-MIL-88, exhibits highly peroxidase-like activity, and AuNPs has the distinct adsorption property to single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). The peroxidase-like activity of Au@Fe-MIL-88 exhibit excellent switchable in response to specific DNA, ssDNA is easily adsorbed on the surface of the Au@Fe-MIL-88 hybrids, resulting in the reduce of the peroxidase-like activity of the hybrids. While it is recovered by the addition of target DNA, and the recovery degree is proportional to the target DNA concentration over the range of 30-150 nM with a detection limit of 11.4 nM. Based on these unique properties, we develop a label-free colorimetric method for DNA hybridization detection. In control experiment, base-mismatched DNA cannot induce recovery of the peroxidase-like activity. This detection method is simple, cheap, rapid and colorimetric. PMID:25702274

  4. An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus.

    PubMed Central

    Zouros, E; Oberhauser Ball, A; Saavedra, C; Freeman, K R

    1994-01-01

    In animals, mitochondrial DNA (mtDNA) inheritance is predominantly maternal. In a few cases incidental transmission of paternal mtDNA was observed and estimated to account for only 10(-4)-10(-3) of an individual's mtDNA content. In contrast, biparental inheritance is common in mussels of the genus Mytilus. Here we present direct evidence that sex and mtDNA inheritance are coupled in Mytilus. Females inherit mtDNA only from their mother, but they transmit it to both daughters and sons. Males inherit mtDNA from both parents, but they transmit to sons only the mtDNA they inherited from their father. In pair matings, this mtDNA inheritance pattern is associated with a strong sex-ratio bias. These findings establish a newly discovered type of cytoplasmic DNA transmission. We also present evidence that the phenomenon breaks down in interspecific hybrids. Images PMID:8052604

  5. DNA structure and function.

    PubMed

    Travers, Andrew; Muskhelishvili, Georgi

    2015-06-01

    The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase.

  6. DNA barcoding for plants.

    PubMed

    de Vere, Natasha; Rich, Tim C G; Trinder, Sarah A; Long, Charlotte

    2015-01-01

    DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.

  7. Complexation Between Cationic Diblock Copolymers and Plasmid DNA

    NASA Astrophysics Data System (ADS)

    Jung, Seyoung; Reineke, Theresa; Lodge, Timothy

    Deoxyribonucleic acids (DNA), as polyanions, can spontaneously bind with polycations to form polyelectrolyte complexes. When the polycation is a diblock copolymer with one cationic block and one uncharged hydrophilic block, the polyelectrolyte complexes formed with plasmid DNA (pDNA) are often colloidally stable, and show great promise in the field of polymeric gene therapy. While the resulting properties (size, stability, and toxicity to biological systems) of the complexes have been studied for numerous cationic diblocks, the fundamentals of the pDNA-diblock binding process have not been extensively investigated. Herein, we report how the cationic block content of a diblock influences the pDNA-diblock interactions. pDNA with 7164 base pairs and poly(2-deoxy-2-methacrylamido glucopyranose)-block-poly(N-(2-aminoethyl) methacrylamide) (PMAG-b-PAEMA) are used as the model pDNA and cationic diblock, respectively. To vary the cationic block content, two PMAG-b-PAEMA copolymers with similar PMAG block lengths but distinct PAEMA block lengths and a PAEMA homopolymer are utilized. We show that the enthalpy change from pDNA-diblock interactions is dependent on the cationic diblock composition, and is closely associated with both the binding strength and the pDNA tertiary structure.

  8. Human DNA repair genes.

    PubMed

    Wood, R D; Mitchell, M; Sgouros, J; Lindahl, T

    2001-02-16

    Cellular DNA is subjected to continual attack, both by reactive species inside cells and by environmental agents. Toxic and mutagenic consequences are minimized by distinct pathways of repair, and 130 known human DNA repair genes are described here. Notable features presently include four enzymes that can remove uracil from DNA, seven recombination genes related to RAD51, and many recently discovered DNA polymerases that bypass damage, but only one system to remove the main DNA lesions induced by ultraviolet light. More human DNA repair genes will be found by comparison with model organisms and as common folds in three-dimensional protein structures are determined. Modulation of DNA repair should lead to clinical applications including improvement of radiotherapy and treatment with anticancer drugs and an advanced understanding of the cellular aging process. PMID:11181991

  9. DNA characterization of Lyme disease spirochetes.

    PubMed Central

    Schmid, G. P.; Steigerwalt, A. G.; Johnson, S.; Barbour, A. G.; Steere, A. C.; Robinson, I. M.; Brenner, D. J.

    1984-01-01

    Lyme disease spirochetes (LDS) have phenotypic characteristics of both treponemes and borreliae. To ascertain whether one or more species of LDS exist, as well as their taxonomic status, we determined the DNA base (G + C) content for three strains of LDS, the DNA relatedness of ten strains isolated in the United States or Europe, and the DNA relatedness of LDS to other spirochetes. The G + C content of the three LDS strains was 28.1-29.0 mol%, most similar to those of Borellia hermsii (30.6 mol %) and Treponema hyodysenteriae (25.6 mol %) among the other spirochetes tested. DNA hybridization studies of nine LDS strains to a reference strain isolated from human blood revealed divergence (unpaired bases) within related nucleotide sequences of only 0.0-1.0 percent, indicating the strains were one species. Similarly, relatedness values of seven strains to the reference strain were high: 58-98 percent (mean, 71 percent) in 50 degrees C reactions and 50-93 percent (mean, 69 percent) in 65 degrees C reactions. Labeled DNA from B. hermsii was 30-40 percent related to three Lyme disease spirochete strains in 50 degrees C reactions and 8-10 percent related in 65 degrees C reactions. In contrast, DNA from the reference LDS strain showed relatedness of only 1 percent to DNAs of two leptospires and only 16 percent to DNA from T. hyodysenteriae. We conclude that LDS are a single species, genetically unlike treponemes or leptospires, which belong in the genus Borrelia. PMID:6516455

  10. Fractal analysis of DNA sequence data

    SciTech Connect

    Berthelsen, C.L.

    1993-01-01

    DNA sequence databases are growing at an almost exponential rate. New analysis methods are needed to extract knowledge about the organization of nucleotides from this vast amount of data. Fractal analysis is a new scientific paradigm that has been used successfully in many domains including the biological and physical sciences. Biological growth is a nonlinear dynamic process and some have suggested that to consider fractal geometry as a biological design principle may be most productive. This research is an exploratory study of the application of fractal analysis to DNA sequence data. A simple random fractal, the random walk, is used to represent DNA sequences. The fractal dimension of these walks is then estimated using the [open quote]sandbox method[close quote]. Analysis of 164 human DNA sequences compared to three types of control sequences (random, base-content matched, and dimer-content matched) reveals that long-range correlations are present in DNA that are not explained by base or dimer frequencies. The study also revealed that the fractal dimension of coding sequences was significantly lower than sequences that were primarily noncoding, indicating the presence of longer-range correlations in functional sequences. The multifractal spectrum is used to analyze fractals that are heterogeneous and have a different fractal dimension for subsets with different scalings. The multifractal spectrum of the random walks of twelve mitochondrial genome sequences was estimated. Eight vertebrate mtDNA sequences had uniformly lower spectra values than did four invertebrate mtDNA sequences. Thus, vertebrate mitochondria show significantly longer-range correlations than to invertebrate mitochondria. The higher multifractal spectra values for invertebrate mitochondria suggest a more random organization of the sequences. This research also includes considerable theoretical work on the effects of finite size, embedding dimension, and scaling ranges.

  11. Fractal Analysis of DNA Sequence Data

    NASA Astrophysics Data System (ADS)

    Berthelsen, Cheryl Lynn

    DNA sequence databases are growing at an almost exponential rate. New analysis methods are needed to extract knowledge about the organization of nucleotides from this vast amount of data. Fractal analysis is a new scientific paradigm that has been used successfully in many domains including the biological and physical sciences. Biological growth is a nonlinear dynamic process and some have suggested that to consider fractal geometry as a biological design principle may be most productive. This research is an exploratory study of the application of fractal analysis to DNA sequence data. A simple random fractal, the random walk, is used to represent DNA sequences. The fractal dimension of these walks is then estimated using the "sandbox method." Analysis of 164 human DNA sequences compared to three types of control sequences (random, base -content matched, and dimer-content matched) reveals that long-range correlations are present in DNA that are not explained by base or dimer frequencies. The study also revealed that the fractal dimension of coding sequences was significantly lower than sequences that were primarily noncoding, indicating the presence of longer-range correlations in functional sequences. The multifractal spectrum is used to analyze fractals that are heterogeneous and have a different fractal dimension for subsets with different scalings. The multifractal spectrum of the random walks of twelve mitochondrial genome sequences was estimated. Eight vertebrate mtDNA sequences had uniformly lower spectra values than did four invertebrate mtDNA sequences. Thus, vertebrate mitochondria show significantly longer-range correlations than do invertebrate mitochondria. The higher multifractal spectra values for invertebrate mitochondria suggest a more random organization of the sequences. This research also includes considerable theoretical work on the effects of finite size, embedding dimension, and scaling ranges.

  12. Mitochondrial regulation of cancer associated nuclear DNA methylation

    SciTech Connect

    Xie Chenghui; Naito, Akihiro; Mizumachi, Takatsugu; Evans, Teresa T.; Douglas, Michael G.; Cooney, Craig A.; Fan Chunyang; Higuchi, Masahiro

    2007-12-21

    The onset and progression of cancer is associated with the methylation-dependent silencing of specific genes, however, the mechanism and its regulation have not been established. We previously demonstrated that reduction of mitochondrial DNA content induces cancer progression. Here we found that mitochondrial DNA-deficient LN{rho}0-8 activates the hypermethylation of the nuclear DNA promoters including the promoter CpG islands of the endothelin B receptor, O{sup 6}-methylguanine-DNA methyltransferase, and E-cadherin. These are unmethylated and the corresponding gene products are expressed in the parental LNCaP containing mitochondrial DNA. The absence of mitochondrial DNA induced DNA methyltransferase 1 expression which was responsible for the methylation patterns observed. Inhibition of DNA methyltransferase eliminated hypermethylation and expressed gene products in LN{rho}0-8. These studies demonstrate loss or reduction of mitochondrial DNA resulted in the induction of DNA methyltransferase 1, hypermethylation of the promoters of endothelin B receptor, O{sup 6}-methylguanine-DNA methyltransferase, and E-cadherin, and reduction of the corresponding gene products.

  13. A high-throughput method for detection of DNA in chloroplasts using flow cytometry

    PubMed Central

    Rowan, Beth A; Oldenburg, Delene J; Bendich, Arnold J

    2007-01-01

    Background The amount of DNA in the chloroplasts of some plant species has been shown recently to decline dramatically during leaf development. A high-throughput method of DNA detection in chloroplasts is now needed in order to facilitate the further investigation of this process using large numbers of tissue samples. Results The DNA-binding fluorophores 4',6-diamidino-2-phenylindole (DAPI), SYBR Green I (SG), SYTO 42, and SYTO 45 were assessed for their utility in flow cytometric analysis of DNA in Arabidopsis chloroplasts. Fluorescence microscopy and real-time quantitative PCR (qPCR) were used to validate flow cytometry data. We found neither DAPI nor SYTO 45 suitable for flow cytometric analysis of chloroplast DNA (cpDNA) content, but did find changes in cpDNA content during development by flow cytometry using SG and SYTO 42. The latter dye provided more sensitive detection, and the results were similar to those from the fluorescence microscopic analysis. Differences in SYTO 42 fluorescence were found to correlate with differences in cpDNA content as determined by qPCR using three primer sets widely spaced across the chloroplast genome, suggesting that the whole genome undergoes copy number reduction during development, rather than selective reduction/degradation of subgenomic regions. Conclusion Flow cytometric analysis of chloroplasts stained with SYTO 42 is a high-throughput method suitable for determining changes in cpDNA content during development and for sorting chloroplasts on the basis of DNA content. PMID:17381841

  14. Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize.

    PubMed

    Oldenburg, Delene J; Bendich, Arnold J

    2004-12-10

    We examined the DNA from chloroplasts obtained from different tissues of juvenile maize seedlings (from eight to 16 days old) and adult plants (50-58 days old). During plastid development, we found a striking progression from complex multigenomic DNA molecules to simple subgenomic molecules. The decrease in molecular size and complexity of the DNA paralleled a progressive decrease in DNA content per plastid. Most surprising, we were unable to detect DNA of any size in most chloroplasts from mature leaves, long before the onset of leaf senescence. Thus, the DNA content per plastid is not constant but varies during development from hundreds of genome copies in the proplastid to undetectable levels in the mature chloroplast. This loss of DNA from isolated, mature chloroplasts was monitored by three independent methods: staining intact chloroplasts with 4',6-diamidino-2-phenylindole (DAPI); staining at the single-molecule level with ethidium bromide after exhaustive deproteinization of lysed chloroplasts; and blot-hybridization after standard DNA isolation procedures. We propose a mechanism for the production of multigenomic chloroplast chromosomes that begins at paired DNA replication origins on linear molecules to generate a head-to-tail linear concatemer, followed by recombination-dependent replication.

  15. Assessing the viability of extended nonmetal atom chains in M(n)F(4n+2) (M=S and Se).

    PubMed

    Popov, Ivan A; Averkiev, Boris B; Starikova, Alyona A; Boldyrev, Alexander I; Minyaev, Ruslan M; Minkin, Vladimir I

    2015-01-26

    Theoretical investigations to evaluate the viability of extended nonmetal atom chains on the basis of molecular models with the general formula Mn F4n+2 (M=S and Se) and corresponding solid-state systems exhibiting direct SS or SeSe bonding were performed. The proposed high-symmetry molecules were found to be minima on the potential energy surface for all Sn F4n+2 systems studied (n=2-9) and for selenium analogues up to n=6. Phonon calculations of periodic structures confirmed the dynamic stability of the -(SF4 -SF4 )∞ - chain, whereas the analogous -(SeF4 -SeF4 )∞ - chain was found to have a number of imaginary phonon frequencies. Chemical bonding analysis of the dynamically stable -(SF4 -SF4 )∞ - structure revealed a multicenter character of the SS and SF bonds. A novel definition and abbreviation (ENAC) are proposed by analogy with extended metal atom chain (EMAC) complexes.

  16. Removal of ZnO nanoparticles in simulated wastewater treatment processes and its effects on COD and NH(4)(+)-N reduction.

    PubMed

    Hou, Linlin; Xia, Jing; Li, Kaiyang; Chen, Jian; Wu, Xiaolei; Li, Xiqing

    2013-01-01

    For many engineered nanoparticles, the primary pathway of release into the environment is via sewage and industrial wastewater discharges. In this work, the removal of uncoated ZnO nanoparticles (ZnO NPs) during simulated wastewater treatment processes and its impact on treatment performance were examined. Simulated primary clarification removed the majority (about 70%) of the dosed ZnO NPs. During simulated sequencing batch reactor (SBR) processes, ZnO NPs were completely removed in each cycle throughout the 11-day experimental duration (two cycles per day). Continuous input of ZnO NPs into the wastewater (at concentrations up to 5 mg L(-1)) did not reduce chemical oxygen demand (COD) removal. NH(4)(+)-N removal was reduced at a dosing concentration of 5 mg L(-1) ZnO NPs per cycle. Inhibition of respiration of nitrifying microorganisms by ZnO NPs corroborated the reduction of NH(4)(+)-N removal. These results indicate that if the wastewater is treated, the release of ZnO NPs into receiving water bodies would be minimal and ZnO NPs would mainly accumulate in biosolids. Uncoated ZnO NPs in wastewater at very high concentrations may have some adverse effects on activated sludge process. PMID:23168621

  17. Magnetism by interfacial hybridization and p-type doping of MoS(2) in Fe(4)N/MoS(2) superlattices: a first-principles study.

    PubMed

    Feng, Nan; Mi, Wenbo; Cheng, Yingchun; Guo, Zaibing; Schwingenschlögl, Udo; Bai, Haili

    2014-03-26

    Magnetic and electronic properties of Fe4N(111)/MoS2(√3 × √3) superlattices are investigated by first-principles calculations, considering two models: (I) Fe(I)Fe(II)-S and (II) N-S interfaces, each with six stacking configurations. In model I, strong interfacial hybridization between Fe(I)/Fe(II) and S results in magnetism of monolayer MoS2, with a magnetic moment of 0.33 μB for Mo located on top of Fe(I). For model II, no magnetism is induced due to weak N-S interfacial bonding, and the semiconducting nature of monolayer MoS2 is preserved. Charge transfer between MoS2 and N results in p-type MoS2 with Schottky barrier heights of 0.5-0.6 eV. Our results demonstrate that the interfacial geometry and hybridization can be used to tune the magnetism and doping in Fe4N(111)/MoS2(√3 × √3) superlattices.

  18. Pressure-driven variations of hydrogen bonding energy in ammonium azide (NH4N3): IR absorption and Raman scattering studies.

    PubMed

    Wu, Xiaoxin; Ma, Fengxian; Ma, Chunli; Cui, Hang; Liu, Zhenxian; Zhu, Hongyang; Wang, Xiaoli; Cui, Qiliang

    2014-07-14

    In this study, high pressure infrared (IR) absorption and Raman scattering studies for ammonium azide (NH4N3) were carried out at room temperature up to 20 GPa and 22 GPa, respectively. For comparison and further assignment, the vibrational spectra at ambient conditions were calculated using CASTEP code, particularly for the far- and mid-IR modes. The recorded vibrational data consistently indicated a pressure-induced phase transition at 2.9 GPa. All observed vibrational modes maintained their identities at the high pressure phase, indicating that NH4N3 was still presented in the form of ammonium cations and azide anions linked by the hydrogen bond (N-H⋯N). Above 2.9 GPa, the relative magnitude of the torsional mode weakened and the N-H symmetric stretch displayed a redshift, indicating strengthened hydrogen bonding energy. The opposite effects were observed above 12 GPa, where the relative magnitude of the torsional mode strengthened and the N-H symmetric stretch reverted to a blueshift, indicating weakened hydrogen bonding energy. It can be concluded that the hydrogen bonding energy exhibited a weakening (0-2.9 GPa), strengthening (2.9-12 GPa), and then again weakening (12-22 GPa) phenomena with the increasing of compression. The hydrogen bonding energy changing with the increase of pressure can be ascribed to a phase transition at 2.9 GPa and a rotational or bending behavior of azide ions at 12 GPa.

  19. Influence of bulking agents on CH4, N2O, and NH3 emissions during rapid composting of pig manure from the Chinese Ganqinfen system*

    PubMed Central

    Sun, Xiang-ping; Lu, Peng; Jiang, Tao; Schuchardt, Frank; Li, Guo-xue

    2014-01-01

    Mismanagement of the composting process can result in emissions of CH4, N2O, and NH3, which have caused severe environmental problems. This study was aimed at determining whether CH4, N2O, and NH3 emissions from composting are affected by bulking agents during rapid composting of pig manure from the Chinese Ganqinfen system. Three bulking agents, corn stalks, spent mushroom compost, and sawdust, were used in composting with pig manure in 60 L reactors with forced aeration for more than a month. Gas emissions were measured continuously, and detailed gas emission patterns were obtained. Concentrations of NH3 and N2O from the composting pig manure mixed with corn stalks or sawdust were higher than those from the spent mushroom compost treatment, especially the sawdust treatment, which had the highest total nitrogen loss among the three runs. Most of the nitrogen was lost in the form of NH3, which accounts for 11.16% to 35.69% of the initial nitrogen. One-way analysis of variance for NH3 emission showed no significant differences between the corn stalk and sawdust treatments, but a significant difference was noted between the spent mushroom compost and sawdust treatments. The introduction of sawdust reduced CH4 emission more than the corn stalks and spent mushroom compost. However, there were no significant differences among the three runs for total carbon loss. All treatments were matured after 30 d. PMID:24711356

  20. Factorial Moments Analyses Show a Characteristic Length Scale in DNA Sequences

    NASA Astrophysics Data System (ADS)

    Mohanty, A. K.; Narayana Rao, A. V. S. S.

    2000-02-01

    A unique feature of most of the DNA sequences, found through the factorial moments analysis, is the existence of a characteristic length scale around which the density distribution is nearly Poissonian. Above this point, the DNA sequences, irrespective of their intron contents, show long range correlations with a significant deviation from the Gaussian statistics, while, below this point, the DNA statistics are essentially Gaussian. The famous DNA walk representation is also shown to be a special case of the present analysis.

  1. Evidence for endoreduplication: germ cell DNA levels prior to chromatin diminution in Mesocyclops edax.

    PubMed

    Rasch, E M; Wyngaard, G A

    2001-06-01

    We studied the functional significance of marked differences in the DNA content of somatic cells and germ line nuclei by static Feulgen-DNA cytophotometry for several species of microcrustaceans that exhibit chromatin diminution during very early stages of embryogenesis. Mature females and males showed many gonadal nuclei with elevated amounts of DNA that persist until dispersal of this "extra" DNA throughout the cytoplasm as fragments and coalescing droplets of chromatin during anaphase of the diminution division.

  2. Recombinant DNA products: Insulin, interferon and growth hormone

    SciTech Connect

    Bollon, A.P.

    1984-01-01

    This book provides the discussion of products of biotechnology of recombinant DNA. The contents include: Recombinant DNA techniques; isolation, cloning, and expression of genes; from somatostatin to human insulin; yeast; an alternative organism for foreign protein production; background in human interferon; preclinical assessment of biological properties of recombinant DNA derived human interferons; human clinical trials of bacteria-derived human ..cap alpha.. interferon.f large scale production of human alpha interferon from bacteria; direct expression of human growth hormone in escherichia coli with the lipoprotein promoter; biological actions in humans of recombinant DNA synthesized human growth hormone; NIH guidelines for research involving recombinant DNA molecules; appendix; viral vectors and the NHY guidelines; FDA's role in approval and regulation of recombinant DNA drugs; and index.

  3. DNA methylation in plants.

    PubMed

    Vanyushin, B F

    2006-01-01

    DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA

  4. Differential Nuclear and Mitochondrial DNA Preservation in Post-Mortem Teeth with Implications for Forensic and Ancient DNA Studies

    PubMed Central

    Higgins, Denice; Rohrlach, Adam B.; Kaidonis, John; Townsend, Grant; Austin, Jeremy J.

    2015-01-01

    Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Futhermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard

  5. Improved PCR Amplification of Broad Spectrum GC DNA Templates

    PubMed Central

    Guido, Nicholas; Starostina, Elena; Leake, Devin; Saaem, Ishtiaq

    2016-01-01

    Many applications in molecular biology can benefit from improved PCR amplification of DNA segments containing a wide range of GC content. Conventional PCR amplification of DNA sequences with regions of GC less than 30%, or higher than 70%, is complex due to secondary structures that block the DNA polymerase as well as mispriming and mis-annealing of the DNA. This complexity will often generate incomplete or nonspecific products that hamper downstream applications. In this study, we address multiplexed PCR amplification of DNA segments containing a wide range of GC content. In order to mitigate amplification complications due to high or low GC regions, we tested a combination of different PCR cycling conditions and chemical additives. To assess the fate of specific oligonucleotide (oligo) species with varying GC content in a multiplexed PCR, we developed a novel method of sequence analysis. Here we show that subcycling during the amplification process significantly improved amplification of short template pools (~200 bp), particularly when the template contained a low percent of GC. Furthermore, the combination of subcycling and 7-deaza-dGTP achieved efficient amplification of short templates ranging from 10–90% GC composition. Moreover, we found that 7-deaza-dGTP improved the amplification of longer products (~1000 bp). These methods provide an updated approach for PCR amplification of DNA segments containing a broad range of GC content. PMID:27271574

  6. Improved PCR Amplification of Broad Spectrum GC DNA Templates.

    PubMed

    Guido, Nicholas; Starostina, Elena; Leake, Devin; Saaem, Ishtiaq

    2016-01-01

    Many applications in molecular biology can benefit from improved PCR amplification of DNA segments containing a wide range of GC content. Conventional PCR amplification of DNA sequences with regions of GC less than 30%, or higher than 70%, is complex due to secondary structures that block the DNA polymerase as well as mispriming and mis-annealing of the DNA. This complexity will often generate incomplete or nonspecific products that hamper downstream applications. In this study, we address multiplexed PCR amplification of DNA segments containing a wide range of GC content. In order to mitigate amplification complications due to high or low GC regions, we tested a combination of different PCR cycling conditions and chemical additives. To assess the fate of specific oligonucleotide (oligo) species with varying GC content in a multiplexed PCR, we developed a novel method of sequence analysis. Here we show that subcycling during the amplification process significantly improved amplification of short template pools (~200 bp), particularly when the template contained a low percent of GC. Furthermore, the combination of subcycling and 7-deaza-dGTP achieved efficient amplification of short templates ranging from 10-90% GC composition. Moreover, we found that 7-deaza-dGTP improved the amplification of longer products (~1000 bp). These methods provide an updated approach for PCR amplification of DNA segments containing a broad range of GC content.

  7. Secure content objects

    DOEpatents

    Evans, William D.

    2009-02-24

    A secure content object protects electronic documents from unauthorized use. The secure content object includes an encrypted electronic document, a multi-key encryption table having at least one multi-key component, an encrypted header and a user interface device. The encrypted document is encrypted using a document encryption key associated with a multi-key encryption method. The encrypted header includes an encryption marker formed by a random number followed by a derivable variation of the same random number. The user interface device enables a user to input a user authorization. The user authorization is combined with each of the multi-key components in the multi-key encryption key table and used to try to decrypt the encrypted header. If the encryption marker is successfully decrypted, the electronic document may be decrypted. Multiple electronic documents or a document and annotations may be protected by the secure content object.

  8. Regulating contents and furnishings.

    PubMed

    Koffel, W E

    1991-01-01

    The criteria in the 1991 edition of the Life Safety Code are a first attempt to address the fire hazards associated with upholstered furniture and mattresses. Recognizing that the criteria do not represent a complete hazard analysis, it is anticipated that the subcommittee will continue its efforts and will evaluate the appropriateness of additional criteria. The NFPA Standards Council also has appointed a Technical Committee on Contents and Furnishings, which will meet in August 1991. This committee will have primary responsibility for developing fire hazard calculation procedures and documents that other committees can use to control the fire hazards of contents and furnishings.

  9. [Effects of enhanced UV-B radiation on physiological metabolism, DNA and protein of crops: a review].

    PubMed

    Li, Yuan; He, Yongmei; Zu, Yanqun

    2006-01-01

    Ozone depletion in stratosphere has led to the increase of solar UV-B radiation reaching to the earth surface, which would affect crops to various extents. This review dealt with the effects of enhanced UV-B radiation on the physiological metabolism, DNA damage and protein content of crops. Enhanced UV-B radiation could increase crops' flavonoid content but decrease their chlorophyll content and photosynthesis, induce gene change, and result in DNA damage and change of protein content.

  10. WormBase: better software, richer content

    PubMed Central

    Schwarz, Erich M.; Antoshechkin, Igor; Bastiani, Carol; Bieri, Tamberlyn; Blasiar, Darin; Canaran, Payan; Chan, Juancarlos; Chen, Nansheng; Chen, Wen J.; Davis, Paul; Fiedler, Tristan J.; Girard, Lisa; Harris, Todd W.; Kenny, Eimear E.; Kishore, Ranjana; Lawson, Dan; Lee, Raymond; Müller, Hans-Michael; Nakamura, Cecilia; Ozersky, Phil; Petcherski, Andrei; Rogers, Anthony; Spooner, Will; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Durbin, Richard; Spieth, John; Stein, Lincoln D.; Sternberg, Paul W.

    2006-01-01

    WormBase (), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism. PMID:16381915

  11. Selenium and spermine alleviate cadmium induced toxicity in the red seaweed Gracilaria dura by regulating antioxidants and DNA methylation.

    PubMed

    Kumar, Manoj; Bijo, A J; Baghel, Ravi S; Reddy, C R K; Jha, Bhavanath

    2012-02-01

    The protective role of exogenously supplied selenium (Se) and polyamines (PAs) such as putrescine (Put) and spermine (Spm) in detoxifying the cadmium (Cd) induced toxicity was studied in the marine red alga Gracilaria dura in laboratory conditions. The Cd exposure (0.4 mM) impede the growth of alga while triggering the reactive oxygen species (ROS viz. O(2)(•-) and H(2)O(2)) generation, inhibition of antioxidant system, and enhancing the lipoxygenase (LOX) activity, malondialdehyde (MDA) level and demethylation of DNA. Additions of Se (50 μM) and/or Spm (1 mM) to the culture medium in contrast to Put, efficiently ameliorated the Cd toxicity by decreasing the accumulation of ROS and MDA contents, while restoring or enhancing the level of enzymatic and nonenzymatic antioxidants and their redox ratio, phycobiliproteins and phytochelatins, over the controls. The isoforms of antioxidant enzymes namely superoxide dismutase (Mn-SOD, ~150 kDa; Fe-SOD ~120 kDa), glutathione peroxidase (GSH-Px, ~120 and 140 kDa), glutathione reductase (GR, ~110 kDa) regulated differentially to Se and/or Spm supplementation. Furthermore, it has also resulted in enhanced levels of endogenous PAs (specially free and bound insoluble Put and Spm) and n-6 PUFAs (C20-3, n-6 and C20-4, n-6). This is for the first time wherein Se and Spm were found to regulate the stabilization of DNA methylation by reducing the events of cytosine demethylation in a mechanism to alleviate the Cd stress in marine alga. The present findings reveal that both Se and Spm play a crucial role in controlling the Cd induced oxidative stress in G. dura.

  12. Ribonucleotides in Bacterial DNA

    PubMed Central

    Schroeder, Jeremy W.; Randall, Justin R.; Matthews, Lindsay A.; Simmons, Lyle A.

    2014-01-01

    In all living cells, DNA is the storage medium for genetic information. Being quite stable, DNA is well-suited for its role in storage and propagation of information, but RNA is also covalently included in DNA through various mechanisms. Recent studies also demonstrate useful aspects of including ribonucleotides in the genome during repair. Therefore, our understanding of the consequences of RNA inclusion into bacterial genomic DNA is just beginning, but with its high frequency of occurrence the consequences and potential benefits are likely to be numerous and diverse. In this review, we discuss the processes that cause ribonucleotide inclusion in genomic DNA, the pathways important for ribonucleotide removal and the consequences that arise should ribonucleotides remain nested in genomic DNA. PMID:25387798

  13. DNA profiles from fingermarks.

    PubMed

    Templeton, Jennifer E L; Linacre, Adrian

    2014-11-01

    Criminal investigations would be considerably improved if DNA profiles could be routinely generated from single fingermarks. Here we report a direct DNA profiling method that was able to generate interpretable profiles from 71% of 170 fingermarks. The data are based on fingermarks from all 5 digits of 34 individuals. DNA was obtained from the fingermarks using a swab moistened with Triton-X, and the fibers were added directly to one of two commercial DNA profiling kits. All profiles were obtained without increasing the number of amplification cycles; therefore, our method is ideally suited for adoption by the forensic science community. We indicate the use of the technique in a criminal case in which a DNA profile was generated from a fingermark on tape that was wrapped around a drug seizure. Our direct DNA profiling approach is rapid and able to generate profiles from touched items when current forensic practices have little chance of success.

  14. Electrocatalysis in DNA Sensors.

    PubMed

    Furst, Ariel; Hill, Michael G; Barton, Jacqueline K

    2014-12-14

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

  15. Electrocatalysis in DNA Sensors

    PubMed Central

    Furst, Ariel; Hill, Michael G.; Barton, Jacqueline K.

    2014-01-01

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

  16. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  17. DNA-based machines.

    PubMed

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures fo