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Sample records for 4n dna content

  1. Enhanced unscheduled DNA synthesis in UV-irradiated human skin explants treated with T4N5 liposomes

    SciTech Connect

    Yarosh, D.B.; Kibitel, J.T.; Green, L.A.; Spinowitz, A. )

    1991-07-01

    Epidermal keratinocytes cultured from explants of skin cancer patients, including biopsies from xeroderma pigmentosum patients, were ultraviolet light-irradiated and DNA repair synthesis was measured. Repair capacity was much lower in xeroderma pigmentosum patients than in normal patients. The extent of DNA repair replication did not decline with the age of the normal patient. Treatment with T4N5 liposomes containing a DNA repair enzyme enhanced repair synthesis in both normal and xeroderma pigmentosum keratinocytes in an irradiation- and liposome-dose dependent manner. These results provide no evidence that aging people or skin cancer patients are predisposed to cutaneous malignancy by a DNA repair deficiency, but do demonstrate that T4N5 liposomes enhance DNA repair in the keratinocytes of the susceptible xeroderma pigmentosum and skin cancer population.

  2. Mitochondrial DNA Content and Lung Cancer Risk

    PubMed Central

    Bonner, Matthew R.; Shen, Min; Liu, Chin-San; DiVita, Margaret; He, Xingzhou; Lan, Qing

    2010-01-01

    Smoky coal contains polycyclic aromatic hydrocarbons (PAHs) and has been strongly implicated in etiology of lung cancer in Xuan Wei, China. While PAHs have been demonstrated to form bulky adducts in nuclear DNA, they have a 90-fold greater affinity for mitochondrial DNA (mtDNA). To compensate for mitochondrial dysfunction or damage, mtDNA content is thought to increase. We conducted a population-based case-control study of lung cancer in Xuan Wei, China hypothesizing that mtDNA content is associated with lung cancer risk. Cases (n = 122) and controls (n = 121) were individually matched on age (±2yrs), sex, village of residence, and type of heating/cooking fuel currently used. Lifetime smoky coal use and potential confounders were determined with questionnaires. mtDNA was extracted from sputum and content was determined with quantitative RT-PCR. Odds ratios (OR) and 95% confidence intervals (95% CI) were calculated with unconditional logistic regression. mtDNA content was dichotomized at the median based on the distribution among the controls. mtDNA content > 157 was associated with a 2-fold increase in lung cancer risk (OR = 1.8; 95% CI = 1.0–3.2) compared with those with ≤157 copies. Risk was higher among those >57 years of age compared with those ≤ 57 years (p interaction = 0.01). In summary, mtDNA content was positively associated with lung cancer risk. Furthermore, there was some evidence that mtDNA content was more strongly associated with lung cancer risk among older individuals. However, due to the small sample size, additional studies are needed to evaluate these associations. PMID:18691788

  3. Synthesis, DNA binding and cleavage activities of copper (II) thiocyanate complex with 4-( N, N-dimethylamino)pyridine and N, N-dimethylformamide

    NASA Astrophysics Data System (ADS)

    Chen, Feng-juan; Xu, Min; Xi, Pin-xian; Liu, Hong-yang; Zeng, Zheng-zhi

    2011-10-01

    Two novel copper(II) thiocyanate complexes with 4-( N, N-dimethylamino) pyridine and N, N-dimethylformamide( 1) and with4-( N, N-dimethylamino) pyridine ( 2) have been synthesized and characterized. The crystal and molecular structures of complexes 1 and 2 were determined by single-crystal X-ray diffraction. Antioxidative activity tests in vitro showed that complex 1 has significant antioxidative activity against hydroxyl free radicals from the Fenton reaction and also oxygen free radicals, which is better than standard antioxidants like vitamin C and mannitol. The interaction of complex 1 with calf thymus DNA was investigated by spectroscopic, cyclic voltammetry, and viscosity measurements. Results suggest that complex 1 can bind to DNA via partial intercalation mode. Moreover, complex 1 has been found to cleavage of plasmid DNA pBR322.

  4. Synthesis, DNA binding and cleavage activities of copper (II) thiocyanate complex with 4-(N,N-dimethylamino)pyridine and N,N-dimethylformamide.

    PubMed

    Chen, Feng-juan; Xu, Min; Xi, Pin-xian; Liu, Hong-yang; Zeng, Zheng-zhi

    2011-10-15

    Two novel copper(II) thiocyanate complexes with 4-(N,N-dimethylamino) pyridine and N,N-dimethylformamide (1) and with 4-(N,N-dimethylamino) pyridine (2) have been synthesized and characterized. The crystal and molecular structures of complexes 1 and 2 were determined by single-crystal X-ray diffraction. Antioxidative activity tests in vitro showed that complex 1 has significant antioxidative activity against hydroxyl free radicals from the Fenton reaction and also oxygen free radicals, which is better than standard antioxidants like vitamin C and mannitol. The interaction of complex 1 with calf thymus DNA was investigated by spectroscopic, cyclic voltammetry, and viscosity measurements. Results suggest that complex 1 can bind to DNA via partial intercalation mode. Moreover, complex 1 has been found to cleavage of plasmid DNA pBR322. PMID:21723777

  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. 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

  7. Relationship between DNA content and nuclear morphology of mature granulocytes.

    PubMed

    Berger, J; Kotelnikov, V M; Kozinec, G I

    1986-01-01

    Increased nuclear segmentation was experimentally induced in rat mature granulocytes. Some mature hypersegmented granulocytes were tetraploid, other hypersegmented granulocytes were diploid. The phenomenon of the formation of tetraploid mature granulocytes has not been observed till the present time. Our data suggest that the increase in nuclear segmentation of granulocytes can be stimulated by elevated DNA content, but the process of nuclear lobe formation is not dependent on cellular content of DNA. PMID:3803627

  8. 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.

  9. Analyzing Schizosaccharomyces pombe DNA Content by Flow Cytometry.

    PubMed

    Boye, Erik; Anda, Silje; Rothe, Christiane; Stokke, Trond; Grallert, Beáta

    2016-01-01

    Flow cytometry can be used to measure the DNA content of individual cells. The data are usually presented as DNA histograms that can be used to examine the cells' progression through the cell cycle. Under standard growth conditions, fission yeast cells do not complete cytokinesis until after G1 phase; therefore, DNA histograms show one major peak representing cells in G1 (2×1C DNA) and G2 phase (1×2C DNA). By analysis of the duration of the fluorescence signal as well as the intensity of the DNA-related signal, it is possible to discriminate between cells in M/G1, S, and G2 This protocol describes how to prepare cells for flow cytometry and analyze them. We also describe the application of barcoding for more accurate comparison of samples. PMID:27250946

  10. 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

  11. 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

  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. 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

  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. 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

  16. 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

  17. 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.

  18. Markovian language model of the DNA and its information content

    PubMed Central

    Srivastava, S.; Baptista, M. S.

    2016-01-01

    This work proposes a Markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and groups of words that share symbolic similarities. Interpreting a node to represent a group of similar words and edges to represent their functional connectivity allows us to construct a network of the grammatical rules governing the appearance of groups of words in the DNA. Our model allows us to predict the transition between groups of words in the DNA with unprecedented accuracy, and to easily calculate many informational quantities to better characterize the DNA. In addition, we reduce the DNA of known bacteria to a network of only tens of nodes, show how our model can be used to detect similar (or dissimilar) genes in different organisms, and which sequences of symbols are responsible for most of the information content of the DNA. Therefore, the DNA can indeed be treated as a language, a Markovian language, where a ‘word’ is an element of a group, and its grammar represents the rules behind the probability of transitions between any two groups. PMID:26909179

  19. 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

  20. 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. PMID:26125928

  1. 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.

  2. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age.

    PubMed

    Meier-Kolthoff, Jan P; Klenk, Hans-Peter; Göker, Markus

    2014-02-01

    The G+C content of a genome is frequently used in taxonomic descriptions of species and genera. In the past it has been determined using conventional, indirect methods, but it is nowadays reasonable to calculate the DNA G+C content directly from the increasingly available and affordable genome sequences. The expected increase in accuracy, however, might alter the way in which the G+C content is used for drawing taxonomic conclusions. We here re-estimate the literature assumption that the G+C content can vary up to 3-5 % within species using genomic datasets. The resulting G+C content differences are compared with DNA-DNA hybridization (DDH) similarities calculated in silico using the GGDC web server, with 70% similarity as the gold standard threshold for species boundaries. The results indicate that the G+C content, if computed from genome sequences, varies no more than 1% within species. Statistical models based on larger differences alone can reject the hypothesis that two strains belong to the same species. Because DDH similarities between two non-type strains occur in the genomic datasets, we also examine to what extent and under which conditions such a similarity could be <70% even though the similarity of either strain to a type strain was ≥ 70%. In theory, their similarity could be as low as 50%, whereas empirical data suggest a boundary closer (but not identical) to 70%. However, it is shown that using a 50% boundary would not affect the conclusions regarding the DNA G+C content. Hence, we suggest that discrepancies between G+C content data provided in species descriptions on the one hand and those recalculated after genome sequencing on the other hand ≥ 1% are due to significant inaccuracies of the applied conventional methods and accordingly call for emendations of species descriptions. PMID:24505073

  3. [Effects of application time and basal/topdressing ratio of nitrogen fertilizer on the spatiotemporal variation of soil NO3- -N and NH4+ -N contents and the grain yield and its quality of wheat].

    PubMed

    Wu, Ji; Guo, Xi-sheng; Yang, Xiao-hu; Huang, Xiao-rong

    2008-11-01

    Field trials were conducted to study the effects of different application time and basal/topdressing ratio of nitrogen fertilizer on the spatiotemporal variation of soil NO3- -N and NH4+ -N contents and the grain yield and its quality of wheat. The results showed that soil NO3- -N and NH4+ -N contents decreased with increasing soil depth. Both the application time and the basal/topdressing ratio of nitrogen fertilizer had significant effects on the NO3- -N and NH4+ -N contents in 0-20 cm soil layer. Compared with basal application, later fertilization and higher topdressing ratio could promote the nitrogen uptake by wheat plant and increase the plant nitrogen recovery significantly, decrease the soil nitrogen recovery during wheat growth, and improve the grain quality significantly, while had less effects on the grain yield. Topdressing too much nitrogen fertilizer at booting stage could result in a significant decrease of grain yield. Under the condition of this experiment, the optimal nitrogen fertilization mode for good wheat grain yield and its quality and good ecological benefits was 5:3:2 of basal application: topdressing at jointing stage: topdressing at booting stage. PMID:19238836

  4. The megakaryocyte DNA content and platelet formation after the sublethal whole body irradiation of rats

    SciTech Connect

    Tanum, G.

    1984-04-01

    The DNA content of rat bone marrow megakaryocytes (MK) was studied by Feulgen photometry, following whole body irradiation with 2 Gy. The DNA measurements were preceded by acetylcholinesterase staining to avoid missing the smaller 2N-8N MK. The number of 2N-8N MK declined immediately following irradiation, whereas the number of 16N-64N MK remained normal for 4 days before decreasing. The number of 2N-8N and 16N-64N MK reached minimum around days 7 and 10, respectively, and thereafter increased to supranormal values at days 14 and 20, respectively. Platelet production, measured by /sup 35/S incorporation into platelets, increased during the first 4 days, then decreased to minimum about day 10. A rise to supranormal values was present at day 20. All values were about normal 30 days after exposure. The observed pattern may be explained as follows: Most of the 16N-64N MK survive the applied dose and maintain their ability to produce platelets. Some of the 2N-4N and 8N MK survive irradiation and transform into platelet-producing MK. No influx of cells from the MK stem cell compartment into the MK compartment can be observed before day 7 after irradiation. One explanation for this time lag may be that thrombocytopenia, which does not occur before then, is an essential stimulus for MK stem cell activation.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. beta 1-4N-acetylgalactosaminyltransferase can synthesize both asialoglycosphingolipid GM2 and glycosphingolipid GM2 in vitro and in vivo: isolation and characterization of a beta 1-4N-acetylgalactosaminyltransferase cDNA clone from rat ascites hepatoma cell line AH7974F.

    PubMed Central

    Hidari, J K; Ichikawa, S; Furukawa, K; Yamasaki, M; Hirabayashi, Y

    1994-01-01

    We have cloned a cDNA encoding beta 1-4N-acetylgalactosaminyltransferase (EC 2.4.1.92) (GalNAc-T) from rat ascites hepatoma of the free-cell type AH7974F. The cell line only expressed asialo-series glycosphingolipids (GSLs) including asialo-GM2 [Taki, T., Hirabayashi, Y., Ishiwata, Y., Matsumoto, M., and Kojima, K. (1979) Biochim. Biophys. Acta 572, 113-120]. The cDNA, pGNA56, was isolated by screening AH7974F cDNA library in lambda gt10 with a probe. The probe was obtained from AH7974F cDNA by PCR using primers with the nucleotide sequence of the human GalNAc-T cDNA. The amino acid sequence deduced from the nucleotide sequence of pGNA56 exhibited 88% similarity to the human GalNAc-T sequence. The enzyme was a typical type II membrane protein, which consisted of a short N-terminal residue, a transmembrane region, and a long C-terminal residue, including the catalytic domain. The substrate specificity of rat GalNAc-T was determined using homogenates from cells into which the cDNA clone was transfected. The enzyme catalysed not only the formation of GM2 and GD2 from GM3 and GD3 respectively, but also asialo-GM2 from CDH. It also acted on GSL substrates, including GM1b, sialylparagloboside and GD1 alpha. On the other hand, the enzyme did not transfer GalNAc to soluble substrates such as glycoproteins and oligosaccharide. The GSL compositional and immunocytochemical analyses of stable transfectants obtained by transfection of the cDNA showed simultaneous expression of asialo-GM2 and GM2 on the plasma membrane. Therefore, we concluded that the formation of asialo-GM2, GM2 and GD2 was catalysed by the single GalNAc-T. Northern-blot hybridization showed that the GalNAc-T mRNA was strongly expressed in rat brain, testis, and spleen. The gene was also expressed in rat normal liver to a lesser extent. We found the GSLs in asialo- and alpha-pathways such as asialo-GM1 and GD1 alpha in the rat tissues by using a sensitive t.l.c.-immunostaining method. These observations also

  10. Ploidy distribution and DNA content variations of Lonicera caerulea (caprifoliaceae) in Japan.

    PubMed

    Miyashita, Tomomi; Araki, Hajime; Hoshino, Yoichiro

    2011-01-01

    Ploidy level and geographical distribution were investigated in Japanese Lonicera caerulea L. Flow cytometric analysis revealed the presence of DNA diploid and DNA tetraploid plants in Japan. Chromosome observation confirmed that diploid and tetraploid plants showed 2n = 2x = 8 and 2n =4x = 36, respectively. The DNA diploid populations were found only in lowland mires, Betsukai, Bekanbeushi, Kushiro and Kiritappu located in eastern Hokkaido. On the other hand, DNA tetraploid populations were distributed in a wide area of Hokkaido, and mainland of Japan. The habitats of DNA tetraploid plants were lowland to alpine region. The DNA content measurement with flow cytometry revealed significant differences in the relative DNA contents among DNA tetraploid populations. The relative DNA content within DNA tetraploid populations varied 1.157-fold at maximum, and might correlate with altitude indicating that DNA contents were smaller as altitude increases. The wide area of distribution in various environments of DNA tetraploid plants suggested the adaptability of the tetraploid plants. Although diploid and tetraploid populations were found, no triploid was detected, indicating crossing difficulty between diploid and tetraploid as confirmed by crossing experiment. PMID:20422248

  11. Lower mitochondrial DNA content relates to high-altitude adaptation in Tibetans.

    PubMed

    Li, Yue; Huang, Wei; Yu, Qin; Cheng, Yao-Ting; Kong, Qing-Peng

    2016-01-01

    Mitochondrial DNA (mtDNA) is crucial to mitochondria in energy production and other physiological functions. When lowlanders arrive at high altitude, the mitochondrial content tends to decrease. However, the mtDNA content of native highlanders share the same feature as lowlanders remains unknown. It is also interesting to dissect the other changes in blood plasma that might accompany the change of mtDNA content. To address these issues, we recruited 241 Tibetan subjects in Tibet and 220 Han subjects in Shaanxi province. Relative mtDNA copy number and blood biochemical indexes were measured. Results show that relative mtDNA copy number in Tibetans is significantly lower as compared to Han subjects; sex, age, blood glucose, triglyceride and total cholesterol show no influence on mtDNA content, but carbon dioxide combining power is negatively correlated with mtDNA content. These results indicate that an increase in CO2 combining power along with lower mtDNA content may provide adaptive potential. PMID:24845439

  12. 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

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

    SciTech Connect

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

    1982-07-01

    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. The authors 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; they 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. They concluded that these strains are diploid.

  14. 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

  15. 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

  16. [Comparative evaluation of dysplasia and early cancer of the stomach based on analysis of DNA content].

    PubMed

    Zolotarevskiĭ, V B; Sklianskaia, O A

    1984-01-01

    DNA content in the tumour cell nuclei was studied in 16 cases of early stomach carcinoma and in the adjacent areas of the foveolar epithelium dysplasia and metaplastic intestinal epithelium. One wave microspectrophotometry was used; the slides were stained with gallocyanin-chrome alum. The number of DNA synthesizing diploid cells was increasing with the increase of the dysplasia degree. The number of tetraploid cells was higher and the signs of aneuploidy appeared in the areas of noninvasive carcinoma. The stem line in early invasive carcinoma was represented by the diploid cells. The increase of cell atypia in tubular and papillary adenocarcinoma is followed by increase of the tetraploid cell number and by the appearance of polyploidy and aneuploidy. Both undifferentiated and goblet-cell carcinomas have similar parameters of the DNA histogram. DNA content allows an objective judgement on the degree of an early carcinoma cell atypia and differentiation of the advanced dysplasia and noninvasive carcinoma. PMID:6098243

  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. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma.

    PubMed

    Gregory, T R

    2001-02-01

    Variation in DNA content has been largely ignored as a factor in evolution, particularly following the advent of sequence-based approaches to genomic analysis. The significant genome size diversity among organisms (more than 200000-fold among eukaryotes) bears no relationship to organismal complexity and both the origins and reasons for the clearly non-random distribution of this variation remain unclear. Several theories have been proposed to explain this 'C-value enigma' (heretofore known as the 'C-value paradox'), each of which can be described as either a mutation pressure' or 'optimal DNA' theory. Mutation pressure theories consider the large portion of non-coding DNA in eukaryotic genomes as either 'junk' or 'selfish' DNA and are important primarily in considerations of the origin of secondary DNA. Optimal DNA theories differ from mutation pressure theories by emphasizing the strong link between DNA content and cell and nuclear volumes. While mutation pressure theories generally explain this association with cell size as coincidental, the nucleoskeletal theory proposes a coevolutionary interaction between nuclear and cell volume, with DNA content adjusted adaptively following shifts in cell size. Each of these approaches to the C-value enigma is problematic for a variety of reasons and the preponderance of the available evidence instead favours the nucleotypic theory which postulates a causal link between bulk DNA amount and cell volume. Under this view, variation in DNA content is under direct selection via its impacts on cellular and organismal parameters. Until now, no satisfactory mechanism has been presented to explain this nucleotypic effect. However, recent advances in the study of cell cycle regulation suggest a possible 'gene nucleus interaction model' which may account for it. The present article provides a detailed review of the debate surrounding the C-value enigma, the various theories proposed to explain it, and the evidence in favour of a

  20. [DNA content in the organs of animals in space flight on the Kosmos-690 satellite].

    PubMed

    Guseĭnov, F T; Komolova, G S; Egorov, I A; Tigranian, R A; Serova, L V

    1978-01-01

    The DNA content in the liver, spleen and bone marrow of white rats exposed to a prolonged gamma-irradiation at a dose of 220 and 800 rad on the 10th day of the 20.5-day space flight and the ground-based synchronous experiment was measured. Space flight factors produced a modifying effect on the postradiation changes in the DNA content. This modifying influence was detected in all organs tested, although in a different degree, and involved an enhancement of the radiation effect which was associated with retardation of postradiation regenerative processes. PMID:713477

  1. Sensitivity to ultraviolet radiation as a function of DNA content in Escherichia coli B/r.

    PubMed Central

    Bronk, B V; Walbridge, D G

    1980-01-01

    Populations of Escherichia coli B/r A were grown to log phase at various growth rates determined by the richness of the medium. The genome content, G, was calculated from log phase doubling times by means of the Cooper-Helmstetter formula. Cell volumes were measured and found to vary linearly with this genome content. Cells with various DNA contents were prepared for ultraviolet irradiation and plated for dark repair under similar conditions. The resulting logarithmic survival curves were all similar in shape: convex up, with straight line portions having approximately the same slope (D0 = 11.4 +/- 0.2 J/m2). The shoulders however increase in width with calculated DNA content giving an extrapolation number which varies roughly as exp(G) or exp (0.6 Gmax). PMID:7020785

  2. 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)

  3. 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

  4. Sustained hypoxia modulates mitochondrial DNA content in the neonatal rat brain.

    PubMed

    Lee, Heung M; Greeley, George H; Englander, Ella W

    2008-03-01

    The effects of placental insufficiency and preterm birth on neurodevelopment can be modeled in experimental settings of neonatal hypoxia in rodents. Here, rat pups were reared in reduced oxygen (9.5%) for 11 days, starting on postnatal day 3 (P3). This led to a significant reduction in brain and body weight gain in hypoxic pups compared to age-matched normoxia-reared controls, plausibly reflecting an inability to fulfill the energetic needs of normal growth and development. Adaptive processes designed to augment energetic capacity in eukaryotes include stimulation of mitochondrial biogenesis. We show that after 11 days of sustained hypoxia, the levels of nuclear respiratory factor-1 and mitochondrial transcription factor A are elevated and the content of mitochondrial DNA (mtDNA) is greater in the hypoxic P14 pup brain compared to normoxic conditions. Corresponding immunohistochemical analyses reveal increased density of mtDNA in large cortical neurons. In contrast, no changes in mtDNA content are observed in the brain of pups reared for 24 h (P3-P4) under hypoxic conditions. Together, these data suggest that prolonged inadequate oxygenation may trigger a compensatory increase in neuronal mitochondrial DNA content to partially mitigate compromised energy homeostasis and reduced energetic capacity in the developing hypoxic brain. PMID:18078825

  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. 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)

  7. Nuclear DNA Content Variation and Species Relationships in the Genus Lupinus (Fabaceae)

    PubMed Central

    NAGANOWSKA, BARBARA; WOLKO, BOGDAN; ŚLIWIŃSKA, ELWIRA; KACZMAREK, ZYGMUNT

    2003-01-01

    The 2C nuclear DNA content has been estimated by flow cytometry in 18 species and botanical forms of the genus Lupinus (family Fabaceae), using propidium iodide as a fluorescent dye. They represented distinct infrageneric taxonomic groups and differed in somatic chromosome numbers. Estimated 2C DNA values ranged from 0·97 pg in L. princei to 2·44 pg in L. luteus, which gives a more than 2·5-fold variation. Statistical analysis of the data obtained resulted in a grouping that supports the generally accepted taxonomic classification of the Old World lupins. The rough-seeded L. princei turned out to be an interesting exception, getting closer to smooth-seeded species. Results of DNA content analyses are discussed with regards to the phylogenetic relationships among the Old World lupins and some aspects of the evolution of the genus. PMID:12853281

  8. 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.

  9. 2C or not 2C: a closer look at cell nuclei and their DNA content.

    PubMed

    Greilhuber, Johann; Dolezel, Jaroslav

    2009-06-01

    The life cycle of animals and plants involves changes in chromosome number (nuclear phase) and sometimes even the karyotype, and consequently the DNA content of a nuclear genome is not static in time. Thus, in order to interpret DNA content data, it is important that the status of the materials from which DNA content is estimated be precisely defined. The previously proposed distinction between "holoploid" (C) and "monoploid" (Cx) genome size covers the most frequent states of plant and animal nuclear genomes. However, restricting nomenclature to just C and Cx still leaves a number of unresolved problems. Here, we propose an extension of the C-value terminology to handle a range of cytogenetic conditions, life cycle segments, and nuclear phases. A set of superscripts and subscripts are used in a formal way to identify life cycle segments and to express the quantitative relationship between these segments. A revision of the current usage of the holoploid chromosome number n was necessary to maintain the intimate link between n and C-value and between the monoploid chromosome number x and Cx-value. In this revision, haplophase individuals (i.e., "haploid" animals and "haploid" spontaneous or experimentally induced land plant sporophytes) have chromosome number n (not 2n, as is the current tradition) and thus nuclear DNA contents based on 1C. However, to avoid an unlimited progression of n levels due to generative polyploidy, zygotic individuals are assigned as 2n starting from the zygote, whatever their ploidy level. Their ploidy is indicated by multiples of the basic chromosome number x. The extended terminology for genome size should eliminate ambiguities in reporting DNA contents in both plants and animals. PMID:19242716

  10. 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

  11. 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

  12. Cell-free circulating mitochondrial DNA content and risk of hepatocellular carcinoma in patients with chronic HBV infection.

    PubMed

    Li, Ling; Hann, Hie-Won; Wan, Shaogui; Hann, Richard S; Wang, Chun; Lai, Yinzhi; Ye, Xishan; Evans, Alison; Myers, Ronald E; Ye, Zhong; Li, Bingshan; Xing, Jinliang; Yang, Hushan

    2016-01-01

    Recent studies have demonstrated a potential link between circulating cell-free mitochondrial DNA (mtDNA) content and cancers. However, there is no study evaluating the association between circulating mtDNA as a non-invasive marker of hepatocellular carcinoma (HCC) risk. We conducted a nested case-control study to determine circulating mtDNA content in serum samples from 116 HBV-related HCC cases and 232 frequency-matched cancer-free HBV controls, and evaluate the retrospective association between mtDNA content and HCC risk using logistic regression and their temporal relationship using a mixed effects model. HCC cases had significantly lower circulating mtDNA content than controls (1.06 versus 2.47, P = 1.7 × 10(-5)). Compared to HBV patients with higher mtDNA content, those with lower mtDNA content had a significantly increased risk of HCC with an odds ratio (OR) of 2.19 (95% confidence interval [CI] 1.28-3.72, P = 0.004). Quartile analyses revealed a significant dose-dependent effect (Ptrend = 0.001) for this association. In a pilot longitudinal sub-cohort of 14 matched cases-control pairs, we observed a trend of dramatically decreased mtDNA content in cases and slightly decreased mtDNA content in controls, with a significant interaction of case-control status with time (Pinteraction = 0.049). Our findings suggest that circulating mtDNA is a potential novel non-invasive biomarker of HCC risk in HBV patients. PMID:27063412

  13. Cell-free circulating mitochondrial DNA content and risk of hepatocellular carcinoma in patients with chronic HBV infection

    PubMed Central

    Li, Ling; Hann, Hie-Won; Wan, Shaogui; Hann, Richard S.; Wang, Chun; Lai, Yinzhi; Ye, Xishan; Evans, Alison; Myers, Ronald E.; Ye, Zhong; Li, Bingshan; Xing, Jinliang; Yang, Hushan

    2016-01-01

    Recent studies have demonstrated a potential link between circulating cell-free mitochondrial DNA (mtDNA) content and cancers. However, there is no study evaluating the association between circulating mtDNA as a non-invasive marker of hepatocellular carcinoma (HCC) risk. We conducted a nested case-control study to determine circulating mtDNA content in serum samples from 116 HBV-related HCC cases and 232 frequency-matched cancer-free HBV controls, and evaluate the retrospective association between mtDNA content and HCC risk using logistic regression and their temporal relationship using a mixed effects model. HCC cases had significantly lower circulating mtDNA content than controls (1.06 versus 2.47, P = 1.7 × 10−5). Compared to HBV patients with higher mtDNA content, those with lower mtDNA content had a significantly increased risk of HCC with an odds ratio (OR) of 2.19 (95% confidence interval [CI] 1.28–3.72, P = 0.004). Quartile analyses revealed a significant dose-dependent effect (Ptrend = 0.001) for this association. In a pilot longitudinal sub-cohort of 14 matched cases-control pairs, we observed a trend of dramatically decreased mtDNA content in cases and slightly decreased mtDNA content in controls, with a significant interaction of case-control status with time (Pinteraction = 0.049). Our findings suggest that circulating mtDNA is a potential novel non-invasive biomarker of HCC risk in HBV patients. PMID:27063412

  14. 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. PMID:27063451

  15. Karyotype and nuclear DNA content of hexa-, octo-, and duodecaploid lines of Bromus subgen. Ceratochloa

    PubMed Central

    2009-01-01

    The subgenus Ceratochloa of the genus Bromus includes a number of closely related allopolyploid forms or species that present a difficult taxonomic problem. The present work combines data concerning chromosome length, heterochromatin distribution and nuclear genome size of different 6x, 8x and 12x accessions in this subgenus. Special attention is paid to the karyotype structure and genomic constitution of duodecaploid plants recently found in South America. Hexaploid lineages possess six almost indistinguishable genomes and a nuclear DNA content between 12.72 pg and 15.10 pg (mean 1Cx value = 2.32 pg), whereas octoploid lineages contain the same six genomes (AABBCC) plus two that are characterized by longer chromosomes and a greater DNA content (1Cx = 4.47 pg). Two duodecaploid accessions found in South America resemble each other and apparently differ from the North American duodecaploid B. arizonicus as regards chromosome size and nuclear DNA content (40.00 and 40.50 pg vs. 27.59 pg). These observations suggest that the South American duodecaploids represent a separate evolutionary lineage of the B. subgenus Ceratochloa, unrecognized heretofore. PMID:21637516

  16. 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

  17. 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

  18. Cytophotometric investigation of DNA and RNA content in nuclei of active Strasburger cells in Pinus nigra var. austriaca (Hoess) Badoux.

    PubMed

    Sauter, J J; Ulrich, H

    1977-01-01

    The nuclei of active, sieve cell-associated Strasburger cells in the secondary phloem of Pinus nigra var. austriaca (Hoess) Badoux have been studied for their structure and DNA and RNA content. No difference in size compared to those of ordinary ray cells was found. The nuclear surface is often increased by an ameboid or lobed shape. The amount of highly decondensed chromatin is greatly increased. Cytophotometric measurements of DNA content of both Feulgen and gallocyanine chromalum-stained nuclei showed normal DNA levels and proved absence of endomitotic polyploidization. RNA content, however, was significantly increased as compared to nuclei of young Strasburger cells and of ordinary ray parenchyma cells. PMID:24420510

  19. 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.

  20. 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. PMID:24853858

  1. Cytochemical evaluation of sperm and lymphocyte DNA content after treatment with 5 N HCl.

    PubMed

    Redi, C A; Garagna, S; Bottiroli, G

    1986-01-01

    In situ as well as extra situm cytochemical methods were used to investigate why the observed Feulgen-DNA value of sperm versus lymphocyte cells is lower than expected. After treatment with 5 N HCl, in situ experiments involving the GCA reaction and the UV cytophotometry showed the loss of DNA in sperm nuclei to be 12% more than that in lymphocyte nuclei. Extra situm study of sperm and lymphocytes treated with 5 N HCl showed the phosphate and DABA contents of sperm to be 35% and 23%, respectively, less than those of lymphocytes. The data suggest that sperm chromatin is much more sensitive than somatic chromatin to HCl depolymerization during the Feulgen reaction, and this can tentatively be attributed to the protein complement of sperm chromatin. PMID:2420758

  2. 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

  3. Comparison of p53 and DNA content abnormalities in adenocarcinoma of the oesophagus and gastric cardia.

    PubMed Central

    Gleeson, C. M.; Sloan, J. M.; McManus, D. T.; Maxwell, P.; Arthur, K.; McGuigan, J. A.; Ritchie, A. J.; Russell, S. E.

    1998-01-01

    This study examined the association between 17p allelic loss, p53 gene mutation, p53 protein expression and DNA aneuploidy in a series of adenocarcinomas arising in the oesophagus and gastric cardia. 17p allelic loss was detected in 79% (15 of 19) of oesophageal and in 83% (29 of 35) of gastric adenocarcinomas. p53 mutations were detected in 70% (14 of 20) and 63% (26 of 41) of oesophageal and of gastric adenocarcinomas respectively. Both tumour types were associated with a predominance of base transitions at CpG dinucleotides. In five cases of oesophageal adenocarcinoma, the same mutation was detected both in tumour and in adjacent dysplastic Barrett's epithelium. Diffuse p53 protein expression was detected in 65% (13 of 20) and 59% (24 of 41) of oesophageal and of gastric tumours, respectively, and was associated with the presence of p53 missense mutation (Chi-squared, P < 0.0001). DNA aneuploidy was detected in 80% (16 of 20) of oesophageal and in 70% (28 of 40) of gastric tumours. No association was found between p53 or DNA content abnormalities and tumour stage or histological subtype. In conclusion, this study detected a similar pattern of p53 alterations in adenocarcinoma of the oesophagus and gastric cardia--molecular data consistent with the observation that these tumours demonstrate similar clinical and epidemiological features. Images Figure 1 Figure 4 PMID:9460999

  4. Different gDNA Content in the Subpopulations of Prostate Cancer Extracellular Vesicles: Apoptotic Bodies, Microvesicles, and Exosomes

    PubMed Central

    Lázaro-Ibáñez, Elisa; Sanz-Garcia, Andres; Visakorpi, Tapio; Escobedo-Lucea, Carmen; Siljander, Pia; Ayuso-Sacido, Ángel; Yliperttula, Marjo

    2014-01-01

    Background Extracellular vesicles (EVs) are cell-derived membrane vesicles. EVs contain several RNAs such as mRNA, microRNAs, and ncRNAs, but less is known of their genomic DNA (gDNA) content. It is also unknown whether the DNA cargo is randomly sorted or if it is systematically packed into specific EV subpopulations. The aim of this study was to analyze whether different prostate cancer (PCa) cell-derived EV subpopulations (apoptotic bodies, microvesicles, and exosomes) carry different gDNA fragments. Methods EV subpopulations were isolated from three PCa cell lines (LNCaP, PC-3, and RC92a/hTERT) and the plasma of PCa patients and healthy donors, and characterized by transmission electron microscopy, nanoparticle tracking analysis and total protein content. gDNA fragments of different genes were detected by real time quantitative PCR and confirmed by DNA sequencing. Results We report that the concentration of EVs was higher in the cancer patients than in the healthy controls. EV subpopulations differed from each other in terms of total protein and DNA content. Analysis of gDNA fragments of MLH1, PTEN, and TP53 genes from the PCa cell-derived EV subpopulations showed that different EVs carried different gDNA content, which could even harbor specific mutations. Altogether, these results suggest that both nucleic acids and proteins are selectively and cell-dependently packed into the EV subtypes. Conclusions EVs derived from PCa cell lines and human plasma samples contain double-stranded gDNA fragments which could be used to detect specific mutations, making EVs potential biomarkers for cancer diagnostics and prognostics. PMID:25111183

  5. 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

  6. 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. PMID:17294697

  7. 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

  8. Myonuclear transcription is responsive to mechanical load and DNA content but uncoupled from cell size during hypertrophy

    PubMed Central

    Kirby, Tyler J.; Patel, Rooshil M.; McClintock, Timothy S.; Dupont-Versteegden, Esther E.; Peterson, Charlotte A.; McCarthy, John J.

    2016-01-01

    Myofibers increase size and DNA content in response to a hypertrophic stimulus, thus providing a physiological model with which to study how these factors affect global transcription. Using 5-ethynyl uridine (EU) to metabolically label nascent RNA, we measured a sevenfold increase in myofiber transcription during early hypertrophy before a change in cell size and DNA content. The typical increase in myofiber DNA content observed at the later stage of hypertrophy was associated with a significant decrease in the percentage of EU-positive myonuclei; however, when DNA content was held constant by preventing myonuclear accretion via satellite cell depletion, both the number of transcriptionally active myonuclei and the amount of RNA generated by each myonucleus increased. During late hypertrophy, transcription did not scale with cell size, as smaller myofibers (<1000 μm2) demonstrated the highest transcriptional activity. Finally, transcription was primarily responsible for changes in the expression of genes known to regulate myofiber size. These findings show that resident myonuclei possess a significant reserve capacity to up-regulate transcription during hypertrophy and that myofiber transcription is responsive to DNA content but uncoupled from cell size during hypertrophy. PMID:26764089

  9. Genetic variants in uracil processing enzymes are associated with abnormal DNA uracil content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction. Maintenance of DNA integrity through DNA repair is critical in cancer prevention. Among the enzymes involved in DNA repair are those that prevent or correct uracil misincorporation in DNA. Repair of misincorporated uracil is important since it can cause double-stranded DNA breaks and o...

  10. DNA content variation in monilophytes and lycophytes: large genomes that are not endopolyploid.

    PubMed

    Bainard, Jillian D; Henry, Thomas A; Bainard, Luke D; Newmaster, Steven G

    2011-08-01

    Less than 1% of known monilophytes and lycophytes have a genome size estimate, and substantially less is known about the presence and prevalence of endopolyploid nuclei in these groups. Thirty-one monilophyte species (including three horsetails) and six lycophyte species were collected in Ontario, Canada. Using flow cytometry, genome size and degree of endopolyploidy were estimated for 37 species. Across the five orders covered, 1Cx-values averaged 4.2 pg in the Lycopodiales, 18.1 pg for the Equisetales, 5.06 pg for a single representative of the Ophioglossales, 14.3 pg for the Osmundales, and 7.06 pg for the Polypodiales. There was no indication of endoreduplication in any of the leaf, stem, or root tissue analyzed. This information is essential to our understanding of DNA content evolution in land plants. PMID:21847691

  11. 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

  12. 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. PMID:12824068

  13. Analysis of Nuclear DNA Content in Capsicum (Solanaceae) by Flow Cytometry and Feulgen Densitometry

    PubMed Central

    MOSCONE, EDUARDO A.; BARANYI, MONIKA; EBERT, IRMA; GREILHUBER, JOHANN; EHRENDORFER, FRIEDRICH; HUNZIKER, ARMANDO T.

    2003-01-01

    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. PMID:12824068

  14. 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. PMID:23619523

  15. Age-related decrease in mtDNA content as a consequence of mtDNA 4977 bp deletion.

    PubMed

    Zabihi Diba, Leila; Mohaddes Ardebili, Seyed Mojtaba; Gharesouran, Jalal; Houshmand, Massoud

    2016-07-01

    As one of the most frequent somatic mutations accumulated during aging in human mitochondrial DNA, the 4977 bp deletion has intrigued scientific interest in recent years. Although many studies have shown a significant increase in the amount of 4977 bp deletion, the findings with respect to an age-dependent escalate of ΔmtDNA4977 bp in blood are still disputatious. Therefore, we investigated the presence of common deletion and mtDNA deletion level in whole blood samples of 100 old individuals (60-90 years). We detected the accumulation of common deletion in 46 old individuals. Consequently, there was statistically significant difference between the aged and young individuals in mitochondrial content (p = 0.01) and deletion levels ranged from 2% to 17% of the total mtDNA (mean: 10% ± 0.02%). We conclude that common deletion has decreased the mtDNA content; however, it is not clearly detectable in the blood as one of the fast replicating tissues comparing with tissues with low mitotic activity. PMID:26152346

  16. Cell cycle synchronization of E. coli using the stringent response, with fluorescence labeling assays for DNA content and replication

    PubMed Central

    Ferullo, Daniel J.; Cooper, Deani L.; Moore, Hayley R.; Lovett, Susan T.

    2009-01-01

    We describe a method for synchronization of the cell cycle in the bacterium E. coli. Treatment of asynchronous cultures with the amino acid analog, DL-serine hydroxamate, induces the stringent response, with concomitant arrest of DNA replication at initiation. Following release of the stringent response, cells initiate DNA replication in synchrony, as determined by flow cytometry for DNA content, Southern blotting and microscopy. This method has the advantage that it can be used in fully wild-type cells, at different growth rates, and may be applicable to other bacterial species with replication control by the stringent response. We also elaborate other methods useful for establishing cell cycle parameters in bacterial populations. We describe flow cytometric methods for analyzing bacterial populations for DNA content using the DNA-specific dye PicoGreen, readily detected by most commercial flow cytometers. We also present an method for incorporation of the nucleotide ethynyl-deoxyuridine, EdU, followed by “click” labeling with fluorescent dyes, which allows us to measure and visualize newly replicated DNA in fixed E. coli K-12 cells under non-denaturing conditions. PMID:19245839

  17. Cell cycle synchronization of Escherichia coli using the stringent response, with fluorescence labeling assays for DNA content and replication.

    PubMed

    Ferullo, Daniel J; Cooper, Deani L; Moore, Hayley R; Lovett, Susan T

    2009-05-01

    We describe a method for synchronization of the cell cycle in the bacterium Escherichia coli. Treatment of asynchronous cultures with the amino acid analog, dl-serine hydroxamate, induces the stringent response, with concomitant arrest of DNA replication at initiation. Following release of the stringent response, cells initiate DNA replication in synchrony, as determined by flow cytometry for DNA content, Southern blotting and microscopy. This method has the advantage that it can be used in fully wild-type cells, at different growth rates, and may be applicable to other bacterial species with replication control by the stringent response. We also elaborate other methods useful for establishing cell cycle parameters in bacterial populations. We describe flow cytometric methods for analyzing bacterial populations for DNA content using the DNA-specific dye PicoGreen, readily detected by most commercial flow cytometers. We also present an method for incorporation of the nucleotide ethynyl-deoxyuridine, EdU, followed by "click" labeling with fluorescent dyes, which allows us to measure and visualize newly replicated DNA in fixed E. coli K-12 cells under non-denaturing conditions. PMID:19245839

  18. Diagnostic and prognostic impact of cytochemically assessed nuclear DNA contents in human adenocarcinomas of the mammary gland.

    PubMed

    Askensten, U

    1988-01-01

    Cytochemical assessments of the nuclear DNA contents in carcinomas of the breast can be used for both prognostic and diagnostic purposes. Two main techniques are currently being used, viz. flow cytometry (FCM) and microspectrophotometry (MSP). An account of their advantages and disadvantages is given. In addition, an old, rather crude, cytophotometric technique can be used for histopathological sections of paraffin-embedded specimens. The principal sampling procedures are fine-needle aspiration biopsy and the so-called imprint technique, where the specimens are made from the cut surface of the freshly excised operation specimen. Paraffin-embedded histopathological material can also be used, applying a newly developed MSP procedure, where isolated nuclei from deparaffinized/disintegrated specimens are analyzed. Most important is that intact cell nuclei, representative for the whole tumour nodule, can be obtained. The simultaneous use of FCM and MSP is also of utmost importance for the reliability in the interpretation of the results. Then, a kind of "DNA malignancy grading" is obtained that in several investigations has proven itself to be an excellent prognosticating tool that can be used for making an adequate choice of therapy for the individual patient. The diagnostic value of the results of the cytochemically assessed nuclear DNA distribution patterns is not so high as the prognostic one. Tumours with a diploid type of nuclear DNA content can be found both among benign and malignant neoplasms. However, a neoplasm with an aneuploid DNA distribution pattern can almost certainly be considered highly malignant. PMID:3066302

  19. 17β-Hydroxysteroid dehydrogenase type 10 predicts survival of patients with colorectal cancer and affects mitochondrial DNA content.

    PubMed

    Amberger, Albert; Deutschmann, Andrea J; Traunfellner, Pia; Moser, Patrizia; Feichtinger, René G; Kofler, Barbara; Zschocke, Johannes

    2016-04-28

    Mitochondrial energy production is reduced in tumor cells, and altered mitochondrial respiration contributes to tumor progression. Synthesis of proteins coded by mitochondrial DNA (mtDNA) requires the correct processing of long polycistronic precursor RNA molecules. Mitochondrial RNase P, composed of three different proteins (MRPP1, HSD10, and MRPP3), is necessary for correct RNA processing. Here we analyzed the role of RNase P proteins in colorectal cancer. High HSD10 expression was found in 28%; high MRPP1 expression in 40% of colorectal cancers, respectively. Expression of both proteins was not significantly associated with clinicopathological parameters. Survival analysis revealed that loss of HSD10 expression is associated with poor prognosis. Cox regression demonstrated that patients with high HSD10 tumors are at lower risk. High HSD10 expression was significantly associated with high mtDNA content in tumor tissue. A causal effect of HSD10 overexpression or knock down with increased or reduced mtDNA levels, respectively, was confirmed in tumor cell lines. Our data suggest that HSD10 plays a role in alterations of energy metabolism by regulating mtDNA content in colorectal carcinomas, and HSD10 protein analysis may be of prognostic value. PMID:26884257

  20. 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

  1. Role of CpG context and content in evolutionary signatures of brain DNA methylation

    PubMed Central

    Xin, Yurong; O’Donnell, Anne H.; Ge, Yongchao; Chanrion, Benjamin; Milekic, Maria; Rosoklija, Gorazd; Stankov, Aleksandar; Arango, Victoria; Dwork, Andrew J.; Gingrich, Jay A.; Haghighi, Fatemeh G.

    2011-01-01

    DNA methylation is essential in brain function and behavior; therefore, understanding the role of DNA methylation in brain-based disorders begins with the study of DNA methylation profiles in normal brain. Determining the patterns and scale of methylation conservation and alteration in an evolutionary context enables the design of focused but effective methylation studies of disease states. We applied an enzymatic-based approach, Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS), which utilizes second-generation sequencing technology to provide an unbiased representation of genome-wide DNA methylation profiles of human and mouse brains. In this large-scale study, we assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. In addition to CpG density, these data show that genomic context is a critical factor in DNA methylation conservation and alteration signatures throughout mammalian brain evolution. We identify key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease. PMID:22048252

  2. 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.

  3. 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.

  4. In vitro embryo production efficiency in cattle and its association with oocyte adenosine triphosphate content, quantity of mitochondrial DNA, and mitochondrial DNA haplogroup.

    PubMed

    Tamassia, M; Nuttinck, F; May-Panloup, P; Reynier, P; Heyman, Y; Charpigny, G; Stojkovic, M; Hiendleder, S; Renard, J-P; Chastant-Maillard, S

    2004-08-01

    Mitochondria have a broad range of functions that affect reproduction, and structural as well as quantitative variation in mtDNA has been associated with gamete quality and reproductive success. To investigate the mitochondria effect on in vitro embryo production, we collected oocytes by ultrasound-guided follicular aspiration from donor cows known to differ in the developmental capacity, measured by the blastocyst formation rate, of their oocytes. To evaluate the potential effects of mtDNA and mitochondrial function on oocyte quality, the donor cows' mtDNA control region was sequenced and, after pairwise comparisons of polymorphisms, animals were grouped into two major haplogroups. The number of mtDNA molecules per oocyte was quantified by real-time PCR, and the adenosine triphosphate (ATP) content was measured in each oocyte to identify variations between haplogroups. Overall, ATP stocks in oocytes of the two haplogroups differed significantly (P < 0.05; means +/- SEM) both at the germinal vesicle and metaphase II stages (2.8 +/- 0.06 pmol vs. 2.6 +/- 0.07 pmol and 2.9 +/- 0.1 pmol vs. 2.3 +/- 0.06 pmol, respectively). The proportion of development to blastocyst was significantly different between haplogroups (22.3 +/- 2.1 % vs. 36.7 +/- 2.9 %). The number of mtDNA molecules per oocyte was highly variable (377 327 +/- 14 104, ranging from 2.0 x 10(3) to 1.2 x 10(6)) but not significantly different between the two haplogroups; significant differences were observed between animals without any apparent relationship to blastocyst production. These data suggest that mitochondria and mtDNA haplogroup affect the developmental capacity of bovine oocytes in vitro. PMID:15084486

  5. Relative DNA content in diploid, polyploid, and multiploid species of Paspalum (Poaceae) with relation to reproductive mode and taxonomy.

    PubMed

    Galdeano, Florencia; Urbani, M H; Sartor, M E; Honfi, A I; Espinoza, F; Quarin, C L

    2016-07-01

    It is generally accepted that polyploids have downsized basic genomes rather than additive values with respect to their related diploids. Changes in genome size have been reported in correlation with several biological characteristics. About 75 % of around 350 species recognized for Paspalum (Poaceae) are polyploid and most polyploids are apomictic. Multiploid species are common with most of them bearing sexual diploid and apomictic tetraploid or other ploidy levels. DNA content in the embryo and the endosperm was measured by flow cytometry in a seed-by-seed analysis of 47 species including 77 different entities. The relative DNA content of the embryo informed the genome size of the accession while the embryo:endosperm ratio of DNA content revealed its reproductive mode. The genome sizes (2C-value) varied from 0.5 to 6.5 pg and for 29 species were measured for the first time. Flow cytometry provided new information on the reproductive mode for 12 species and one botanical variety and supplied new data for 10 species concerning cytotypes reported for the first time. There was no significant difference between the mean basic genome sizes (1Cx-values) of 32 sexual and 45 apomictic entities. Seventeen entities were diploid and 60 were polyploids with different degrees. There were no clear patterns of changes in 1Cx-values due to polyploidy or reproductive systems, and the existing variations are in concordance with subgeneric taxonomical grouping. PMID:26965283

  6. 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

  7. 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

  8. 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

  9. 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

  10. Synthesis and Cytostatic Evaluation of 4-N-Alkanoyl and 4-N-Alkyl Gemcitabine Analogues

    PubMed Central

    Pulido, Jesse; Sobczak, Adam J.; Balzarini, Jan; Wnuk, Stanislaw F.

    2014-01-01

    Couplings of gemcitabine with the functionalized carboxylic acids (C9-C13) or reactions of 4-N-tosylgemcitabine with the corresponding alkyl amines afforded 4-N-alkanoyl and 4-N-alkyl gemcitabine derivatives. The analogues with a terminal hydroxyl group on the alkyl chain were efficiently fluorinated under conditions that are compatible with protocols for 18F labeling. The 4-N-alkanoylgemcitabines showed potent cytostatic activities in the low nM range against a panel of tumor cell lines while cytotoxicity of the 4-N-alkylgemcitabines were in the low μM range. The cytotoxicity for the 4-N-alkanoylgemcitabine analogues were reduced approximately by two orders of magnitude in the 2′-deoxycytidine kinase (dCK)-deficient CEM/dCK- cell line whereas cytotoxicity of the 4-N-alkylgemcitabines were only 2-5 times lower. None of the compounds acted as efficient substrates for cytosolic dCK, and therefore, the 4-N-alkanoyl analogues need to be converted first to gemcitabine to display a significant cytostatic potential, while 4-N-alkyl derivatives attain the modest activity without “measurable” conversion to gemcitabine. PMID:24341356

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Barcoding, types and the Hirudo files: using information content to critically evaluate the identity of DNA barcodes.

    PubMed

    Kvist, Sebastian; Oceguera-Figueroa, Alejandro; Siddall, Mark E; Erséus, Christer

    2010-12-01

    Species identifications based on DNA barcoding rely on the correct identity of previously barcoded specimens, but little attention has been given to whether deposited barcodes include correspondence to the species' name-bearing type. The information content associated with COX1 sequences in the two most commonly used repositories of barcodes, GenBank and the Barcode of Life Data System (BOLD), is often insufficient for subsequent evaluation of the robustness of the identification procedure. We argue that DNA barcoding and taxonomy alike will benefit from more information content in the annotations of barcoded specimens as this will allow for validation and re-evaluation of the initial specimen identification. The aim should be to closely connect specimens from which reference barcodes are generated with the holotype through straight-forward taxonomy, and geographical and genetic correlations. Annotated information should also include voucher specimens and collector/identifier information. We examine two case studies based on empirical data, in which barcoding and taxonomy benefit from increased information content. On the basis of data from the first case study, we designate a barcoded neotype of the European medicinal leech, Hirudo medicinalis, on morphological and geographical grounds. PMID:21171864

  17. 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

  18. MITOCHONDRIAL DNA IN THE OOGAMOCHLAMYS CLADE (CHLOROPHYCEAE): HIGH GC CONTENT AND UNIQUE GENOME ARCHITECTURE FOR GREEN ALGAE(1).

    PubMed

    Borza, Tudor; Redmond, Erin K; Laflamme, Mark; Lee, Robert W

    2009-12-01

    Most mitochondrial genomes in the green algal phylum Chlorophyta are AT-rich, circular-mapping DNA molecules. However, mitochondrial genomes from the Reinhardtii clade of the Chlorophyceae lineage are linear and sometimes fragmented into subgenomic forms. Moreover, Polytomella capuana, from the Reinhardtii clade, has an elevated GC content (57.2%). In the present study, we examined mitochondrial genome conformation and GC bias in the Oogamochlamys clade of the Chlorophyceae, which phylogenetic data suggest is closely related to the Reinhardtii clade. Total DNA from selected Oogamochlamys taxa, including four Lobochlamys culleus (H. Ettl) Pröschold, B. Marin, U. G. Schlöss. et Melkonian strains, Lobochlamys segnis (H. Ettl) Pröschold, B. Marin, U. G. Schlöss. et Melkonian, and Oogamochlamys gigantea (O. Dill) Pröschold, B. Marin, U. G. Schlöss. et Melkonian, was subjected to Southern blot analyses with cob and cox1 probes, and the results suggest that the mitochondrial genome of these taxa is represented by multiple-sized linear DNA fragments with overlapping homologies. On the basis of these data, we propose that linear mitochondrial DNA with a propensity to become fragmented arose in an ancestor common to the Reinhardtii and Oogamochlamys clades or even earlier in the evolutionary history of the Chlorophyceae. Analyses of partial cob and cox1 sequences from these Oogamochlamys taxa revealed an unusually high GC content (49.9%-65.1%) and provided evidence for the accumulation of cob and cox1 pseudogenes and truncated sequences in the mitochondrial genome of all L. culleus strains examined. PMID:27032590

  19. Quantification of the DNA content of structurally abnormal X chromosomes and X chromosome aneuploidy using high resolution bivariate flow karyotyping.

    PubMed

    Trask, B; van den Engh, G; Nussbaum, R; Schwartz, C; Gray, J

    1990-01-01

    Quantification of the Hoechst and chromomycin A3 fluorescence intensities of mitotic human chromosomes isolated from karyotypically normal and abnormal cells was performed with a dual beam flow cytometer. The resultant flow karyotypes contain information about the relative DNA content and base composition of chromosomes and their relative frequencies in the mitotic cell sample. The relative copy number of X and Y chromosomes was determined for 38 normal males and females and 6 cell lines with X or Y chromosome aneuploidy. Flow karyotype diagnoses corresponded with conventional cytogenetic results in all cases. We show that chromosome DNA content can be derived from peak position in Hoechst vs. chromomycin flow karyotypes. These values are linearly related to propidium iodide staining intensity as measured with flow cytometry and to the binding of gallocyanin chrome alum to phosphate groups as measured with slide-based scanning photometry. Cell lines with deleted or dicentric X chromosomes ranging in length from 0.53 to 1.95 times normal were analyzed by using flow cytometry. The measured difference in DNA content between a normal X and each of the structurally abnormal chromosomes was linearly correlated to the difference predicted from cytogenetics and/or probe analyses. Deletions of 3-5 Mb, which were at and below the detection limits of conventional cytogenetics, could be quantified by flow karyotyping in individuals with X-linked diseases such as Duchenne muscular dystrophy, choroideremia, and ocular albinism/ichthyosis. The results show that the use of flow karyotyping to quantify the size of restricted regions of the genome can complement conventional cytogenetics and other physical mapping techniques in the study of genetic disorders. PMID:2106419

  20. 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...

  1. GENE CONTENT AND ORGANIZATION OF AN 85-KBP DNA SEGMENT FROM THE GENOME OF SPIROPLASMA KUNKELII

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spiroplasma kunkelii is a cell wall-less phloem-inhabiting bacterium that causes corn stunt disease. As a part of the S. kunkelii Genome Sequencing Project, we analyzed an 85 kbp DNA segment from the pathogenic S. kunkelii strain CR2-3x. This genome segment contains 101 open reading frames (ORFs). ...

  2. INCREASED 8-HYDROXY GUANINE CONTENT OF CHLOROPLAST DNA FROM OZONE TREATED PLANTS

    EPA Science Inventory

    The mechanism of ozone-mediated plant injury is not know but has been postulated to involve oxygen free radicals. Hydroxyl free radicals react with DNA causing formation of many products, one of which is 8-hydroxyguanine. By using high performance liquid chromatography with elect...

  3. C-value paradox in angiosperm plant species. I. Sensitivity to DNase I in species with different 2C DNA content.

    PubMed

    Olszewska, M J

    1992-01-01

    The experimental conditions for DNAase I digestion in situ for plant nuclei have been presented. Cytophotometric measurements of DNA loss performed on Feulgen-stained nuclei of three species differing in 2C DNA, heterochromatin and condensed euchromatin contents have shown that the lower 2C DNA amount the higher is DNase I sensitivity. Heterochromatin and some fractions of euchromatin are DNase I resistant. Microdensitometric measurements along M chromosome in Vicia faba have demonstrated the sites hypersensitive to DNase I. PMID:1483532

  4. Clonability and gene distribution on human chromosome 21: reflections of junk DNA content?

    PubMed

    Gardiner, K

    1997-12-31

    Data from transcriptional mapping of human chromosome 21 have been compiled from a number of sources. Regardless of the gene identification technique used, a consistent picture has developed: the centromere proximal half of 21q, which contains 50% of the DNA (20 Mb), harbors only 10% of the expressed sequences. Because of the variety of gene isolation techniques used, this result is unlikely to arise simply from methodological artefacts, biases in clonability or tissue specificity of expression. This region is known to be AT-rich and to contain APP, the largest gene (spanning 300 kb) currently analyzed on 21q. Interesting preliminary data from analysis of the Fugu rubripes homolog of APP has shown an unusually high, 50-fold, compaction of intron size, raising the intriguing possibility that >90% of the DNA in the human gene may be functionless. Thus, data from a variety of approaches suggest that a large part of 21q very likely has neither coding capacity nor associated regulatory function. By these criteria, it is a good candidate for a repository of junk DNA. PMID:9461378

  5. 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

  6. 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.

  7. 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...

  8. 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...

  9. 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

  10. 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

  11. 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)

  12. Changes in nuclear, nucleolar and cytoplasmic RNA content during growth and differentiation of root parenchyma cells in plant species with different dynamics of DNA endoreplication.

    PubMed

    Marciniak, K; Bilecka, A

    1985-01-01

    Using cytophotometric method, after staining preparations with gallocyanin RNA content was examined in nucleus, nucleolus and cytoplasm of six species of angiospermal plants in successive (1-7 mm) segments of root representing successive zones of differentiation. During the cell cycle, RNA content duplicates in the nucleus, nucleolus and cytoplasm of meristematic cells. On the other hand, during growth and differentiation of parenchyma cells in species with endoreplication the content of nucleolar RNA does not increase in proportion with DNA content. High level of endoreplication is connected with high nucleolar RNA content and low cytoplasmic RNA content. In species without endoreplication at low nucleolar RNA content, a considerable growth of cytoplasmic RNA content takes place. PMID:2417894

  13. Flow cytometric analysis and microsatellite genotyping reveal extensive DNA content variation in Trypanosoma cruzi populations and expose contrasts between natural and experimental hybrids

    PubMed Central

    Lewis, Michael D.; Llewellyn, Martin S.; Gaunt, Michael W.; Yeo, Matthew; Carrasco, Hernán J.; Miles, Michael A.

    2009-01-01

    Trypanosoma cruzi exhibits remarkable genetic heterogeneity. This is evident at the nucleotide level but also structurally, in the form of karyotypic variation and DNA content differences between strains. Although natural populations of T. cruzi are predominantly clonal, hybrid lineages (TcIId and TcIIe) have been identified and hybridisation has been demonstrated in vitro, raising the possibility that genetic exchange may continue to shape the evolution of this pathogen. The mechanism of genetic exchange identified in the laboratory is unusual, apparently involving fusion of diploid parents followed by genome erosion. We investigated DNA content diversity in natural populations of T. cruzi in the context of its genetic subdivisions by using flow cytometric analysis and multilocus microsatellite genotyping to determine the relative DNA content and estimate the ploidy of 54 cloned isolates. The maximum difference observed was 47.5% between strain Tu18 cl2 (TcIIb) and strain C8 cl1 (TcI), which we estimated to be equivalent to ∼73 Mb of DNA. Large DNA content differences were identified within and between discrete typing units (DTUs). In particular, the mean DNA content of TcI strains was significantly less than that for TcII strains (P < 0.001). Comparisons of hybrid DTUs TcIId/IIe with corresponding parental DTUs TcIIb/IIc indicated that natural hybrids are predominantly diploid. We also measured the relative DNA content of six in vitro-generated TcI hybrid clones and their parents. In contrast to TcIId/IIe hybrid strains these experimental hybrids comprised populations of sub-tetraploid organisms with mean DNA contents 1.65–1.72 times higher than the parental organisms. The DNA contents of both parents and hybrids were shown to be relatively stable after passage through a mammalian host, heat shock or nutritional stress. The results are discussed in the context of hybridisation mechanisms in both natural and in vitro settings. PMID:19393242

  14. 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.

  15. Effects of Spent Pot Liner on mitotic activity and nuclear DNA content in meristematic cells of Allium cepa.

    PubMed

    Andrade-Vieira, Larissa Fonseca; de Campos, José Marcello Salabert; Davide, Lisete Chamma

    2012-09-30

    Industrial waste usually contains complex mixtures of mutagenic chemicals. Spent Pot Liner (SPL) is a complex solid waste from the aluminum industry, which is composed of organics, fluoride salts, inorganic cyanides, metals, and sodium. Due to the toxicity of these compounds, this study sought to use cytogenetics and flow cytometry to assess the effects of SPL on cell cycle parameters and DNA content in meristematic cells of Allium cepa. Three concentrations of leachates from SPL-soil mixtures were used for the study: 0, 10, and 25%. Roots were collected and analyzed after 4, 8, 12, 24, and 36 h of exposure to the above SPL leachates. The results showed an overall mitodepressive effect accompanied by an increased percentage of condensed nuclei and genomic instability as evidenced by the presence of cellular/chromosomal abnormalities. Terminal deoxynucleotidyl transferase dUTP nick end labeling revealed nuclei with fragmented DNA, a marker of programmed cell death. This study also addressed the question of reversibility of the effects of SPL and found that 36 h of exposure to 25% SPL seemed to be the point at which the effects on the induction of apoptosis became irreversible. PMID:22634111

  16. 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.

  17. 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

  18. 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)

  19. 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

  20. 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. PMID:20222712

  1. 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.

  2. Changes in nuclear and nucleolar protein content during the growth and differentiation of root parenchyma cells in plant species with different DNA-endoreplication dynamics.

    PubMed

    Marciniak, K; Bilecka, A

    1986-01-01

    Using cytophotometric procedures, we measured the nuclear and nucleolar protein content of successive zones of growth and differentiation in consecutive (1-7 mm) root segments obtained from eight species of the Angiospermae after staining the preparations with Feulgen-Naphthol Yellow S (F-NYS). In meristematic cells the nuclear and nucleolar protein content was found to double during the cell cycle. In species in which differentiation occurs at the same time as nuclear DNA endoreplication, i.e. Vicia faba subsp. minor, V. faba subsp. major, Pisum sativum, Hordeum vulgare and Amaryllis belladonna, the pool of nuclear proteins observed during the G2 phase of the cell cycle was seen in the differentiated zone in nuclei containing 8C DNA. Species in which differentiation is not accompanied by the process of nuclear DNA endoreplication, i.e. Levisticum officinale, Tulipa kaufmanniana and Haemanthus katharinae, exhibited the highest nuclear proteins content during the G2 phase of the cell cycle; comparably high values were not found in the differentiated zone. A decrease in nucleolar protein content was observed during the process of differentiation, this tendency being more evident in the studied species that do not exhibit endoreplication. PMID:3733472

  3. Comparative flow cytometric analysis of DNA-bound PCNA and DNA content as estimators of S-phase cells in cell cultures.

    PubMed

    Bustamante, A S; Guervós, M A; de los Toyos, J R; Dolbeare, F; Sampedro, A

    1996-07-01

    Flow cytometric estimations of S-phase cells were carried out on cultures from three different cell lines and in frozen aliquots. A PCNA-extraction protocol was applied. Measurements of the S fraction estimated from bivariate PCNA/DNA analysis after detergent extraction of DNA non-bound PCNA were compared with those obtained from total DNA histograms (Vindelöv and Christensen's technique, methanol-fixed whole cells and PCNA-extracted nuclei). No significant differences between methods, or between fresh and frozen specimens, were found in the measurements of the percentage of S-phase cells. Nevertheless, nuclei yield following PCNA extraction was highly variable, ranging from 63% to 10% (mean: 26%). In some cases, the extraction was not complete and samples had to be discarded. Usually, boundaries between S-phase events and G0/G1 or G2/M subpopulations were not clearly defined. Because of these shortcomings, and the fact that is more costly and time consuming, the estimation of the S-phase fraction by means of bivariate DNA-bound PCNA/total DNA flow cytometric studies does not seem to surpass that obtained from standard DNA cell cycle analyses. PMID:8844110

  4. COMPARISON OF RAPID METHODS FOR THE EXTRACTION OF BACTERIAL DNA FROM COLONIC AND CECAL LUMEN CONTENTS OF THE PIG

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The increasing use of DNA methodologies to study the microflora of the pig gastrointestinal tract requires an efficient recovery of bacterial DNA from intestinal samples. Thus, the objective of this study was to determine which extraction methods are most effective for colonic and cecal lumen sampl...

  5. Base-content dependence of emission enhancements, quantumyields, and lifetimes of cyanine dyes bound to double-strand DNA: Photophysical properties of monomeric and bichromophoric DNA stains

    SciTech Connect

    Netzel, T.L.; Nafisi, K.; Zhao, M.; Lenhard, J.R.; Johnson, I.

    1995-12-21

    This paper reports fluorescence quantum yield, emission enhancement, and emission lifetime measurements for 10 cyanine dyes complexed to calf thymus DNA (CT-DNA), (dAdT){sub 10}, and (dGdC){sub 6} duplexes. Six of the dyes are linked bichromophores with four cationic charges per molecule, and four are monomers with two cationic charges per molecule. All of the dyes exhibit either bi- or triexponential emission decay kinetics reflecting different dye/ds DNA modes of binding, and the average radiative lifetime for the bichromophores bound to ds DNA is 5.1{+-}0.8 ns. These results are consistent with expectations that binding-induced restriction of torsion about the central methine bridge is responsible for the large emission enhancements of these dyes. Scrutiny of the lengths of average emission lifetime for these 10 dyes on (dAdT){sub 10} and (dGdC){sub 6} duplexes finds that they do not vary as expected if electron transfer (ET) emission quenching were an important process. There are also differences in emission quantum yield between dyes with pyridinium and quinolinium structural components when bound to (dAdT){sub 10} and (dGdC){sub 6} duplexes. These differences are very distinct for the monomeric dyes where pyridinium dyes have 4-fold greater emission yields on (dAdT){sub 10} duplexes and quinolinium dyes have 2-fold greater emission yields on (dGdC){sub 6} duplexes. 68 refs., 7 figs., 6 tabs.

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

    PubMed Central

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

    1993-01-01

    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) PMID:8357263

  7. “Indefinite for Dysplasia” in Barrett's Esophagus: Inflammation and DNA Content Abnormality are Significant Predictors of Early Detection of Neoplasia

    PubMed Central

    Choi, Won-Tak; Emond, Mary J; Rabinovitch, Peter S; Ahn, Joseph; Upton, Melissa P; Westerhoff, Maria

    2015-01-01

    Background: Dysplasia arising from Barrett's esophagus precedes esophageal adenocarcinoma (EAC). Cases that are difficult to diagnose as dysplastic, especially in the setting of inflammation, may be designated “indefinite for dysplasia (IND).” Although flow cytometric analysis of DNA content has shown some promise in detecting EAC, there are few reports that have specifically evaluated the outcome of IND. Aims and methods: We analyzed a series of 96 IND patients seen at the University of Washington between 2005 and 2013 to determine the outcome of IND and to identify factors (including histologic features and DNA flow cytometric data) associated with subsequent detection of neoplasia. Results: Twenty-five percent of IND cases were found to have low-grade dysplasia, high-grade dysplasia (HGD), or EAC within 1 year, with 37% and 47% detected within 2 and 3 years, respectively. The 1-, 2-, and 3-year detection rates of HGD or EAC were 10%, 13%, and 20%, respectively. Active inflammation (hazard ratio (HR)=3.4, P=0.0005) and abnormal DNA content (HR=5.7, P=0.003) were significant risk factors of neoplasia. When active inflammation and DNA flow cytometric results were considered together, the HR for the combined markers was 18.8 (P<0.0001). The sensitivity and specificity of the combined markers for predicting detection of subsequent neoplasia within 3 years were 100% and 60%, respectively, with 100% negative and 89% positive predictive values. Conclusions: Histology with the support of DNA flow cytometry can identify a subset of IND patients who may have a higher risk for subsequent detection of neoplasia. PMID:25761942

  8. 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...

  9. 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

  10. The content of DNA and RNA in microparticles released by Jurkat and HL-60 cells undergoing in vitro apoptosis

    SciTech Connect

    Reich, Charles F.; Pisetsky, David S.

    2009-03-10

    Microparticles are small membrane-bound vesicles that are released from apoptotic cells during blebbing. These particles contain DNA and RNA and display important functional activities, including immune system activation. Furthermore, nucleic acids inside the particle can be analyzed as biomarkers in a variety of disease states. To elucidate the nature of microparticle nucleic acids, DNA and RNA released in microparticles from the Jurkat T and HL-60 promyelocytic cell lines undergoing apoptosis in vitro were studied. Microparticles were isolated from culture media by differential centrifugation and characterized by flow cytometry and molecular approaches. In these particles, DNA showed laddering by gel electrophoresis and was present in a form that allowed direct binding by a monoclonal anti-DNA antibody, suggesting antigen accessibility even without fixation. Analysis of RNA by gel electrophoresis showed intact 18s and 28s ribosomal RNA bands, although lower molecular bands consistent with 28s ribosomal RNA degradation products were also present. Particles also contained messenger RNA as shown by RT-PCR amplification of sequences for {beta}-actin and GAPDH. In addition, gel electrophoresis showed the presence of low molecular weight RNA in the size range of microRNA. Together, these results indicate that microparticles from apoptotic Jurkat and HL-60 cells contain diverse nucleic acid species, indicating translocation of both nuclear and cytoplasmic DNA and RNA as particle release occurs during death.

  11. [High resolution analysis of replication foci by conventional fluorescent microscopy. I. A study of complexity and DNA content of the foci].

    PubMed

    Chagin, V O; Rozanov, Iu M; Solov'eva, L V; Tomilin, N V

    2004-01-01

    Newly replicated DNA segments (RDS) have been shown to form discrete foci in the mammalian nucleus. Comparison of the number of such foci in formaldehyde-fixed cell nucleus with estimated number of simultaneously active replication forks (RF) suggests that each replication focus contains a cluster of about 10 to 20 closely associated RF. That implied the cluster of synchronously activated replicons as the primary unit of mammalian DNA replication. It still remains unclear whether such clustering of RF does mean adjacency of the replicons in a genomic location (structural clustering, model 1), or it arises from transient clustering of the replicons from different DNA domains at the functioning replication machinery (functional clustering, model 2). In this study we used conventional fluorescence microscopy of the hypotonically treated nuclei preparations to investigate replication foci at the optical resolution limit. Human K562 cells were labeled with 5'-iododeoxyuridine for different time periods. We synchronized the cell culture with hydroxyurea to be able to measure an average increase in DNA content during labeling period using DNA cytometry. Under these conditions, RDS appear as multiple small foci (mini-foci, MF). Further studies revealed that most of such mini-foci of replication represent optical diffraction spots, which are standard in size and different in brightness. The number of the "spots" and variation of their brightness mostly depend on the extent of hypotonic treatment. Flow cytometry control of the synchronized cells peak movement allowed us to measure mean DNA content of the MF. In case of most effective hypotonic treatment, a MF contains about 40 Kbp of labeled DNA, and the general number of the MF approaches the number of replicons that are simultaneously active in a given moment of S-phase. Influence of the effect of hypotonic treatment on overall number of observed MF suggests that replication foci in early and mid S-phase cells do not

  12. 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

  13. Inhibition of oncogenic epidermal growth factor receptor kinase triggers release of exosome-like extracellular vesicles and impacts their phosphoprotein and DNA content.

    PubMed

    Montermini, Laura; Meehan, Brian; Garnier, Delphine; Lee, Wan Jin; Lee, Tae Hoon; Guha, Abhijit; Al-Nedawi, Khalid; Rak, Janusz

    2015-10-01

    Cancer cells emit extracellular vesicles (EVs) containing unique molecular signatures. Here, we report that the oncogenic EGF receptor (EGFR) and its inhibitors reprogram phosphoproteomes and cargo of tumor cell-derived EVs. Thus, phosphorylated EGFR (P-EGFR) and several other receptor tyrosine kinases can be detected in EVs purified from plasma of tumor-bearing mice and from conditioned media of cultured cancer cells. Treatment of EGFR-driven tumor cells with second generation EGFR kinase inhibitors (EKIs), including CI-1033 and PF-00299804 but not with anti-EGFR antibody (Cetuximab) or etoposide, triggers a burst in emission of exosome-like EVs containing EGFR, P-EGFR, and genomic DNA (exo-gDNA). The EV release can be attenuated by treatment with inhibitors of exosome biogenesis (GW4869) and caspase pathways (ZVAD). The content of P-EGFR isoforms (Tyr-845, Tyr-1068, and Tyr-1173), ERK, and AKT varies between cells and their corresponding EVs and as a function of EKI treatment. Immunocapture experiments reveal the presence of EGFR and exo-gDNA within the same EV population following EKI treatment. These findings suggest that targeted agents may induce cancer cells to change the EV emission profiles reflective of drug-related therapeutic stress. We suggest that EV-based assays may serve as companion diagnostics for targeted anticancer agents. PMID:26272609

  14. Karnyothrips flavipes, a previously unreported predatory thrips of the coffee berry borer: DNA-based gut content analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new predator of the coffee berry borer, Hypothenemus hampei, was found in the coffee growing area of Kisii in Western Kenya. Field observations, laboratory trials and gut content analysis using molecular tools have confirmed the role of the predatory thrips Karnyothrips flavipes Jones (Phlaeothrip...

  15. 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.

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

    DOE PAGESBeta

    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

  17. Characterizing the DNA Damage Response by Cell Tracking Algorithms and Cell Features Classification Using High-Content Time-Lapse Analysis

    PubMed Central

    Georgescu, Walter; Osseiran, Alma; Rojec, Maria; Liu, Yueyong; Bombrun, Maxime; Tang, Jonathan; Costes, Sylvain V.

    2015-01-01

    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 many DSB

  18. 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

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

    SciTech Connect

    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.

    1988-09-01

    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). The authors have cloned the cDNA for one of the drug-detoxifying enzymes overexpressed in multidrug-resistant MCF7 cells (Adr/sup R/ 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 Adr/sup R/ MCF7 cells is associated with overexpression but not with amplification of the gene. They 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 Adr/sup R/ MCF7 cells, they examined several other breast cancer cell lines that were not selected for drug resistance. In each of these cell lines they found an inverse association between GST/pi/ expression and ER content. They also examined RNA from 21 primary breast cancers and found a similar association between GST/pi/ expression and ER content in vivo. 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.

  20. Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae)

    PubMed Central

    2013-01-01

    Background Homosporous ferns are distinctive amongst the land plant lineages for their high chromosome numbers and enigmatic genomes. Genome size measurements are an under exploited tool in homosporous ferns and show great potential to provide an overview of the mechanisms that define genome evolution in these ferns. The aim of this study is to investigate the evolution of genome size and the relationship between genome size and spore size within the apomictic Asplenium monanthes fern complex and related lineages. Results Comparative analyses to test for a relationship between spore size and genome size show that they are not correlated. The data do however provide evidence for marked genome size variation between species in this group. These results indicate that Asplenium monanthes has undergone a two-fold expansion in genome size. Conclusions Our findings challenge the widely held assumption that spore size can be used to infer ploidy levels within apomictic fern complexes. We argue that the observed genome size variation is likely to have arisen via increases in both chromosome number due to polyploidy and chromosome size due to amplification of repetitive DNA (e.g. transposable elements, especially retrotransposons). However, to date the latter has not been considered to be an important process of genome evolution within homosporous ferns. We infer that genome evolution, at least in some homosporous fern lineages, is a more dynamic process than existing studies would suggest. PMID:24354467

  1. 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. PMID:12083257

  2. Rapid genomic DNA changes in allotetraploid fish hybrids.

    PubMed

    Wang, J; Ye, L H; Liu, Q Z; Peng, L Y; Liu, W; Yi, X G; Wang, Y D; Xiao, J; Xu, K; Hu, F Z; Ren, L; Tao, M; Zhang, C; Liu, Y; Hong, Y H; Liu, S J

    2015-06-01

    Rapid genomic change has been demonstrated in several allopolyploid plant systems; however, few studies focused on animals. We addressed this issue using an allotetraploid lineage (4nAT) of freshwater fish originally derived from the interspecific hybridization of red crucian carp (Carassius auratus red var., ♀, 2n=100) × common carp (Cyprinus carpio L., ♂, 2n=100). We constructed a bacterial artificial chromosome (BAC) library from allotetraploid hybrids in the 20th generation (F20) and sequenced 14 BAC clones representing a total of 592.126 kb, identified 11 functional genes and estimated the guanine-cytosine content (37.10%) and the proportion of repetitive elements (17.46%). The analysis of intron evolution using nine orthologous genes across a number of selected fish species detected a gain of 39 introns and a loss of 30 introns in the 4nAT lineage. A comparative study based on seven functional genes among 4nAT, diploid F1 hybrids (2nF1) (first generation of hybrids) and their original parents revealed that both hybrid types (2nF1 and 4nAT) not only inherited genomic DNA from their parents, but also demonstrated rapid genomic DNA changes (homoeologous recombination, parental DNA fragments loss and formation of novel genes). However, 4nAT presented more genomic variations compared with their parents than 2nF1. Interestingly, novel gene fragments were found for the iqca1 gene in both hybrid types. This study provided a preliminary genomic characterization of allotetraploid F20 hybrids and revealed evolutionary and functional genomic significance of allopolyploid animals. PMID:25669608

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. Purification of stearidonic acid (18:4(n-3)) and hexadecatetraenoic acid (16:4(n-3)) from algal fatty acid with lipase and medium pressure liquid chromatography.

    PubMed

    Ishihara, K; Murata, M; Kaneniwa, M; Saito, H; Komatsu, W; Shinohara, K

    2000-11-01

    Stearidonic acid (18:4(n-3)) and hexadecatetraenoic acid (16:4(n-3)) are included in some edible marine algae such as Undaria pinnatifida and Ulva pertusa with relatively high compositions (up to 40%) of total fatty acids. In order to prepare 16:4(n-3) and 18:4(n-3) enriched fatty acid concentrates, we screened for a suitable lipase which concentrates these acids by the removal of other fatty acids in the selective esterification reaction reported by Shimada et al. (Shimada et al. (1997), J. Am. Oil Chem. Soc., 74, 1465-1470). In combination with the lipase reaction and reversed-phase medium pressure liquid chromatography, we purified 18:4(n-3) and 16:4(n-3) to more than 95% purity. PMID:11193415

  11. 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

  12. [The development of a test-system for the quantitative and qualitative evaluation of DNA content in criminalistic objects by the real-time polymerase chain reaction].

    PubMed

    Lapenkov, M I; Plakhina, N V; Alekseev, Ia I; Varlamov, D A

    2011-01-01

    An original test-system for the preliminary quantitative and qualitative evaluation of isolated DNA is proposed by the polymerase chain reaction in real time (PCR-RT) based on the TaqMan technology. This test-system permits to simultaneously measure the amount of DNA in the sample, identify the genetic gender, and detect PCR inhibitors. The method has been approbated in the practical work of forensic medical experts. PMID:21735715

  13. Convention on nomenclature for DNA cytometry

    SciTech Connect

    Hiddemann, W.; Schumann, J.; Andreeff, M.; Barlogie, B.; Herman, C.J.; Leif, R.C.; Mayall, B.H.; Murphy, R.F.; Sandberg, A.A.

    1984-01-01

    The Committee on Nomenclature of the Society for Analytical Cytology presents guidelines for the analysis of DNA content by cytometry. These guidelines cover: staining of DNA; cytogenetic and cytometric terminology; DNA index; resolution of measurements; and cytometric standards.

  14. 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.

  15. 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

  16. 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

  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. DNA as information.

    PubMed

    Wills, Peter R

    2016-03-13

    This article reviews contributions to this theme issue covering the topic 'DNA as information' in relation to the structure of DNA, the measure of its information content, the role and meaning of information in biology and the origin of genetic coding as a transition from uninformed to meaningful computational processes in physical systems. PMID:26857666

  19. Microstructural Aspects of Irradiation Damage in A508 Gr 4N Forging Steel: Composition and Flux Effects

    SciTech Connect

    M.G. Burke; R.J. Stofanak; J.M. Hyde; C.A. English; W.L. Server

    2002-10-09

    Neutron irradiation can promote significant changes in the microstructure and associated mechanical properties of low alloy steels. In particular, irradiation can induce the formation of non-equilibrium phases and segregation, which may lead to a degradation in toughness. In this study, the microstructural changes caused by neutron irradiation have been characterized in A508 Grade (Gr) 4N-type steels ({approx}3.5% Ni) using a variety of state-of-the-art analytical techniques including 3D-Atom Probe Field-Ion Microscopy and Small Angle Neutron Scattering, along with post-irradiation annealing studies combining Positron Annihilation Lineshape Analysis and hardness measurements. Important differences between conventional and ''superclean'' A508 Gr 4N steel have been identified in this investigation. The data indicate that Ni is not the controlling factor in the irradiation damage behavior of these materials; rather, the Mn content of the steel is a dominant factor in the irradiation-induced microstructural development of solute-related hardening features.

  20. Search for resonances in 4n, 7H and 9He via transfer reactions

    SciTech Connect

    Fortier, S.; Tryggestad, E.; Rich, E.; Beaumel, D.; Becheva, E.; Blumenfeld, Y.; Delaunay, F.; Frascaria, N.; Guillot, J.; Hammache, F.; Khan, E.; Lima, V.; Scarpaci, J. A.

    2007-05-22

    Investigation of unbound nuclear systems 9He, 7H and 4n was performed at GANIL-SPIRAL using the 8He beam at 15.3 A MeV and a CD2 target. The missing mass spectra were deduced from kinetic energies and emission angles of light ejectiles detected by the Silicon array MUST. In addition to previously known low-lying narrow resonant states in 9He, the d(8He,p) reaction displays a structure just above neutron emission threshold, identified with the 'true' ground state of 9He. The analysis of angular distributions shows that the inversion of s1/2 and p1/2 neutron shells previously observed in 11Be and 10Li also exists in the lightest N=7 isotone 9He. The d(8He,3He) and d(8He,6Li) reactions were used to search for resonant states in the t+4n (7H) and 4n systems, respectively. The missing mass spectrum of the 4n system does not give evidence for the existence of a bound 'tetraneutron'. However the comparison with the results of 5-body phase-space calculations emphasizes the existence of correlations in the 4n system. The broad structure observed at {approx_equal}2 MeV above the t+4n emission threshold is proposed to be the ground state of 7H.

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

    PubMed

    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. PMID:27211286

  2. 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

  3. 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.

  4. 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. PMID:26651516

  5. 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. PMID:26979316

  6. Ab initio study of thermodynamic, electronic, magnetic, structural, and elastic properties of Ni4N allotropes

    NASA Astrophysics Data System (ADS)

    Hemzalová, P.; Friák, M.; Šob, M.; Ma, D.; Udyansky, A.; Raabe, D.; Neugebauer, J.

    2013-11-01

    We have employed parameter-free density functional theory calculations to study the thermodynamic stability and structural parameters as well as elastic and electronic properties of Ni4N in eight selected crystallographic phases. In agreement with the experimental findings, the cubic structure with Pearson symbol cP5, space group Pm3¯m (221) is found to be the most stable and it is also the only thermodynamically stable structure at T=0 K with respect to decomposition to the elemental Ni crystal and N2 gas phase. We determine structural parameters, bulk moduli, and their pressure derivatives for all eight allotropes. The thermodynamic stability and bulk modulus is shown to be anticorrelated. Comparing ferromagnetic and nonmagnetic states, we find common features between the magnetism of elemental Ni and studied ferromagnetic Ni4N structures. For the ground-state Ni4N structure and other two Ni4N cubic allotropes, we predict a complete set of single-crystalline elastic constants (in the equilibrium and under hydrostatic pressure), the Young and area moduli, as well as homogenized polycrystalline elastic moduli obtained by different homogenization methods. We demonstrate that the elastic anisotropy of the ground-state Ni4N is qualitatively opposite to that in the elemental Ni, i.e., these materials have hard and soft crystallographic directions interchanged. Moreover, one of the studied metastable cubic phases is found auxetic, i.e., exhibiting negative Poisson ratio.

  7. Synthesis and electromagnetic properties of nanodendritic γ‧-Fe4N

    NASA Astrophysics Data System (ADS)

    Zhu, Mengna; Yu, Meijie; Mao, Qiong; Li, Fazhan; Wang, Chengguo

    2016-02-01

    Nanodendritic γ‧-Fe4N was successfully synthesized through a nitriding process from dendritic α-Fe2O3, which was prepared by hydrothermal method using potassium ferricyanide (K3[Fe(CN)6]) as iron source. The structure and electromagnetic properties of this material were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), vibrating sample magnetometer (VSM) and vector network analyzer (VNA). The results revealed that the dendritic morphology can be mostly inherited from α-Fe2O3 to γ‧-Fe4N by controlling the nitriding temperature, duration and nitrogen potential precisely. The dendritic γ‧-Fe4N has the saturation magnetization of 146emu/g and the coercive force of 94Oe at 300K. The maximum reflection loss is ‑12dB at 3GHz with the thickness of 3.0mm for the composite sample.

  8. Defined DNA/nanoparticle conjugates.

    PubMed

    Ackerson, Christopher J; Sykes, Michael T; Kornberg, Roger D

    2005-09-20

    Glutathione monolayer-protected gold clusters were reacted by place exchange with 19- or 20-residue thiolated oligonucleotides. The resulting DNA/nanoparticle conjugates could be separated on the basis of the number of bound oligonucleotides by gel electrophoresis and assembled with one another by DNA-DNA hybridization. This approach overcomes previous limitations of DNA/nanoparticle synthesis and yields conjugates that are precisely defined with respect to both gold and nucleic acid content. PMID:16155122

  9. 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

  10. DNA Media Storage

    PubMed Central

    Bogard, Christy M.; Rouchka, Eric C.

    2010-01-01

    In 1994, University of Southern California computer scientist Dr. Leonard Adelman solved the Hamiltonian Path Problem using DNA as a computational mechanism. He proved the principle that DNA computing could be used to solve computationally complex problems. Because of the limitations in discovery time, resource requirements, and sequence mismatches, DNA computing has not yet become a commonly accepted practice. However, advancements are continually being discovered that are evolving the field of DNA Computing. Practical applications of DNA are not restricted to computation alone. This research presents a novel approach in which DNA could be used as a means of storing files. Through the use of Multiple Sequence Alignment combined with intelligent heuristics, the most probabilistic file contents can be determined with minimal errors. PMID:20622994

  11. DNA Media Storage.

    PubMed

    Bogard, Christy M; Rouchka, Eric C

    2007-09-01

    In 1994, University of Southern California computer scientist Dr. Leonard Adelman solved the Hamiltonian Path Problem using DNA as a computational mechanism. He proved the principle that DNA computing could be used to solve computationally complex problems. Because of the limitations in discovery time, resource requirements, and sequence mismatches, DNA computing has not yet become a commonly accepted practice. However, advancements are continually being discovered that are evolving the field of DNA Computing. Practical applications of DNA are not restricted to computation alone. This research presents a novel approach in which DNA could be used as a means of storing files. Through the use of Multiple Sequence Alignment combined with intelligent heuristics, the most probabilistic file contents can be determined with minimal errors. PMID:20622994

  12. Fabrication and physical properties of [Fe/Fe4N]N multilayers with high saturation magnetization

    NASA Astrophysics Data System (ADS)

    Yu, B.; Lin, L.; Ma, B.; Zhang, Z. Z.; Jin, Q. Y.; Wang, J. P.

    2016-05-01

    [Fe/Fe4N]N multilayers with high saturation magnetization were prepared on MgO(200) substrate, by the DC reactive magnetron sputtering and then annealed at higher temperature. Their structural and magnetic properties were investigated. Epitaxial growth of α-Fe and γ'-Fe4N were demonstrated on MgO, and then excellent [Fe/Fe4N]N was obtained. Though the saturation magnetizations of the as-deposited [Fe/Fe4N]N are slightly below the average value of those of α-Fe and γ'-Fe4N, the saturation magnetization of the annealed [Fe(3.04 nm)/Fe4N(3.04 nm)]5 increases up to 1850 emu/cc, 32 % larger than that of α-Fe film. N atom diffusion from the γ'-Fe4N to the α-Fe layer at high temperature greatly improves the saturation magnetization.

  13. 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

  14. Conversion of 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium tosylate (DAST) from a Simple Optical Material to a Versatile Optoelectronic Material.

    PubMed

    Xu, Xiangdong; Sun, Ziqiang; Fan, Kai; Jiang, Yadong; Huang, Rui; Wen, Yuejiang; He, Qiong; Ao, Tianhong

    2015-01-01

    4-N,N-dimethylamino-4'-N'-methyl-stilbazolium tosylate (DAST) is an important optical material, but its poor conductivity limits applications in devices. To tackle this problem, we designed, prepared, and systematically investigated novel binary composite films that are composed of two-dimensional (2D) DAST and 2D graphene. Results indicate that both electrical and optical properties of DAST can be significantly improved by graphene addition. The negative steric effects of big DAST molecules that greatly trouble ex-situ synthesis can be efficiently overcome by in-situ synthesis, thus leading to better film quality and higher physical properties. Consequently, the in-situ composite film exhibits a low sheet resistance of 7.5 × 10(6) ohm and high temperature coefficient of resistance of -2.79% K(-1), close to the levels of the most important bolometric materials for uncooled infrared detectors. Particularly, a new low temperature reduction of graphene oxide induced by DAST, which is further enhanced by in-situ process, was discovered. This work presents valuable information about the DAST-graphene composite films, their chemical structures, mechanisms, physical properties, and comparison on in-situ and ex-situ syntheses of graphene-based composites, all of which will be helpful for not only theoretically studying the DAST and graphene materials and expanding their applications, but also for seeking new optoelectronic sensitive materials. PMID:26192068

  15. Superconductivity in Ban+2Ir4nGe12n+4 (n=1,2) with cage structure and softening of low-lying localized mode

    NASA Astrophysics Data System (ADS)

    Guo, Jiangang; Yamaura, Jun-ichi; Lei, Hechang; Matsuishi, Satoru; Qi, Yanpeng; Hosono, Hideo

    2013-10-01

    We report on new superconductors Ban+2Ir4nGe12n+4 (n = 1, 2) with critical temperatures Tc = 6.1 and 3.2 K, respectively, along with their crystal structures, electron transport, and specific heat. The compounds are composed of alternating Ba@Ir8Ge16 and Ba@Ir2Ge16 cages, both of which are larger in the n = 1 sample than in the n = 2 sample. The normal-state heat capacity reveals two low-lying vibration modes associated with guest Ba cations, and both characteristic temperatures in Ba3Ir4Ge16 are smaller than those in Ba4Ir8Ge28. Meanwhile, the density functional theory calculations reveal that the Ge-4p bands dominated the Fermi level in both samples. We propose that the softening of localized phonons due to expansion of the cage strengthens the electron-phonon coupling between Ba cations and Ge anions, leading to the higher Tc in Ba3Ir4Ge16.

  16. 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.

  17. 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).

  18. Cleaving DNA with DNA

    NASA Astrophysics Data System (ADS)

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-03-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

  19. 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.

  20. Adsorptive performance and catalytic activity of superparamagnetic Fe3O4@nSiO2@mSiO2 core-shell microspheres towards DDT.

    PubMed

    Liu, Feng; Tian, Hua; He, Junhui

    2014-04-01

    Due to specific properties, core-shell Fe3O4@SiO2 and core-shell-shell Fe3O4@nSiO2@mSiO2 nanostructures have been extensively investigated for the contamination treatment of wastewater. However, these reported materials were usually used as advanced adsorbents or catalyst-supports. In this study, we demonstrate that magnetic mesoporous silica Fe3O4@nSiO2@mSiO2 microspheres can not only exhibit excellent adsorptive performance for removal of DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane) from aqueous media, but also display high catalytic activity. Over 97% of DDT could be quickly removed from aqueous media in 60 min. At 60°C the DDE (1,1-dichloro-2,2-bis(4-chlorophenyl) ethylene) content increases greatly as DDT disappears completely, and is decomposed completely after thermal treatment at a relatively low temperature of 450°C. The obtained magnetic mesoporous silica nanoparticles were characterized by X-ray diffraction, transmission electron microscopy, nitrogen adsorption-desorption measurements and vibrating sample magnetometer. The results indicate that Fe3O4@nSiO2@mSiO2 microspheres show strong superparamagnetism and have high specific surface area (577 m(2) g(-1)). PMID:24491332

  1. 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

  2. DNA repair

    SciTech Connect

    Friedberg, E.C.; Hanawalt, P.C. )

    1988-01-01

    Topics covered in this book included: Eukaryote model systems for DNA repair study; Sensitive detection of DNA lesions and their repair; and Defined DNA sequence probes for analysis of mutagenesis and repair.

  3. A spectral study of 2-formylimidazole 4N-substituted thiosemicarbazones and their copper(II) complexes

    NASA Astrophysics Data System (ADS)

    West, Douglas X.; Lockwood, Mark A.; Albert, Julyan N.; Liberta, Anthony E.

    1993-11-01

    Copper(II) complexes of 2-formylimidazole 4N-methyl-, 4N-dimethyl- 4N-ethyl- and 3-hexa-methyleneiminylthiosemicarbazone, along with two nickel(II) complexes of the latter thiosemicarbazone, have been synthesized. Infrared, electronic, NMR and ESR spectra have been used to characterize the complexes and the uncomplexed thiosemicarbazones. None of the complexes or thiosemicarbazones possess growth inhibitory activity against Aspergillus niger and Paecilomyces variotii.

  4. 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.

  5. 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.

  6. 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.}

  7. Pulsating strings from two-dimensional CFT on (T4)N / S (N)

    NASA Astrophysics Data System (ADS)

    Cardona, Carlos

    2015-04-01

    We propose a state from the two-dimensional conformal field theory on the orbifold (T4)N / S (N) as a dual description for a pulsating string moving in AdS3. We show that, up to first order in the deforming parameter, the energy in both descriptions has the same dependence on the mode number, but with a non-trivial function of the coupling.

  8. 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.

  9. 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.

  10. 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.

  11. Sequencing mitochondrial DNA polymorphisms by hybridization

    SciTech Connect

    Chee, M.S.; Lockhart, D.J.; Hubbell, E.

    1994-09-01

    We have investigated the use of DNA chips for genetic analysis, using human mitochondrial DNA (mtDNA) as a model. The DNA chips are made up of ordered arrays of DNA oligonucleotide probes, synthesized on a glass substrate using photolithographic techniques. The synthesis site for each different probe is specifically addressed by illumination of the substrate through a photolithographic mask, achieving selective deprotection Nucleoside phosphoramidites bearing photolabile protecting groups are coupled only to exposed sites. Repeated cycles of deprotection and coupling generate all the probes in parallel. The set of 4{sup N} N-mer probes can be synthesized in only 4N steps. Any subset can be synthesized in 4N steps. Any subset can be synthesized in 4N or fewer steps. Sequences amplified from the D-loop region of human mitochondrial DNA (mtDNA) were fluorescently labelled and hybridized to DNA chips containing probes specific for mtDNA. Each nucleotide of a 1.3 kb region spanning the D loop is represented by four probes on the chip. Each probe has a different base at the position of interest: together they comprise a set of A, C, G and T probes which are otherwise identical. In principle, only one probe-target hybrid will be a perfect match. The other three will be single base mismatches. Fluorescence imaging of the hybridized chip allows quantification of hybridization signals. Heterozygous mixtures of sequences can also be characterized. We have developed software to quantitate and interpret the hybridization signals, and to call the sequence automatically. Results of sequence analysis of human mtDNAs will be presented.

  12. 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

  13. 4-N,N-Dimethylaminopyridine promoted selective oxidation of methyl aromatics with molecular oxygen.

    PubMed

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

    2012-01-01

    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. PMID:22466855

  14. 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.

  15. 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.

  16. 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}

  17. Theory and Application of DNA Histogram Analysis.

    ERIC Educational Resources Information Center

    Bagwell, Charles Bruce

    The underlying principles and assumptions associated with DNA histograms are discussed along with the characteristics of fluorescent probes. Information theory was described and used to calculate the information content of a DNA histogram. Two major types of DNA histogram analyses are proposed: parametric and nonparametric analysis. Three levels…

  18. 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)

  19. Defined DNA/nanoparticle conjugates

    NASA Astrophysics Data System (ADS)

    Ackerson, Christopher J.; Sykes, Michael T.; Kornberg, Roger D.

    2005-09-01

    Glutathione monolayer-protected gold clusters were reacted by place exchange with 19- or 20-residue thiolated oligonucleotides. The resulting DNA/nanoparticle conjugates could be separated on the basis of the number of bound oligonucleotides by gel electrophoresis and assembled with one another by DNA-DNA hybridization. This approach overcomes previous limitations of DNA/nanoparticle synthesis and yields conjugates that are precisely defined with respect to both gold and nucleic acid content. Freely available online through the PNAS open access option.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. The Drosophila melanogaster homologue of the human histo-blood group Pk gene encodes a glycolipid-modifying α1,4-N-acetylgalactosaminyltransferase

    PubMed Central

    2004-01-01

    Insects express arthro-series glycosphingolipids, which contain an α1,4-linked GalNAc residue. To determine the genetic basis for this linkage, we cloned a cDNA (CG17223) from Drosophila melanogaster encoding a protein with homology to mammalian α1,4-glycosyltransferases and expressed it in the yeast Pichia pastoris. Culture supernatants from the transformed yeast were found to display a novel UDP-GalNAc:GalNAcβ1,4GlcNAcβ1-R α-N-acetylgalactosaminyltransferase activity when using either a glycolipid, p-nitrophenylglycoside or an N-glycan carrying one or two terminal β-N-acetylgalactosamine residues. NMR and MS in combination with glycosidase digestion and methylation analysis indicate that the cloned cDNA encodes an α1,4-N-acetylgalactosaminyltransferase. We hypothesize that this enzyme and its orthologues in other insects are required for the biosynthesis of the N5a and subsequent members of the arthro-series of glycolipids as well as of N-glycan receptors for Bacillus thuringiensis crystal toxin Cry1Ac. PMID:15130086

  6. 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…

  7. Laboratory study of CH4-N2 clathrate hydrates applied to Titan's surface conditions

    NASA Astrophysics Data System (ADS)

    Nna Mvondo, D.; Tobie, G.; Le Menn, E.; Bollengier, O.; Grasset, O.

    2013-12-01

    It is proposed that clathrate hydrates may be present at the surface of Titan (Choukroun et al., 2013, 2010). At Titan's surface pressure, pure methane and ethane hydrate (as well as other guests) could exist in the sI structure and nitrogen hydrate as sII structure. The large reservoir of several guest compounds in Titan's atmosphere is expected to result in the formation of multicomponent (compound) clathrate hydrates, as sII or sH structures, stable relative to water ice on the surface of Titan, and with faster expected growth kinetics relative to pure hydrate (Osegovic et al., 2005). Compound hydrate could be a likely sink for many chemicals occurring on Titan's surface. We note that experimental studies on the formation and thermodynamics of the methane-water system, at low and high pressures applied to Titan have been carried out (Lunine and Stevenson; 1985; Choukroun et al., 2013, 2010 and references therein). However, laboratory work on mixing of methane with other compounds in the clathrate phase (ethane, N2, CO2, etc...) applied to Titan conditions (and other icy moons) has still to be addressed. In this context, we have studied the formation and spectral signatures of CH4-N2 clathrate hydrates at temperature and pressure conditions relevant for Titan's surface. Clathrate hydrates samples have been synthesized in an autoclave combined with a cooling system and a multi-gas mixer. Few ml of deionized water was introduced in the autoclave and pressurized with the N2 and CH4 gaseous species for a couple of days, at controlled low temperature and low pressure of the formation and stability of clathrate hydrates. Their formation has been monitored by gas chromatography. Their spectral characterization at low temperature was performed by infrared (FTIR) reflectance spectroscopy. Raman spectroscopy was also used to give constraints on the composition, structure and cage occupancy of the formed clathrates. Here we present the results obtained for different mixing

  8. Perinatal transmission of human papilomavirus DNA

    PubMed Central

    Rombaldi, Renato L; Serafini, Eduardo P; Mandelli, Jovana; Zimmermann, Edineia; Losquiavo, Kamille P

    2009-01-01

    The purpose was to study the perinatal transmission of human papillomavirus DNA (HPV-DNA) in 63 mother-newborn pairs, besides looking at the epidemiological factors involved in the viral DNA transmission. The following sampling methods were used: (1) in the pregnant woman, when was recruited, in cervix and clinical lesions of the vagina, vulva and perineal region; (2) in the newborn, (a) buccal, axillary and inguinal regions; (b) nasopharyngeal aspirate, and (c) cord blood; (3) in the children, buccal was repeated in the 4th week and 6th and 12th month of life. HPV-DNA was identified using two methodologies: multiplex PCR (PGMY09 and MY11 primers) and nested-PCR (genotypes 6/11, 16, 18, 31, 33, 42, 52 and 58). Perinatal transmission was considered when concordance was found in type-specific HPV between mother/newborn or mother/child. HPV-DNA genital was detected in 49 pregnant women submitted to delivery. Eleven newborns (22.4%, n = 11/49) were HPV-DNA positive. In 8 cases (16.3%, n = 8/49) there was type specific HPV concordance between mother/newborn samples. At the end of the first month of life three children (6.1%, n = 3/49) became HPV-DNA positive, while two remained positive from birth. In 3 cases (100%, n = 3/3) there was type specific HPV concordance between mother/newborn samples. In the 6th month, a child (2%, n = 1/49) had become HPV-DNA positive between the 1st and 6th month of life, and there was type specific HPV concordance of mother/newborn samples. All the HPV-DNA positive children (22.4%, n = 11/49) at birth and at the end first month of life (6.1%, n = 3/49) became HPV-DNA negative at the age of 6 months. The HPV-DNA positive child (2%, n = 1/49) from 1st to the 6th month of life became HPV-DNA negative between the 6th and 12th month of life and one child had anogenital warts. In the twelfth month all (100%, n = 49/49) the children studied were HPV-DNA negative. A positive and significant correlation was observed between perinatal transmission

  9. DNA Immunization

    PubMed Central

    Wang, Shixia; Lu, Shan

    2013-01-01

    DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed. PMID:24510291

  10. 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

  11. 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.

  12. 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

  13. 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

  14. Surface layer in composites containing 4- n-octyl-4'-cyanobiphenyl. FTIR spectroscopic characterization

    NASA Astrophysics Data System (ADS)

    Frunza, L.; Kosslick, H.; Bentrup, U.; Pitsch, I.; Fricke, R.; Frunza, S.; Schönhals, A.

    2003-06-01

    Composites containing 4- n-octyl-4'-cyanobiphenyl (8CB) either confined to nanopores of molecular sieves with very large pores or coating silica nanoparticles of aerosil type at high silica-to-8CB ratios are investigated by IR spectroscopy. Band shape analysis was performed in wavenumber regions in which the peaks due to CN stretching, CH stretching and CH out-of-plane vibrations appear. Some of molecules confined to molecular sieves show spectroscopic features characteristic to a bulk-like 8CB matter located in the centre of the pores or in the inter-grain space. Other features of the IR spectra are due to 8CB molecules located in the surface layer, mostly forming hydrogen bonds between their CN groups and surface OH groups. Another part of the 8CB molecules in the surface layer may also interact by π electrons of the aromatic rings. Hydrogen bonding is less hindered for the molecules of the surface layers onto aerosil particles than inside pores of the molecular sieves. Comparison is also made with the case of composites based on molecular sieves with small pores.

  15. Intermolecular potential energy surface and thermophysical properties of the CH4-N2 system

    NASA Astrophysics Data System (ADS)

    Hellmann, Robert; Bich, Eckard; Vogel, Eckhard; Vesovic, Velisa

    2014-12-01

    A five-dimensional potential energy surface (PES) for the interaction of a rigid methane molecule with a rigid nitrogen molecule was determined from quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the CCSD(T) level of theory was utilized to compute a total of 743 points on the PES. The interaction energies were calculated using basis sets of up to quadruple-zeta quality with bond functions and were extrapolated to the complete basis set limit. An analytical site-site potential function with nine sites for methane and five sites for nitrogen was fitted to the interaction energies. The PES was validated by calculating the cross second virial coefficient as well as the shear viscosity and binary diffusion coefficient in the dilute-gas limit for CH4-N2 mixtures. An improved PES was obtained by adjusting a single parameter of the analytical potential function in such a way that quantitative agreement with the most accurate experimental values of the cross second virial coefficient was achieved. The transport property values obtained with the adjusted PES are in good agreement with the best experimental data.

  16. [Raman spectroscopic studies on CO2-CH4-N2 mixed-gas hydrate system].

    PubMed

    Zhang, Bao-yong; Liu, Chuan-hai; Wu, Qiang; Gao, Xia

    2014-06-01

    Accurate determination of coal mine gas separation product characteristics is the key for gas separation application based on hydrate technology. Gas hydrate was synthesized from two types of gas compositions (CO2-CH4-N2). The separation products were measured by in situ Raman spectroscopy. The crystal structure of mixed-gas hydrate was determined, and the cavity occupancy and hydration index were calculated, based on the object molecular various vibrational mode, "loose cage-tight cage" model and the Raman bands area ratio, combined with the model of van der Waals-Platteeuw. The results show that the mixed-gas hydrates are both structure I for the two gas samples; Large cages of mixed-gas hydrate are nearly occupied by guest molecules, and the large cavity occupancies are 98.57% and 98.52%, respectively; but small cages are not easy to be occupied, and the small cavity occupancies are 29.93% and 33.87%, respectively; hydration index of the two gas samples hydrate is 7.14 and 6.98, respectively, which is greater than the theoretical value of structure I. PMID:25358164

  17. Intermolecular potential energy surface and thermophysical properties of the CH4-N2 system.

    PubMed

    Hellmann, Robert; Bich, Eckard; Vogel, Eckhard; Vesovic, Velisa

    2014-12-14

    A five-dimensional potential energy surface (PES) for the interaction of a rigid methane molecule with a rigid nitrogen molecule was determined from quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the CCSD(T) level of theory was utilized to compute a total of 743 points on the PES. The interaction energies were calculated using basis sets of up to quadruple-zeta quality with bond functions and were extrapolated to the complete basis set limit. An analytical site-site potential function with nine sites for methane and five sites for nitrogen was fitted to the interaction energies. The PES was validated by calculating the cross second virial coefficient as well as the shear viscosity and binary diffusion coefficient in the dilute-gas limit for CH4-N2 mixtures. An improved PES was obtained by adjusting a single parameter of the analytical potential function in such a way that quantitative agreement with the most accurate experimental values of the cross second virial coefficient was achieved. The transport property values obtained with the adjusted PES are in good agreement with the best experimental data. PMID:25494743

  18. 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.

  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. Synthesis and photophysical properties of the photoactivatable cationic porphyrin 5-(4-N-dodecylpyridyl)-10,15,20-tri(4-N-methylpyridyl)-21H,23H-porphyrin tetraiodide for anti-malaria PDT.

    PubMed

    Stallivieri, Aurélie; Le Guern, Florent; Vanderesse, Régis; Meledje, Esme; Jori, Giulio; Frochot, Céline; Acherar, Samir

    2015-07-01

    This article describes a new synthetic method for obtaining three water soluble porphyrins. The more sophisticated porphyrin [5-(4-N-dodecylpyridyl)-10,15,20-tri(4-N-methylpyridyl)-21H,23H-porphyrin tetraiodide], also named C12 porphyrin, was obtained through a three step methodology. The improvements, compared to syntheses described in the literature, mostly concern the purification procedures. The photophysical properties of the three porphyrins are described and the C12 porphyrin presents a very good (1)O2 yield compared to its chemical intermediates. This porphyrin seems to be a very promising candidate for PDT applications. PMID:26066986

  1. DNA ALTERATIONS

    EPA Science Inventory

    The exposure of an organism to genotoxic chemicals may induce a cascade of genetic events. nitially, structural alterations to DNA are formed. ext, the DNA damage is processed and subsequently expressed in mutant gene products. inally, diseases result from the genetic damage. he ...

  2. 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. PMID:24054668

  3. Growth evolution of γ‧-Fe4N films on GaN(0001) and their interfacial structure

    NASA Astrophysics Data System (ADS)

    Kimura, Masamitsu; Hasegawa, Shigehiko

    2016-05-01

    We report the growth parameter dependence of structural and magnetic properties of γ‧-Fe4N thin films on GaN(0001) grown by plasma-assisted molecular beam epitaxy, particularly focusing on their interfacial structure. Reflection high-energy electron diffraction (RHEED) and X-ray diffraction reveal that γ‧-Fe4N(111) layers are grown at the interface, while the succeeding layers are preferentially oriented to (111) or (100) depending on the growth conditions. The RHEED observation during the interface formation and the cross-sectional transmission electron microscopy observation indicate that the γ‧-Fe4N(111)/GaN interface is abrupt. On the basis of the present findings, we propose the structural model for the interface.

  4. 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.

  5. NiCo2O4/N-doped graphene as an advanced electrocatalyst for oxygen reduction reaction

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Li, Huiyong; Wang, Haiyan; He, Kejian; Wang, Shuangyin; Tang, Yougen; Chen, Jiajie

    2015-04-01

    Developing low-cost catalyst for high-performance oxygen reduction reaction (ORR) is highly desirable. Herein, NiCo2O4/N-doped reduced graphene oxide (NiCo2O4/N-rGO) hybrid is proposed as a high-performance catalyst for ORR for the first time. The well-formed NiCo2O4/N-rGO hybrid is studied by cyclic voltammetry (CV) curves and linear-sweep voltammetry (LSV) performed on the rotating-ring-disk-electrode (RDE) in comparison with N-rGO-free NiCo2O4 and the bare N-rGO. Due to the synergistic effect, the NiCo2O4/N-rGO hybrid exhibits significant improvement of catalytic performance with an onset potential of -0.12 V, which mainly favors a direct four electron pathway in ORR process, close to the behavior of commercial carbon-supported Pt. Also, the benefits of N-incorporation are investigated by comparing NiCo2O4/N-rGO with NiCo2O4/rGO, where higher cathodic currents, much more positive half-wave potential and more electron transfer numbers are observed for the N-doping one, which should be ascribed to the new highly efficient active sites created by N incorporation into graphene. The NiCo2O4/N-rGO hybrid could be used as a promising catalyst for high power metal/air battery.

  6. Positron annihilation studies of 4-n-butyl-4'-isothiocyanato-1,1'-biphenyl.

    PubMed

    Dryzek, E; Juszyńska, E; Zaleski, R; Jasińska, B; Gorgol, M; Massalska-Arodź, M

    2013-08-01

    Positron annihilation lifetime spectroscopy (PALS) measurements were performed between 93 and 293 K in order to study the supercooled smectic-E (Sm-E) phase of 4-n-butyl-4'-isothiocyanato-1,1'-biphenyl (4TCB), the ordered molecular crystal of 4TCB, and the phase transition between the Sm-E phase and the ordered molecular crystal of 4TCB. The phase transition was well reflected in the abrupt increase of the ortho-positronium (o-Ps) lifetime and intensity. The value of the o-Ps lifetime in the Sm-E liquid crystalline phase of 4TCB, i.e., 2.21 ns at room temperature, was explained by the formation of bubbles induced by Ps atoms, which are created due to a liquidlike state of the butyl chains of 4TCB molecules in the Sm-E phase. The temperature dependence of the o-Ps intensity for the supercooled Sm-E phase can be explained by thermal generation of sites where bubbles are formed; an activation energy equal to 0.30±0.02 eV was estimated. This value was compared with the activation energies of molecular motions. The o-Ps lifetime in the ordered molecular crystal was interpreted as originating from the annihilation of o-Ps confined in molecular vacancy-type imperfections in the crystal lattice. The value of the o-Ps pickoff annihilation between 1.8 and 1.9 ns is in accordance with the size of the molecular vacancy for the 4TCB crystal lattice. Its intensity is lower than 5%. The isothermal crystallization of the 4TCB Sm-E phase was observed by PALS. The low-dimensional crystal growth was concluded from the Avrami equation fitted to the time dependence of the o-Ps intensity, which resulted in an Avrami exponent equal to 1.73. PMID:24032853

  7. 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.

  8. 4-n-butylresorcinol, a depigmenting agent used in cosmetics, reacts with tyrosinase.

    PubMed

    Garcia-Jimenez, Antonio; Teruel-Puche, Jose Antonio; Ortiz-Ruiz, Carmen Vanessa; Berna, Jose; Tudela, Jose; Garcia-Canovas, Francisco

    2016-08-01

    4-n-Butylresorcinol (BR) is considered the most potent inhibitor of tyrosinase, which is why it is used in cosmetics as a depigmenting agent. However, this work demonstrates that BR is a substrate of this enzyme. The Em (met-tyrosinase) form is not active on BR, but Eox (oxy-tyrosinase) can act on this molecule, hydroxylating it to o-diphenol. In turn, this is oxidized to an o-quinone, which isomerizes to a red p-quinone. Thus, for tyrosinase to act on this compound, a mechanism to generate Eox in the medium is required, which can be achieved by means of hydrogen peroxide or ascorbic acid. A kinetic analysis of the proposed mechanism allows its kinetic characterization: catalytic constant kcatBR (8.49 ± 0.20 s(-1) ) and Michaelis-constant KMBR (60.26 ± 8.76 μM). These findings are compared with those for other monophenolic substrates of tyrosinase. Studies of BR docking to the Em form of the enzyme show that the hydroxyl group in C-1 position is oriented toward the copper atom A (CuA), as in it is L-tyrosine. As regards Eox , BR is oriented with the carbon in C-6 position ready to be hydroxylated. The reaction of BR originates o-quinones, which isomerize to p-quinones, which in turn, could react with thiol compounds, a finding that could have important implications for pharmacology and the cosmetic industry. © 2016 IUBMB Life, 68(8):663-672, 2016. PMID:27342394

  9. [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

  10. 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.

  11. Structure, phase transitions, dielectric and spectroscopic studies of the 2-aminopyrimidinium salts: [(2-NH 2C 4N 2H 3) 2H][ClO 4] and [2-NH 2C 4N 2H 4][BF 4

    NASA Astrophysics Data System (ADS)

    Czupiński, O.; Wojtaś, M.; Ciunik, Z.; Jakubas, R.

    2006-01-01

    Crystal structure of the 2-aminopyrimidinium derivatives: [(2-NH 2C 4N 2H 3) 2H][ClO 4] (I) and [2-NH 2C 4N 2H 4][BF 4] (II) has been determined at 100 K (I) and 293 K (II) by means of single crystal X-ray diffraction as monoclinic space group, P2/c and P2/n, respectively. The asymmetric part of the unit cell of (I) contains two symmetry independent 2-aminopyrimidine forming one dimeric cation and one disordered perchlorate anion. The structure of (II) consists of 2-aminopyrimidinium cation, [2-NH 2C 4N 2H 4] +, protonated at a pyrimidine ring-N atom and [BF 4] - anion. Differential scanning calorimetry (DSC) on perchlorate derivative ( 1:1), [2-NH 2C 4N 2H 3][ClO 4] (III)—being isomorphic to tetrafluoroborate one (I) at room temperature, reveals two phase transitions of first order: at 250/275 K and 390/410 K (cooling-heating, respectively), whereas the analog (II) only one transition at high temperatures—343/385 K. The dielectric studies in the frequency range 75 kHz - 10 MHz disclose relaxation process at high temperatures in salt (I). Infrared spectra of polycrystalline [2-NH 2C 4N 2H 4][BF 4] have been studied in the temperature range 300-420 K. Substantial changes in the temperature evolution of frequencies of internal modes of the 2-aminopyrimidinium cations and [BF 4] - anions near 390 K are due to the variations in the motion of both moieties and hydrogen bond configuration. The experimental studies indicate that all phase transitions taking place in studied 2-aminopyrimidinium derivatives are classified as an order-disorder.

  12. 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.

  13. tetra neutron system studied by exothermic double-charge exchange reaction 4He(8He, 8Be)4n

    NASA Astrophysics Data System (ADS)

    Kisamori, Keiichi; Sharaq06 Collaboration

    2014-09-01

    A possible existence of the tetra-neutron system as a resonance state is still an open and fascinating question, while theoretical papers using ab-initio calculation suggests that the bound tetra-neutron does not exist. We have performed a missing-mass spectroscopy of the 4n system via the exothermic double-charge exchange reaction 4He(8He,8Be)4n. The experiment was carried out at the RIBF at RIKEN using the SHARAQ spectrometer and the liquid He target system. Since the secondary beam, 8He at 190A MeV, has a large internal energy, it is possible to produce the 4n system in small momentum transfers of less than 20 MeV/c. In the present analysis, a new analytical framework to treat multi-particles under high beam rate condition (2 MHz) was developed for good statistics. At the SHARAQ spectrometer, 8Be can be identified by measuring the invariant mass of the coincident two-alpha particle with a good signal-to-noise ratio. About several tens of candidate events are obtained above the 4n threshold. We will show the preliminary result of missing-msss spectrum and discuss the shape of spectrum.

  14. 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.

  15. Structure, Phase Transitions, and Isotope Effects in [(CH3)4N]2PuCl6.

    PubMed

    Wilson, Richard E

    2015-11-01

    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 Fd3̅c a = 26.012(3) Å. At 360 K, the structure is in space group Fm3̅m, 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 Fm3̅m to Fd3̅c 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. PMID:26225472

  16. Transition from half metal to semiconductor in Li doped g-C{sub 4}N{sub 3}

    SciTech Connect

    Hashmi, Arqum; Hu, Tao; Hong, Jisang

    2014-03-28

    We have investigated the structural and magnetic properties of Li doped graphitic carbon nitride (g-C{sub 4}N{sub 3}) using the van der Waals density functional theory. A free standing g-C{sub 4}N{sub 3} was known to show a half metallic state with buckling geometry, but this feature completely disappears in the presence of Li doping. Besides this structural modification, very interestingly, we have obtained that the Li doped g-C{sub 4}N{sub 3} shows dramatic change in its electronic structure. Both ferromagnetic and nonmagnetic states are almost degenerated in one Li atom doped system. However, the transition from half metallic state to semiconductor is observed with further increase of Li concentration and the calculated energy gap is 1.97 eV. We found that Li impurity plays as a donor element and charge transfer from the Li atom to neighboring N atoms induces a band gap. Overall, we have observed that the electronic and magnetic properties of g-C{sub 4}N{sub 3} are substantially modified by Li doping.

  17. 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

  18. 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)

  19. [4-(n-Dimethylaminostyryl)-1-methylpyridinium fluorescence in a living cell].

    PubMed

    Morozova, G I; Dobretsov, G E; Dubur, G Ia; Dubur, R R; Golitsyn, V M

    1981-08-01

    A fluorescent compound 4-(p-dimethylinostyryl)-1-methylpyridinium (DSM) has been synthesized, having the absorption maximum about 450 nm and the fluorescence maximum about 590 nm in a water solution. A considerable increase of its fluorescence intensity is found in DNA solutions. The binding of DSM with membranes leads to a shift of its fluorescence maximum to 550 nm. Polychromatic properties of DSM (green fluorescence in membranes, rich yellow - in energized mitochondria, red-orange - in nuclei) are found in DSM stained cells. DSM fluorescence is sensitive to changes in the energized state of cells; the uncupler dinitrophenol or respiration inhibitors-cyanide and amital-cause a strong decrease in the DSM fluorescence intensity in mitochondria. It is ascertained that DSM itself has a low toxicity with respect to cell energy: it had no influence on the mobility of Tetrahymena pyriformis during 23 hours after staining. Thus, DSM may be used as a fluorescent probe for live cells. PMID:7029833

  20. Anti-sense DNA d(GGCCCC)n expansions in C9ORF72 form i-motifs and protonated hairpins.

    PubMed

    Kovanda, Anja; Zalar, Matja; Šket, Primož; Plavec, Janez; Rogelj, Boris

    2015-01-01

    The G4C2 hexanucleotide repeat expansion mutation (HREM) in C9ORF72, represents the most common mutation associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Three main disease mechanisms have been proposed to date: C9ORF72 haploinsufficiency, RNA toxicity, and accumulation of dipeptide repeat proteins. Pure GC content of the HREM potentially enables the formation of various non-B DNA structures such as G-quadruplexes and i-motifs. These structures are proposed to act as promoters and regulatory elements affecting replication, transcription and translation of the surrounding region. G-quadruplexes have already been shown on the G-rich sense DNA and RNA strands (G4C2)n, the structure of the anti-sense (G2C4)n strand remains unresolved. Similar C-rich sequences may, under acidic conditions, form i-motifs consisting of two parallel duplexes in a head to tail orientation held together by hemi-protonated C(+)-C pairs. We show that d(G2C4)n repeats do form i-motif and protonated hairpins even under near-physiological conditions. Rather than forming a DNA duplex, i-motifs persist even in the presence of the sense strand. This preferential formation of G-quadruplex and i-motif/hairpin structures over duplex DNA, may explain HREM replicational and transcriptional instability. Furthermore, i-motifs/hairpins can represent a novel pharmacological target for C9ORF72 associated ALS and FTLD. PMID:26632347

  1. Anti-sense DNA d(GGCCCC)n expansions in C9ORF72 form i-motifs and protonated hairpins

    PubMed Central

    Kovanda, Anja; Zalar, Matja; Šket, Primož; Plavec, Janez; Rogelj, Boris

    2015-01-01

    The G4C2 hexanucleotide repeat expansion mutation (HREM) in C9ORF72, represents the most common mutation associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Three main disease mechanisms have been proposed to date: C9ORF72 haploinsufficiency, RNA toxicity, and accumulation of dipeptide repeat proteins. Pure GC content of the HREM potentially enables the formation of various non-B DNA structures such as G-quadruplexes and i-motifs. These structures are proposed to act as promoters and regulatory elements affecting replication, transcription and translation of the surrounding region. G-quadruplexes have already been shown on the G-rich sense DNA and RNA strands (G4C2)n, the structure of the anti-sense (G2C4)n strand remains unresolved. Similar C-rich sequences may, under acidic conditions, form i-motifs consisting of two parallel duplexes in a head to tail orientation held together by hemi-protonated C+-C pairs. We show that d(G2C4)n repeats do form i-motif and protonated hairpins even under near-physiological conditions. Rather than forming a DNA duplex, i-motifs persist even in the presence of the sense strand. This preferential formation of G-quadruplex and i-motif/hairpin structures over duplex DNA, may explain HREM replicational and transcriptional instability. Furthermore, i-motifs/hairpins can represent a novel pharmacological target for C9ORF72 associated ALS and FTLD. PMID:26632347

  2. Cloning and expression of porcine β1,4 N-acetylgalactosaminyl transferase encoding a new xenoreactive antigen

    PubMed Central

    Byrne, Guerard W; Du, Zeji; Stalboerger, Paul; Kogelberg, Heide; McGregor, Christopher G A

    2014-01-01

    Background Xenograft rejection of pigs organs with an engineered mutation in the GGTA-1 gene (GTKO) remains a predominantly antibody mediated process which is directed to a variety of non-Gal protein and carbohydrate antigens. We previously used an expression library screening strategy to identify six porcine endothelial cell cDNAs which encode pig antigens that bind to IgG induced after pig-to-primate cardiac xenotransplantation. One of these gene products was a glycosyltransferase with homology to the bovine β1,4 N-acetylgalactosaminyltransferase (B4GALNT2). We now characterize the porcine B4GALNT2 gene sequence, genomic organization, expression, and functional significance. Methods The porcine B4GALNT2 cDNA was recovered from the original library isolate, subcloned, sequenced, and used to identify a bacterial artificial chromosome (BAC) containing the entire B4GALNT2 locus from the Children's Hospital Oakland Research Institute BACPAC Resource Centre (#AC173453). PCR primers were designed to map the intron/exon genomic organization in the BAC clone. A stable human embryonic kidney (HEK) cell line expressing porcine B4GALNT2 (HEK-B4T) was produced. Expression of porcine B4GALNT2 in HEK-B4T cells was characterized by immune staining and siRNA transfection. The effects of B4GALNT2 expression in HEK-B4T cells was measured by flow cytometry and complement mediated lysis. Antibody binding to HEK and HEK-B4T cells was used to detect an induced antibody response to the B4GALNT2 produced glycan and the results were compared to GTKO PAEC specific non-Gal antibody induction. Expression of porcine B4GALNT2 in pig cells and tissues was measured by qualitative and quantitative real time reverse transcriptase PCR and by Dolichos biflorus agglutinin (DBA) tissue staining. Results The porcine B4GALNT2 gene shares a conserved genomic organization and encodes an open reading frame with 76 and 70% amino acid identity to the human and murine B4GALNT2 genes, respectively. The B4

  3. Unravelling DNA

    NASA Astrophysics Data System (ADS)

    Conroy, Rs; Danilowicz, C.

    2004-04-01

    The forces involved in the biology of life are carefully balanced between stopping thermal fluctuations ripping our DNA apart and having bonds weak enough to allow enzymes to function. The application of recently developed techniques for measuring piconewton forces and imaging at the nanometre scale on a molecule-by-molecule basis has dramatically increased the impact of single-molecule biophysics. This article describes the most commonly used techniques for imaging and manipulating single biomolecules. Using these techniques, the mechanical properties of DNA can be investigated, for example through measurements of the forces required to stretch and unzip the DNA double helix. These properties determine the ease with which DNA can be folded into the cell nucleus and the size and complexity of the accompanying cellular machinery. Part of this cellular machinery is enzymes, which manipulate, repair and transcribe the DNA helix. Enzymatic function is increasingly being investigated at the single molecule level to give better understanding of the forces and processes involved in the genetic cycle. One of the challenges is to transfer this understanding of single molecules into living systems. Already there have been some notable successes, such as the development of techniques for gene expression through the application of mechanical forces to cells, and the imaging and control of viral infection of a cell. This understanding and control of DNA has also been used to design molecules, which can self-assemble into a range of structures.

  4. Gas phase dicyanoacetylene (C4N2) on Titan: New experimental and theoretical spectroscopy results applied to Cassini CIRS data

    NASA Astrophysics Data System (ADS)

    Jolly, A.; Cottini, V.; Fayt, A.; Manceron, L.; Kwabia-Tchana, F.; Benilan, Y.; Guillemin, J.-C.; Nixon, C.; Irwin, P.

    2015-03-01

    Dicyanoacetylene has not been observed so far in the gas phase in Titan's atmosphere but this molecule is still on the list of the detected species, on the basis of the correspondence between a solid phase feature measured at 478 cm-1 in the laboratory and a spectral feature observed by Voyager. In this work, the infrared spectrum of gaseous C4N2 has been investigated to improve our knowledge of the band intensities and the line parameters for this molecule. Results of previously investigated bands have been revised and the intensity of the ν9 band at 107 cm-1, measured for the first time, was found to be the strongest absorption in the whole infrared domain. We have also improved the analysis of the complex rotational and hot band structure of C4N2 in order to obtain the first line lists for both bending modes ν8 and ν9. Using our radiative transfer code including the new line list of the strong ν9 band, we have searched for the signature of C4N2 at 107 cm-1 in the atmosphere of Titan utilizing Titan CIRS far infrared spectra. Despite averaging a large number of CIRS spectra at northern latitudes during the very favorable Titan winter, no gaseous C4N2 could be detected. At the 1-σ level we obtain an abundance upper limit of 5.3 × 10-10 for the limb average which is lower than or comparable to previously inferred values. As a consequence, the absence or very low amount of gaseous C4N2 makes quite puzzling its presence in the solid phase with an abundance compatible with the observed spectral feature at 478 cm-1.

  5. 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 ...

  6. 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

  7. Bulk size crystal growth, spectroscopic, dielectric and surface studies of 4-N,N-dimethylamino-4-N'-methylstilbazolium m-nitrobenzenesulfonate (DSMNS): A potential THz crystal of stilbazolium family.

    PubMed

    Antony Raj, A; John Sundaram, S; Gunaseelan, R; Sagayaraj, P

    2015-10-01

    The synthesis and growth of a potentially useful and efficient nonlinear optical organic single crystal of 4-N,N-dimethylamino-4-N'-methylstilbazolium m-nitrobenzenesulfonate (DSMNS) is reported. The growth experiment involved the slope nucleation method coupled with slow cooling as well as slow solvent evaporation techniques. Single crystal X-ray diffraction (XRD), Fourier transform infrared (FT-IR), FT-Raman and nuclear magnetic resonance (NMR) techniques have been employed to ascertain the structure and composition of the crystal. Second harmonic generation (SHG) efficiency of the sample has been examined by Kurtz and Perry powder test. Thermogravimetry (TG), differential thermal analysis (DTA) and differential scanning calorimetry (DSC) techniques are employed to investigate the thermal behavior of the grown crystal. The frequency/temperature dependent dielectric properties of the organic crystal of DSMNS are studied. The surface features of the grown crystal are investigated by chemical etching study and atomic force microscopy (AFM). PMID:26010563

  8. 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

  9. 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.

  10. qPCR-based mitochondrial DNA quantification: influence of template DNA fragmentation on accuracy.

    PubMed

    Jackson, Christopher B; Gallati, Sabina; Schaller, André

    2012-07-01

    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 (λnDNA) and mtDNA (λmtDNA) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number. PMID:22683632

  11. 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

  12. 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.

  13. 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.

  14. DNA codes

    SciTech Connect

    Torney, D. C.

    2001-01-01

    We have begun to characterize a variety of codes, motivated by potential implementation as (quaternary) DNA n-sequences, with letters denoted A, C The first codes we studied are the most reminiscent of conventional group codes. For these codes, Hamming similarity was generalized so that the score for matched letters takes more than one value, depending upon which letters are matched [2]. These codes consist of n-sequences satisfying an upper bound on the similarities, summed over the letter positions, of distinct codewords. We chose similarity 2 for matches of letters A and T and 3 for matches of the letters C and G, providing a rough approximation to double-strand bond energies in DNA. An inherent novelty of DNA codes is 'reverse complementation'. The latter may be defined, as follows, not only for alphabets of size four, but, more generally, for any even-size alphabet. All that is required is a matching of the letters of the alphabet: a partition into pairs. Then, the reverse complement of a codeword is obtained by reversing the order of its letters and replacing each letter by its match. For DNA, the matching is AT/CG because these are the Watson-Crick bonding pairs. Reversal arises because two DNA sequences form a double strand with opposite relative orientations. Thus, as will be described in detail, because in vitro decoding involves the formation of double-stranded DNA from two codewords, it is reasonable to assume - for universal applicability - that the reverse complement of any codeword is also a codeword. In particular, self-reverse complementary codewords are expressly forbidden in reverse-complement codes. Thus, an appropriate distance between all pairs of codewords must, when large, effectively prohibit binding between the respective codewords: to form a double strand. Only reverse-complement pairs of codewords should be able to bind. For most applications, a DNA code is to be bi-partitioned, such that the reverse-complementary pairs are separated

  15. 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.

  16. 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

  17. 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

  18. 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. PMID:27078739

  19. Germ cell DNA quantification shortly after IR laser radiation.

    PubMed

    Bermúdez, D; Carrasco, F; Diaz, F; Perez-de-Vargas, I

    1991-01-01

    The immediate effect of IR laser radiation on rat germ cells was studied by cytophotometric quantification of the nuclear DNA content in testicular sections. Two different levels of radiation were studied: one according to clinical application (28.05 J/cm2) and another known to increase the germ cell number (46.80 J/cm2). The laser beam induced changes in the germ cell DNA content depending on the cell type, the cell cycle phase and the doses of radiation energy applied. Following irradiation at both doses the percentage of spermatogonia showing a 4c DNA content was increased, while the percentage of these with a 2c DNA content was decreased. Likewise, the percentages of primary spermatocytes with a DNA content equal to 4c (at 28.05 J/cm2), between 2c and 4c (at 46.80 J/cm2) and higher than 4c (at both doses) were increased. No change in the mean spermatid DNA content was observed. Nevertheless, at 46.80 J/cm2 the percentages of elongated spermatids with a c or 2c DNA content differed from the controls. Data show that, even at laser radiation doses used in therapy, the germ cell DNA content is increased shortly after IR laser radiation. PMID:1772145

  20. [Comparison of heterotrophic nitrification and aerobic denitrification system by strain qy37 and its accelerating removal characteristic of NH4+ -N].

    PubMed

    Zhang, Pei-yu; Qu, Yang; Yu, De-shuang; Guo, Sha-sha; Yang, Rui-xia

    2010-08-01

    The characterization in nitrogen removal of a heterotrophic nitrification-aerobic denitrification bacteria (qy37) was studied. A strain coded as qy37 which had simultaneous heterotrophic nitrifying and aerobic denitrifying ability was screened. In the light of its morphological and physiological characters as well as their sequence analysis of the 16S rDNA, strain qy37 was identified as Pseudomonas sp.. In heterotrophic nitrifying system utilized ammonium chloride as nitrogen source, the concentration of NH4+ -N reduced from 138.52 mg/L to 7.88 mg/L and COD reduced from 2408.39 to 1177.49 mg/L by strain qy37 in 32 hours, the maximum accumulation of NH2OH and NO2- -N were 9.42 mg/L and 0.02 mg/L respectively, it was speculated that NH2OH was transformed to N2O and N2 directly by strain qy37. In aerobic denitrifying system utilized sodium nitrite as nitrogen source, the concentration of NO2- -N reduced from 109.25 mg/L to 2.59 mg/L by strain qy37 in 24 hours, and the maximum accumulation of NH2OH was 3.28 mg/L. Compared with heterotrophic nitrifying system, aerobic denitrifying system had a higher bacterial growth whereas the lower removal rate of TN and COD, as well as the accumulation of NH2OH. NO3- -N was also detected in aerobic denitrifying system. It is considered that the upgrowth of bacterium and utilization of energy in aerobic denitrifying system were more efficient than that in heterotrophic nitrifying system. In heterotrophic nitrification-aerobic denitrification system, the removal rate of NH4+ -N improved 37.31% in 16 hours than that in heterotrophic nitrifying system, the accumulation of NH2OH was less but N2O was higher than that in both heterotrophic nitrifying system and aerobic denitrifying system. PMID:21090299

  1. Optical properties of g-C4N3/BN bilayer film: A first-principles study

    NASA Astrophysics Data System (ADS)

    Son, Jicheol; Hashmi, Arqum; Hong, Jisang

    2015-11-01

    Using first-principles method, we explored the frequency dependent dielectric function, refractive index, reflectivity, optical conductivity, loss function, and absorption coefficient of g-C4N3/BN bilayer system. Here, the dependences of the optical properties on the electric field polarization were also explored. Because the dielectric function strongly depended on the electric polarization, we obtained anisotropic optical properties. For instance, the dielectric function was frequency independent for perpendicular electric polarization while a frequency dependent dielectric function was observed for parallel electric polarization. A high refractive index larger than 2 was obtained for parallel polarization in the infrared and the visible frequency ranges, whereas a constant refractive index of approximately 1.5 was observed for perpendicular polarization. We found that the electromagnetic wave propagating perpendicular to the film surface had a very small reflectivity at ultraviolet frequencies, this property could be utilized for applications as anti-reflection ultraviolet coatings. In addition, the g-C4N3/BN bilayer may produce no meaningful joule heating for in-plane wave propagation because of its extremely weak optical conductivity. We propose that optical phonons may generated by incident ultraviolet waves. In addition, the bilayer system may be transparent in the visible range. Overall, we found that metal-free, transparent, half-metallic g-C4N3 films could be utilized for spintronics and optical device applications.

  2. Electronic structure and magnetic properties of Mn, Co, and Ni substitution of Fe in Fe4N

    NASA Astrophysics Data System (ADS)

    Monachesi, Patrizia; Björkman, Torbjörn; Gasche, Thomas; Eriksson, Olle

    2013-08-01

    The magnetic properties of Mn, Co, and Ni substituted Fe4N are calculated from first principles theory. It is found that the generalized gradient approximation reproduces with good accuracy the magnetic moment and equilibrium volume for the parent Fe4N structure, with the atomic moment largest for the Fe atom furthest away from the N atom (Fe I site), approaching a value of 3 μB/atom, whereas the Fe atom closer to the N atom (Fe II site) has a moment closer to that of bcc Fe. The substitution of Fe for Mn, Co, or Ni, shows an intricate behavior in which the Mn substitution clearly favors the Fe II site, Ni favors substitution on the Fe I site, and Co shows no strong preference for either lattice site. The Ni and Co substitution results in a ferromagnetic coupling to the Fe atoms, whereas Mn couples antiferromagnetically on the Fe II site and ferromagnetically on the Fe I site. For all types of doping, the total magnetic moment is enhanced compared to Fe4N only in the energetically very unfavorable case of Mn doping at the Fe I site.

  3. Microwave absorption of gamma'-Fe2.6 Ni1.4N nanoparticles derived from nitriding counterpart precursor.

    PubMed

    Huang, H; Wang, F; Lv, B; Xue, F H; Guo, D Y; Park, W J; Lee, W J; Dong, X L

    2012-04-01

    Gamma-Fe2.6Ni1.4 nanoparticles were prepared by the arc-discharge method as the precursor and its nitride counterpart of gamma'-Fe2.6Ni14N nanoparticles was synthesized directly through a thermal ammonolysis reaction at the temperature of 673 K for two hours. The resultant product was identified as a homogeneous ternary nitride with nearly spherical shape and average size of about 60.0 nm. The electromagnetic characteristics of gamma'-Fe2.6Ni1.4N derivant and gamma-Fe2.6Ni1.4 precursor have been studied in the frequency range of 2-18 GHz. Compared with the precursor, gamma'-Fe2.6Ni1.4N nanoparticles exhibits an enhanced electromagnetic absorption property resulted from the increased dielectric loss by nitriding process. The optimal reflection loss (RL) of gamma'-Fe2.6Ni1.4N nanoparticles/paraffin composite can reach -39.9 dB at 5.2 GHz in a thickness of 2.29 mm, and the frequency band corresponding RL < -10 dB is over 2.6-18 GHz in the thickness range of 0.78-4.20 mm. PMID:22849063

  4. Identification of the enzyme responsible for N-acetylation of norfloxacin by Microbacterium sp. Strain 4N2-2.

    PubMed

    Kim, Dae-Wi; Feng, Jinhui; Chen, Huizhong; Kweon, Ohgew; Gao, Yuan; Yu, Li-Rong; Burrowes, Vanessa J; Sutherland, John B

    2013-01-01

    Microbacterium sp. 4N2-2, isolated from a wastewater treatment plant, converts the antibacterial fluoroquinolone norfloxacin to N-acetylnorfloxacin and three other metabolites. Because N-acetylation results in loss of antibacterial activity, identification of the enzyme responsible is important for understanding fluoroquinolone resistance. The enzyme was identified as glutamine synthetase (GS); N-acetylnorfloxacin was produced only under conditions associated with GS expression. The GS gene (glnA) was cloned, and the protein (53 kDa) was heterologously expressed and isolated. Optimal conditions and biochemical properties (K(m) and V(max)) of purified GS were characterized; the purified enzyme was inhibited by Mn(2+), Mg(2+), ATP, and ADP. The contribution of GS to norfloxacin resistance was shown by using a norfloxacin-sensitive Escherichia coli strain carrying glnA derived from Microbacterium sp. 4N2-2. The GS of Microbacterium sp. 4N2-2 was shown to act as an N-acetyltransferase for norfloxacin, which produced low-level norfloxacin resistance. Structural and docking analysis identified potential binding sites for norfloxacin at the ADP binding site and for acetyl coenzyme A (acetyl-CoA) at a cleft in GS. The results suggest that environmental bacteria whose enzymes modify fluoroquinolones may be able to survive in the presence of low fluoroquinolone concentrations. PMID:23104417

  5. Metallic Co4N Porous Nanowire Arrays Activated by Surface Oxidation as Electrocatalysts for the Oxygen Evolution Reaction.

    PubMed

    Chen, Pengzuo; Xu, Kun; Fang, Zhiwei; Tong, Yun; Wu, Junchi; Lu, Xiuli; Peng, Xu; Ding, Hui; Wu, Changzheng; Xie, Yi

    2015-12-01

    Designing highly efficient electrocatalysts for oxygen evolution reaction (OER) plays a key role in the development of various renewable energy storage and conversion devices. In this work, we developed metallic Co4N porous nanowire arrays directly grown on flexible substrates as highly active OER electrocatalysts for the first time. Benefiting from the collaborative advantages of metallic character, 1D porous nanowire arrays, and unique 3D electrode configuration, surface oxidation activated Co4N porous nanowire arrays/carbon cloth achieved an extremely small overpotential of 257 mV at a current density of 10 mA cm(-2), and a low Tafel slope of 44 mV dec(-1) in an alkaline medium, which is the best OER performance among reported Co-based electrocatalysts to date. Moreover, in-depth mechanistic investigations demonstrate the active phases are the metallic Co4N core inside with a thin cobalt oxides/hydroxides shell during the OER process. Our finding introduces a new concept to explore the design of high-efficiency OER electrocatalysts. PMID:26437900

  6. 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.

  7. Identification of the Enzyme Responsible for N-Acetylation of Norfloxacin by Microbacterium sp. Strain 4N2-2

    PubMed Central

    Kim, Dae-Wi; Feng, Jinhui; Chen, Huizhong; Kweon, Ohgew; Gao, Yuan; Yu, Li-Rong; Burrowes, Vanessa J.

    2013-01-01

    Microbacterium sp. 4N2-2, isolated from a wastewater treatment plant, converts the antibacterial fluoroquinolone norfloxacin to N-acetylnorfloxacin and three other metabolites. Because N-acetylation results in loss of antibacterial activity, identification of the enzyme responsible is important for understanding fluoroquinolone resistance. The enzyme was identified as glutamine synthetase (GS); N-acetylnorfloxacin was produced only under conditions associated with GS expression. The GS gene (glnA) was cloned, and the protein (53 kDa) was heterologously expressed and isolated. Optimal conditions and biochemical properties (Km and Vmax) of purified GS were characterized; the purified enzyme was inhibited by Mn2+, Mg2+, ATP, and ADP. The contribution of GS to norfloxacin resistance was shown by using a norfloxacin-sensitive Escherichia coli strain carrying glnA derived from Microbacterium sp. 4N2-2. The GS of Microbacterium sp. 4N2-2 was shown to act as an N-acetyltransferase for norfloxacin, which produced low-level norfloxacin resistance. Structural and docking analysis identified potential binding sites for norfloxacin at the ADP binding site and for acetyl coenzyme A (acetyl-CoA) at a cleft in GS. The results suggest that environmental bacteria whose enzymes modify fluoroquinolones may be able to survive in the presence of low fluoroquinolone concentrations. PMID:23104417

  8. 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…

  9. DNA computing.

    PubMed

    Gibbons, A; Amos, M; Hodgson, D

    1997-02-01

    DNA computation is a novel and exciting recent development at the interface of computer science and molecular biology. We describe the current activity in this field following the seminal work of Adleman, who recently showed how techniques of molecular biology may be applied to the solution of a computationally intractable problem. PMID:9013647

  10. DNA Music.

    ERIC Educational Resources Information Center

    Miner, Carol; della Villa, Paula

    1997-01-01

    Describes an activity in which students reverse-translate proteins from their amino acid sequences back to their DNA sequences then assign musical notes to represent the adenine, guanine, cytosine, and thymine bases. Data is obtained from the National Institutes of Health (NIH) on the Internet. (DDR)

  11. 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)

  12. 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

  13. [Effect of different nitrogen forms and ratio on growth and active ingredient content of Platycodon grandiflorum].

    PubMed

    Duan, Yun-jing; Wang, Kang-cai; Niu, Ling-hui; Li, Ke; Su, Yun-yun

    2015-10-01

    To providing evidence about nitrogen adequate application of Platycodon grandiflorum, the pot culture experiment was conducted to study the effect of nitrogen on the growth, physiological metabolism and the quality of P. grandiflorum. The activity of NR, GS and SOD, POD and CAT were determined. And the nitrate and ammonium nitrogen content, photosynthetic characteristics, active components of P. grandiflorum were determined. The results showed that the nitrate nitrogen content and P. biomass reached its maximum value, when NH4(+)-N/NO3(-) -N was 0: 100, the activity of NR. The activity of GS was the highest at the NH4(+) -N/NO3(-) -N ratio of 25:75 and ammonium nitrogen content was the highest at 75:25. The activity of SOD decreased and then increased with the increasing of NO3(-) -N. At the NH4(+) -N/NO3(-) -N ratio of 25: 75, the activity of CAT had its maximum value and the content of MDA had the minimum value. At the same time, the content of platycodon D was the highest at this treatment. The studies had shown that different nitrogen forms and ratio had a significant effect on the characteristics of photosynthetic physiology, nitrogen metabolism and resistance adjustment, growth and the quality of P. grandiflorum. The NH4(+) -N/NO3(-) -N ratio of 25: 75 was a suitable ratio of nitrogen forms for the growth of P. Grandiflorum and accumulating the content of platycodon D. PMID:26975097

  14. 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

  15. 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

  16. Preparation, structure and photoluminescence properties of Eu{sup 2+} and Ce{sup 3+}-doped SrYSi{sub 4}N{sub 7}

    SciTech Connect

    Li, Y.Q. . E-mail: y.q.li@tue.nl; Fang, C.M.; With, G. de; Hintzen, H.T. . E-mail: h.t.hintzen@tue.nl

    2004-12-01

    Undoped and Eu{sup 2+} or Ce{sup 3+}-doped SrYSi{sub 4}N{sub 7} were synthesized by solid-state reaction method at 1400-1660{sup o}C under nitrogen/hydrogen atmosphere. The crystal structure was refined from the X-ray powder diffraction data by the Rietveld method. SrYSi{sub 4}N{sub 7} and EuYSi{sub 4}N{sub 7}, being isotypic with the family of compounds MYbSi{sub 4}N{sub 7} (M=Sr, Eu, Ba) and BaYSi{sub 4}N{sub 7,} crystallize with the hexagonal symmetry: space group P6{sub 3}mc (No. 186), Z=2, a=6.0160 (1)A, c=9.7894 (1)A, V=306.83(3)A{sup 3}; and a=6.0123 (1)A, c=9.7869 (1)A, V=306.37(1)A{sup 3}, respectively. Photoluminescence properties have been studied for Sr{sub 1-x}Eu{sub x}YSi{sub 4}N{sub 7} (x=0-1) and SrY{sub 1-x}Ce{sub x}Si{sub 4}N{sub 7} (x=0-0.03) at room temperature. Eu{sup 2+}-doped SrYSi{sub 4}N{sub 7} shows a broad yellow emission band peaking around 548-570nm, while Ce{sup 3+}-doped SrYSi{sub 4}N{sub 7} exhibits a blue emission band with a maximum at about 450nm. SrYSi{sub 4}N{sub 7}:Eu{sup 2+} can be very well excited by 390nm radiation, which makes this material attractive as conversion phosphor for LED lighting applications.

  17. 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

  18. 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

  19. 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.

  20. Interaction peculiarities of 5,10,15,20-tetrakis(4-N-methylpyridil) tetra iodide porphyrin with albumin

    NASA Astrophysics Data System (ADS)

    Lebedeva, N. Sh.; Malkova, E. A.; Popova, T. E.; Kutyrev, A. E.; Syrbu, S. A.; Parfenyuk, E. V.; Vyugin, A. I.

    2014-01-01

    In present work interactions of bovine serum albumin with 5,10,15,20-tetrakis(4-N-methylpyridil) tetra iodide porphyrin have been studied by electron absorption and fluorescence spectroscopy. The studies were carried out in aqueous media at different pH and in water-dimethylformamide mixtures containing up to 0.19 M of the organic solvent. It has been demonstrated that the porphyrin forms stable complexes with BSA in which the porphyrin is located subdomains IB and IIA. The stability constants of the complexes is practically independent of pH.

  1. Photophysics of 4- N, N-dimethylamino cinnamaldehyde in AOT reverse micelles and exploration of its position and orientation

    NASA Astrophysics Data System (ADS)

    Panja, Subhasis; Chakravorti, Sankar

    2003-01-01

    An attempt has been made in this Letter to locate the position and orientation of 4- N, N-dimethylamino cinnamaldehyde (DMACA) inside sodium bis(2-ethylhexyl) sulfosuccinate (AOT)- n-heptane reverse micelle based on change in photophysical properties of DMACA compared to that in n-heptane. It has been proposed that the possibility of finding the donor moiety inside the small water pool of reverse micelle is maximum while the acceptor group straddles in the remaining part of the reverse micelle. The micropolarity in the vicinity of the donor moiety has been computed in terms of dielectric constant with varying water pool size.

  2. G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triad·water complex and implication for small-molecule binding

    PubMed Central

    Heddi, Brahim; Martín-Pintado, Nerea; Serimbetov, Zhalgas; Kari, Teuku Mahfuzh Aufar; Phan, Anh Tuân

    2016-01-01

    G-quadruplexes are non-canonical structures of nucleic acids, in which guanine bases form planar G-tetrads (G·G·G·G) that stack on each other in the core of the structure. G-quadruplexes generally contain multiple times of four (4n) guanines in the core. Here, we study the structure of G-quadruplexes with only (4n - 1) guanines in the core. The solution structure of a DNA sequence containing 11 guanines showed the formation of a parallel G-quadruplex involving two G-tetrads and one G-triad with a vacant site. Molecular dynamics simulation established the formation of a stable G-triad·water complex, where water molecules mimic the position of the missing guanine in the vacant site. The concept of forming G-quadruplexes with missing guanines in the core broadens the current definition of G-quadruplex-forming sequences. The potential ability of such structures to bind different metabolites, including guanine, guanosine and GTP, in the vacant site, could have biological implications in regulatory functions. Formation of this unique binding pocket in the G-triad could be used as a specific target in drug design. PMID:26673723

  3. Evaluation of a novel material, Diomics X-Swab™, for collection of DNA.

    PubMed

    Marshall, Pamela L; Stoljarova, Monika; Larue, Bobby L; King, Jonathan L; Budowle, Bruce

    2014-09-01

    Success of DNA typing is related to the amount of target material recovered from an evidentiary item. Generally, the more DNA that is recovered, the better the chance is of obtaining a typing result that will be robust and reliable. One method of collecting stain materials is by swabbing. Recovery of DNA from a number of commercially available swabs is not an efficient process. The X-Swab™ (Diomics Corporation, La Jolla, CA) is a unique bio-specimen collection material with highly absorptive properties and can be dissolved during certain extraction conditions. Therefore, more DNA may be collected from a substrate and be released from the swab matrix than other swabs. The ability to recover DNA from X-Swab material and success in STR typing were compared with the Copan 4N6FLOQSwab™ (Brescia, Italy), a device which utilizes a proprietary flocked-swab technology to maximize DNA collection and elution efficiency. Both types of swabs were impregnated with known amounts of DNA and body fluids and allowed to air dry. In addition, blood was placed onto glass slides, allowed to dry and collected using both types of swabs. DNA recovery was assessed by DNA quantitation and by STR typing. Results suggested that X-Swab material yielded greater DNA recovery, particularly of low quantity samples (defined as diluted neat samples), compared with the 4N6FLOQSwab. Results also indicated that X-Swab material itself enhances yield of PCR products. PMID:25016249

  4. Lack of genotoxic properties of the hair-dye component N-methyl-amino-2-nitro-4-N',N'-bis-(2-hydroxyethyl)-aminobenzene, in mammalian cells in vitro, and in yeasts.

    PubMed

    Loprieno, N; Mariani, L; Rusciano, D

    1983-02-01

    N-Methyl-amino-2-nitro-4-N',N'-bis-(2-hydroxyethyl)-aminobenzene is a hair-dye ingredient. Its potential ability to induce gene mutations, in the yeast S. pombe and in cultured mammalian CH-V79 cells, mitotic gene conversion in the yeast S. cerevisiae, and unscheduled DNA synthesis in cultured human HeLa cells was evaluated. The chemical proved unable to induce detectable genotoxic effects according to these tests. The present data, together with others that show that the chemical is not mutagenic in Salmonella typhimurium or Drosophila, and is not clastogenic in mammalian cytogenetic assays (in vitro or in vivo), strongly support the non-genotoxicity of the chemical. PMID:6402693

  5. 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.

  6. Temperature profile of a stoichiometric ch4/N2O flame from laser excited fluorescence measurements on OH

    SciTech Connect

    Anderson, W.R.; Decker, L.J.; Kotlar, A.J.

    1982-07-01

    The temperature profile of a stoichiometric CH/sub 4//N/sub 2/O flame over a porous plug, atmospheric-pressure burner has been measured using laser excited fluorescence of the OH radical. The technique of rotationally resolved fluorescence excitation scans was extended to the (1,1) vibrational band of the A doublet sigma plus - X doublet pi system to avoid problems of laser beam depletion and self-absorption encountered by this group and previous workers using the (O,O) band. Absorption spectra were obtained in addition to fluorescence spectra. A least squares curve-fitting technique which accounts for the various types of line broadening was developed and applied to two absorption lines in the (O,O) band. The resulting temperature profile is compared to that from fluorescence data reduced using Boltzmann plots. The more complicated curve-fitting approach was later applied to five lines in the spectrum using several combinations of fluorescence and absorption data. Results of all the aforementioned methods were compared to those from OH band reversal and N2 vibrational Raman measurements at the same point in the post flame gases. Excellent agreement was achieved. The results are discussed with emphasis on both the fluorescence diagnostics and the characteristics of the CH/sub 4//N/sub 2/O flame on the porous-plug burner.

  7. Distinct DNA methylomes of newborns and centenarians

    PubMed Central

    Heyn, Holger; Li, Ning; Ferreira, Humberto J.; Moran, Sebastian; Pisano, David G.; Gomez, Antonio; Diez, Javier; Sanchez-Mut, Jose V.; Setien, Fernando; Carmona, F. Javier; Puca, Annibale A.; Sayols, Sergi; Pujana, Miguel A.; Serra-Musach, Jordi; Iglesias-Platas, Isabel; Formiga, Francesc; Fernandez, Agustin F.; Fraga, Mario F.; Heath, Simon C.; Valencia, Alfonso; Gut, Ivo G.; Wang, Jun; Esteller, Manel

    2012-01-01

    Human aging cannot be fully understood in terms of the constrained genetic setting. Epigenetic drift is an alternative means of explaining age-associated alterations. To address this issue, we performed whole-genome bisulfite sequencing (WGBS) of newborn and centenarian genomes. The centenarian DNA had a lower DNA methylation content and a reduced correlation in the methylation status of neighboring cytosine—phosphate—guanine (CpGs) throughout the genome in comparison with the more homogeneously methylated newborn DNA. The more hypomethylated CpGs observed in the centenarian DNA compared with the neonate covered all genomic compartments, such as promoters, exonic, intronic, and intergenic regions. For regulatory regions, the most hypomethylated sequences in the centenarian DNA were present mainly at CpG-poor promoters and in tissue-specific genes, whereas a greater level of DNA methylation was observed in CpG island promoters. We extended the study to a larger cohort of newborn and nonagenarian samples using a 450,000 CpG-site DNA methylation microarray that reinforced the observation of more hypomethylated DNA sequences in the advanced age group. WGBS and 450,000 analyses of middle-age individuals demonstrated DNA methylomes in the crossroad between the newborn and the nonagenarian/centenarian groups. Our study constitutes a unique DNA methylation analysis of the extreme points of human life at a single-nucleotide resolution level. PMID:22689993

  8. 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. PMID:26139135

  9. 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.

  10. 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.

  11. Nuclear and mitochondrial DNA quantification of various forensic materials.

    PubMed

    Andréasson, H; Nilsson, M; Budowle, B; Lundberg, H; Allen, M

    2006-12-01

    Due to the different types and quality of forensic evidence materials, their DNA content can vary substantially, and particularly low quantities can impact the results in an identification analysis. In this study, the quantity of mitochondrial and nuclear DNA was determined in a variety of materials using a previously described real-time PCR method. DNA quantification in the roots and distal sections of plucked and shed head hairs revealed large variations in DNA content particularly between the root and the shaft of plucked hairs. Also large intra- and inter-individual variations were found among hairs. In addition, DNA content was estimated in samples collected from fingerprints and accessories. The quantification of DNA on various items also displayed large variations, with some materials containing large amounts of nuclear DNA while no detectable nuclear DNA and only limited amounts of mitochondrial DNA were seen in others. Using this sensitive real-time PCR quantification assay, a better understanding was obtained regarding DNA content and variation in commonly analysed forensic evidence materials and this may guide the forensic scientist as to the best molecular biology approach for analysing various forensic evidence materials. PMID:16427750

  12. Wrinkled DNA.

    PubMed Central

    Arnott, S; Chandrasekaran, R; Puigjaner, L C; Walker, J K; Hall, I H; Birdsall, D L; Ratliff, R L

    1983-01-01

    The B form of poly d(GC):poly d(GC) in orthorhombic microcrystallites in oriented fibers has a secondary structure in which a dinucleotide is the repeated motif rather than a mononucleotide as in standard, smooth B DNA. One set of nucleotides (probably GpC) has the same conformations as the smooth form but the alternate (CpG) nucleotides have a different conformation at C3'-O3'. This leads to a distinctive change in the orientation of the phosphate groups. Similar perturbations can be detected in other poly d(PuPy):poly d(PuPy) DNAs such as poly d(IC):poly d(IC) and poly d(AT):poly d(AT) in their D forms which have tetragonal crystal environments. This suggests that such perturbations are intrinsic to all stretches of duplex DNA where purines and pyrimidines alternate and may play a role in the detection and exploitation of such sequences by regulatory proteins. Images PMID:6572358

  13. 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.

  14. PCR-Based Analysis of Mitochondrial DNA Copy Number, Mitochondrial DNA Damage, and Nuclear DNA Damage.

    PubMed

    Gonzalez-Hunt, Claudia P; Rooney, John P; Ryde, Ian T; Anbalagan, Charumathi; Joglekar, Rashmi; Meyer, Joel N

    2016-01-01

    Because of the role that 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Shedding Light on Avian Influenza H4N6 Infection in Mallards: Modes of Transmission and Implications for Surveillance

    PubMed Central

    VanDalen, Kaci K.; Franklin, Alan B.; Mooers, Nicole L.; Sullivan, Heather J.; Shriner, Susan A.

    2010-01-01

    Background Wild mallards (Anas platyrhychos) are considered one of the primary reservoir species for avian influenza viruses (AIV). Because AIV circulating in wild birds pose an indirect threat to agriculture and human health, understanding the ecology of AIV and developing risk assessments and surveillance systems for prevention of disease is critical. Methodology/Principal Findings In this study, mallards were experimentally infected with an H4N6 subtype of AIV by oral inoculation or contact with an H4N6 contaminated water source. Cloacal swabs, oropharyngeal swabs, fecal samples, and water samples were collected daily and tested by real-time RT-PCR (RRT-PCR) for estimation of viral shedding. Fecal samples had significantly higher virus concentrations than oropharyngeal or cloacal swabs and 6 month old ducks shed significantly more viral RNA than 3 month old ducks regardless of sample type. Use of a water source contaminated by AIV infected mallards, was sufficient to transmit virus to naïve mallards, which shed AIV at higher or similar levels as orally-inoculated ducks. Conclusions Bodies of water could serve as a transmission pathway for AIV in waterfowl. For AIV surveillance purposes, water samples and fecal samples appear to be excellent alternatives or additions to cloacal and oropharyngeal swabbing. Furthermore, duck age (even within hatch-year birds) may be important when interpreting viral shedding results from experimental infections or surveillance. Differential shedding among hatch-year mallards could affect prevalence estimates, modeling of AIV spread, and subsequent risk assessments. PMID:20877466

  3. Hydration of ds-DNA and ss-DNA by Neutron Quasielastic Scattering

    PubMed Central

    Bastos, M.; Castro, V.; Mrevlishvili, G.; Teixeira, J.

    2004-01-01

    Quasielastic neutron scattering measurements were performed in hydrated samples of ds-DNA and ss-DNA. The samples were hydrated in a high relative humidity atmosphere, and their final water content was 0.559 g H2O/g ds-DNA and 0.434 g H2O/g ss-DNA. The measurements were performed at 8 and 5.2 Å for the ds-DNA sample, and at 5.2 Å for the ss-DNA sample. The temperature was in both cases 298 K. Analysis of the obtained data indicates that in the ds-DNA sample we can distinguish two types of protons—those belonging to water molecules strongly attached to the ds-DNA surface and another fraction belonging to water that diffuses isotropically in a sphere of radius 2.8 Å, with a local diffusion coefficient of 2.2 × 10−5 cm2 s−1. For ss-DNA, on the other hand, no indication was found of motionally restricted or confined water. Further, the fraction of protons strongly attached to the ds-DNA surface corresponds to 0.16 g H2O/g ds-DNA, which equals the amount of water that is released by ds-DNA upon thermal denaturation, as studied by one of us (G.M.) by differential scanning calorimetry. This value also equals the difference between the critical hydration values of ds-DNA and ss-DNA, also determined by DSC. These results represent, thus, a completely independent measurement of water characteristics and behavior in ds- and ss-DNA at critical hydration values, and therefore substantiate the previous suggestions/conclusions of the results obtained by calorimetry. PMID:15189878

  4. Influence of the substitution of the manganese for iron in the Fe sub 4 N lattice on particle formation and magnetic properties

    SciTech Connect

    Siberchicot, B.; Matar, S.F.; Fournes, L.; Demazeau, G.; Hagenmuller, P. )

    1990-01-01

    Moessbauer resonance studies on Mn-substituted Fe{sub 4}N show that manganese occupies statistically both iron sites in the lattice. Replacement of Fe by Mn modifies the crystal growth process of Fe{sub 4}N magnetic particles and leads to improvement of the extrinsic magnetic properties, i.e., H{sub c} and {sigma}{sub r}/{sigma}{sub s}, required for magnetic recording applications.

  5. 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

  6. 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. PMID:24757789

  7. Structural characterisation of human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol, lactose, 3'-sulfo-lactose, and 2'-fucosyllactose.

    PubMed

    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

  8. Low-template DNA: A single DNA analysis or two replicates?

    PubMed

    Gittelson, Simone; Steffen, Carolyn R; Coble, Michael D

    2016-07-01

    This study investigates the following two questions: (1) Should the DNA analyst concentrate the DNA extract into a single amplification or should he/she split it up to do two replicates? (2) Given the electropherogram obtained from a first analysis, is it worthwhile for the DNA analyst to invest in obtaining a second replicate? A decision-theoretic approach addresses these questions by quantitatively expressing the expected net gain (ENG) of each DNA analysis of interest. The results indicate that two replicates generally have a greater ENG than a single DNA analysis for DNA quantities capable of producing two replicates having an average allelic peak height as low as 43rfu. This supports the position that two replicates increase the information content with regard to a single analysis. PMID:27131143

  9. Mitochondrial DNA replacement versus nuclear DNA persistence

    NASA Astrophysics Data System (ADS)

    Serva, Maurizio

    2006-10-01

    In this paper we consider two populations whose generations are not overlapping and whose size is large. The number of males and females in both populations is constant. Any generation is replaced by a new one and any individual has two parents concerning nuclear DNA and a single one (the mother) concerning mtDNA. Moreover, at any generation some individuals migrate from the first population to the second. In a finite random time T, the mtDNA of the second population is completely replaced by the mtDNA of the first. In the same time, the nuclear DNA is not completely replaced and a fraction F of the ancient nuclear DNA persists. We compute both T and F. Since this study shows that complete replacement of mtDNA in a population is compatible with the persistence of a large fraction of nuclear DNA, it may have some relevance for the 'out of Africa'/multiregional debate in palaeoanthropology.

  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. 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;...

  12. The DNA-based human karyotype.

    PubMed

    Mayall, B H; Carrano, A V; Moore, D H; Ashworth, L K; Bennett, D E; Mendelsohn, M L

    1984-07-01

    Image cytometry and computer analysis are used to determine the relative DNA content and the DNA-based centromeric index of the 24 chromosomes of the human karyotype. A two-step procedure is used. Chromosomes of cells in metaphase first are stained with quinacrine and identified visually by their fluorescent Q-band patterns. They then are stained for DNA using gallocyanin-chrome alum. The chromosome images are scanned and recorded as digital values of optical density by an CYDAC image cytometric microscope system, CYDAC. The digital images are processed by computer to measure for each chromosome the relative DNA stain contents of the whole chromosome and of the p and q arms and the DNA-based centromeric index. About ten cells are analyzed for each of the donors, who are phenotypically normal men and women. The chromosome measurements are pooled by chromosome type for each donor and are compared among donors. The means of the chromosome measurements give the DNA-based human karyotype. Analysis of the DNA-based data shows that some chromosomes or portions of chromosomes vary significantly among donors. These variants do not correlate with detectable morphologic polymorphisms, such as Q- or C-band variants; thus they represent new and otherwise undetectable chromosome polymorphisms whose genetic basis and clinical significance are yet to be determined. PMID:6205836

  13. Quantifying quality in DNA self-assembly

    NASA Astrophysics Data System (ADS)

    Wagenbauer, Klaus F.; Wachauf, Christian H.; Dietz, Hendrik

    2014-04-01

    Molecular self-assembly with DNA is an attractive route for building nanoscale devices. The development of sophisticated and precise objects with this technique requires detailed experimental feedback on the structure and composition of assembled objects. Here we report a sensitive assay for the quality of assembly. The method relies on measuring the content of unpaired DNA bases in self-assembled DNA objects using a fluorescent de-Bruijn probe for three-base ‘codons’, which enables a comparison with the designed content of unpaired DNA. We use the assay to measure the quality of assembly of several multilayer DNA origami objects and illustrate the use of the assay for the rational refinement of assembly protocols. Our data suggests that large and complex objects like multilayer DNA origami can be made with high strand integration quality up to 99%. Beyond DNA nanotechnology, we speculate that the ability to discriminate unpaired from paired nucleic acids in the same macromolecule may also be useful for analysing cellular nucleic acids.

  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. 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

  16. 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

  17. 34 CFR Plans - Contents

    Code of Federal Regulations, 2010 CFR

    1997-07-01

    ... 34 Education 2 1997-07-01 1997-07-01 false Contents Plans State Plans ASSISTANCE TO STATES FOR THE...-General § 300.111 Content of plan. Each State plan must contain the provisions required in §§ 300.121-300.154. State Plans—Contents...

  18. 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...

  19. 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…

  20. 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

  1. 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.

  2. 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

  3. 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

  4. DNA-modified electrodes fabricated using copper-free click chemistry for enhanced protein detection.

    PubMed

    Furst, Ariel L; Hill, Michael G; Barton, Jacqueline K

    2013-12-31

    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

  5. Preparation and characterization of imogolite/DNA hybrid hydrogels.

    PubMed

    Jiravanichanun, Nattha; Yamamoto, Kazuya; Kato, Kenichi; Kim, Jungeun; Horiuchi, Shin; Yah, Weng-On; Otsuka, Hideyuki; Takahara, Atsushi

    2012-01-01

    Imogolite is one of the clay minerals contained in volcanic ash soils. The novel hybrid hydrogels were prepared from imogolite nanofibers and DNA by utilizing strong interaction between the aluminol groups on imogolite surface and phosphate groups of DNA. The hybrid hydrogels of imogolite and DNA were prepared in various feed ratios, and their physicochemical properties and molecular aggregation states were investigated in both dispersion and gel states. The maximum DNA content in the hybrid gels was shown in equivalent molar ratio of imogolite and DNA. The physical properties of the hybrid gels were changed by varying DNA blend ratios. In the dispersion state, the hybrid gels showed a fibrous structure of imogolite, whereas a continuous network structure was observed in pure imogolite, indicating that the hybrid with DNA enhanced the dispersion of imogolite. In the gel state, DNA and imogolite nanofibers formed a 3D network structure. PMID:22148683

  6. 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)

  7. 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. PMID:25355529

  8. Sensitive detection of mercury and copper ions by fluorescent DNA/Ag nanoclusters in guanine-rich DNA hybridization.

    PubMed

    Peng, Jun; Ling, Jian; Zhang, Xiu-Qing; Bai, Hui-Ping; Zheng, Liyan; Cao, Qiu-E; Ding, Zhong-Tao

    2015-02-25

    In this work, we designed a new fluorescent oligonucleotides-stabilized silver nanoclusters (DNA/AgNCs) probe for sensitive detection of mercury and copper ions. This probe contains two tailored DNA sequence. One is a signal probe contains a cytosine-rich sequence template for AgNCs synthesis and link sequence at both ends. The other is a guanine-rich sequence for signal enhancement and link sequence complementary to the link sequence of the signal probe. After hybridization, the fluorescence of hybridized double-strand DNA/AgNCs is 200-fold enhanced based on the fluorescence enhancement effect of DNA/AgNCs in proximity of guanine-rich DNA sequence. The double-strand DNA/AgNCs probe is brighter and stable than that of single-strand DNA/AgNCs, and more importantly, can be used as novel fluorescent probes for detecting mercury and copper ions. Mercury and copper ions in the range of 6.0-160.0 and 6-240 nM, can be linearly detected with the detection limits of 2.1 and 3.4 nM, respectively. Our results indicated that the analytical parameters of the method for mercury and copper ions detection are much better than which using a single-strand DNA/AgNCs. PMID:25305618

  9. Sensitive detection of mercury and copper ions by fluorescent DNA/Ag nanoclusters in guanine-rich DNA hybridization

    NASA Astrophysics Data System (ADS)

    Peng, Jun; Ling, Jian; Zhang, Xiu-Qing; Bai, Hui-Ping; Zheng, Liyan; Cao, Qiu-E.; Ding, Zhong-Tao

    2015-02-01

    In this work, we designed a new fluorescent oligonucleotides-stabilized silver nanoclusters (DNA/AgNCs) probe for sensitive detection of mercury and copper ions. This probe contains two tailored DNA sequence. One is a signal probe contains a cytosine-rich sequence template for AgNCs synthesis and link sequence at both ends. The other is a guanine-rich sequence for signal enhancement and link sequence complementary to the link sequence of the signal probe. After hybridization, the fluorescence of hybridized double-strand DNA/AgNCs is 200-fold enhanced based on the fluorescence enhancement effect of DNA/AgNCs in proximity of guanine-rich DNA sequence. The double-strand DNA/AgNCs probe is brighter and stable than that of single-strand DNA/AgNCs, and more importantly, can be used as novel fluorescent probes for detecting mercury and copper ions. Mercury and copper ions in the range of 6.0-160.0 and 6-240 nM, can be linearly detected with the detection limits of 2.1 and 3.4 nM, respectively. Our results indicated that the analytical parameters of the method for mercury and copper ions detection are much better than which using a single-strand DNA/AgNCs.

  10. 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.

  11. [Characteristics of high solid content sludge with microwave irradiation].

    PubMed

    Qiao, Wei; Wang, Wei; Xun, Rui; Zhou, Gang; Wan, Xiao; Xia, Zhou

    2008-06-01

    This paper focus on changes of high solid content sludge (7%, 9% and 13%) hydrolysis with microwave irradiation also anaerobic biodegradation of treated sludge was tested by biochemical methane potential (BMP) procedure. Results showed that microwave irradiation provided a rapid temperature increasing. Hydrolysis accelerated the solubilization of volatile suspended solid (VSS) and suspended solid (SS). COD, TOC, NH4+-N, TN, and TP concentration of liquor sludge increased, while pH decreased. Sludge solid content was found to be the most influential parameter. VSS and SS dissolving ratio of sludge with 13% solid content were lower than sludge with 7% and 9% solid content. 23% of VSS and 18% of SS dissolved for 9% sludge at 170 degrees C with 5 min, SCOD of liquor was 41 g/L, and concentration of TOC and NH4+-N were 30 g/L and 1 g/L respectively. Biodegradation of treated sludge improved. Methane production of 9% sludge at 170 degrees C with 5 min and 10 min were 27% and 30.8% higher than that of untreated sludge. Hydrolysis time increasing from 5 min to 10 min brought an improvement of 4%, 3.6% and 5.7% methane production at 120 degrees C, 150 degrees C and 170 degrees C. PMID:18763510

  12. 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

  13. Naturalising Representational Content.

    PubMed

    Shea, Nicholas

    2013-05-01

    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

  14. 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.

  15. Solid-state combinatorial screening of ARSi4N7:Eu2+ (A = Sr, Ba, Ca; R = Y, La, Lu) phosphors.

    PubMed

    Park, Woon Bae; Son, Kyung Hyun; Singh, Satendra Pal; Sohn, Kee-Sun

    2012-10-01

    A double-ternary combinatorial chemistry (combi-chem) library was visualized in terms of structure, PL intensity, and color chromaticity for a nitride phosphor system, ARSi4N7:Eu(2+) (A = Sr, Ca, Ba; R = Y, La, Lu), so as to obtain a quantitative structure and property relationship (QSPR) in a systematic manner. Most of the samples constituting the double-ternary combi-chem library turned out to have ARSi4N7 structures with a P63mc space group. However, several phases such as Ca2Si5N8 with a Cc space group, LaSi3N5 with a P212121 space group, R6Si11N20O with a P31c space group, etc., coexisted. Aside from the green luminescence from the well-known SrYSi4N7:Eu(2+) and BaYSi4N7:Eu(2+) phosphors, their solid solutions (Sr,Ba)Si4N7:Eu(2+) proved to possess better PL properties. In addition, novel phosphors with an acceptable green PL intensity and color chromaticity were discovered in the ALuSi4N7:Eu(2+) side of the double-ternary combi-chem library. The Ca-rich side did not constitute a single-phase ARSi4N7 structure with a P63mc space group, and therefore the red emission in the Ca-rich side proved to originate from well-known Ca2Si5N8:Eu(2+) phosphors, which resided in the sample as a minor phase. PMID:22920282

  16. Polybacterial Periodontal Pathogens Alter Vascular and Gut BH4/nNOS/NRF2-Phase II Enzyme Expression.

    PubMed

    Gangula, Pandu; Ravella, Kalpana; Chukkapalli, Sasanka; Rivera, Mercedes; Srinivasan, Shanthi; Hale, Ashley; Channon, Keith; Southerland, Janet; Kesavalu, Lakshmyya

    2015-01-01

    Periodontal disease is a highly prevalent chronic inflammatory disease and is associated with complex microbial infection in the subgingival cavity. Recently, American Heart Association supported a century old association between periodontal disease and atherosclerotic vascular disease. We have recently shown that polybacterial periodontal infection led to aortic atherosclerosis and modulation of lipid profiles; however the underlying mechanism(s) has not been yet demonstrated. Altered nitric oxide (NO) synthesis and tetrahydrobiopterin (BH4), a cofactor for nitric oxide synthases (NOS) has long been shown to be associated with vascular dysfunction and gastrointestinal motility disorders. We sought to examine the mechanism of periodontal infection leading to altered vascular and gastrointestinal smooth muscle relaxation, focusing on the BH4/nNOS pathways. In addition, we also have investigated how the antioxidant system (NRF2-Phase II enzyme expression) in vascular and GI specimens is altered by oral infection. Eight week old male ApoEnull mice were either sham-infected or infected orally for 16 weeks with a mixture of major periodontal bacteria Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia to induce experimental periodontitis. Serum, vascular (mesenteric), stomach, and colon specimens were collected at the end of periodontal pathogen infection. Bacterial infection induced significant (p<0.05) reductions in the levels of BH4,in ratio of BH4:BH2+B and also in nitric oxide levels compared to sham-infected controls. In addition, we identified a significant (p<0.05) reduction in eNOS dimerization, nNOS dimerization and protein expression of BH4 biosynthesis enzymes; GCH-1, DHFR and NRF2 & Phase II enzymes in infected mice versus controls in both mesenteric artery and colon tissues. However, we found no differences in nNOS/BH4 protein expression in stomach tissues of infected and sham-infected mice. This suggests that a polybacterial infection

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Mixed ligand palladium(II) complexes of 6-methoxy-2-oxo-1,2-dihydroquinoline-3-carbaldehyde 4N-substituted thiosemicarbazones with triphenylphosphine co-ligand: synthesis, crystal structure and biological properties.

    PubMed

    Ramachandran, Eswaran; Senthil Raja, Duraisamy; Bhuvanesh, Nattamai S P; Natarajan, Karuppannan

    2012-11-21

    A series of new 6-methoxy-2-oxo-1,2-dihydroquinoline-3-carbaldehyde 4N-substituted thiosemicarbazone ligands (H2L1–H2L5) and their corresponding palladium(II) complexes [Pd(L1)(PPh3)] (1), [Pd(L2)(PPh3)] (2), [Pd(HL3)(PPh3)]Cl (3), [Pd(L4)(PPh3)] (4) and [Pd(L5)(PPh3)] (5), have been synthesized in order to evaluate the effect of terminal N-substitution in thiosemicarbazone moiety on coordination behaviour and biological activity. The new ligands and their corresponding complexes were characterized by analytical and various spectral techniques. The molecular structure of the complexes 2–5 were characterized by single crystal X-ray diffraction studies which revealed that the ligands H2L2, H2L4 and H2L5 are coordinated to palladium(II) as binegative tridentate (ONS2−) by forming six and five member rings whereas, the ligand H2L3 coordinated to Pd(II) as uninegative tridentate (ONS−). The interactions of the new complexes with calf thymus DNA (CT-DNA) have been evaluated by absorption and ethidium bromide (EB) competitive studies which revealed that complexes 1–5 could interact with CT-DNA through intercalation. Further, the interactions of the complexes with bovine serum albumin (BSA) were also investigated using UV-visible, fluorescence and synchronous fluorescence spectroscopic methods, which showed that the new complexes could bind strongly with BSA. Antioxidant studies showed that all the complexes have a strong antioxidant activity against 2-2′-diphenyl-1-picrylhydrazyl (DPPH) radical and 2,2′-azino-3-ethylbenzthiazoline-6-sulfonic acid diammonium salt (ABTS) cation radical. In addition, in vitro cytotoxicity of the complexes against human lung cancer (A549) cell line was assayed which showed that 4 has higher cytotoxic activity than the rest of the complexes and cisplatin. PMID:22864662

  2. 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.

  3. A novel cobalt(II)-selective potentiometric sensor based on p-(4-n-butylphenylazo)calix[4]arene.

    PubMed

    Kumar, Pankaj; Shim, Yoon-Bo

    2009-01-15

    A new poly(vinyl chloride)-based membranes containing p-(4-n-butylphenylazo)calix[4]arene (I) as an electroactive material along with sodiumtetraphenylborate (NaTPB), and dibutyl(butyl)phosphonate in the ratio 10:100:1:200 (I:DBBP:NaTPB:PVC) (w/w) was used to fabricate a new cobalt(II)-selective sensor. It exhibited a working concentration range of 9.2 x 10(-6) to 1.0 x 10(-1)M, with a Nernstian slope of 29.0+/-1.0 mV/decade of activity and the response time of 25s. This sensor shows the detection limit of 4.0 x 10(-6)M. Its potential response remains unaffected of pH in the range, 4.0-7.2, and the cell assembly can be used successfully in partially non-aqueous medium (up to 10%, v/v) without significant change in the slope of working concentration range. The sensor has a lifetime of about 3 months and exhibits excellent selectivity over a number of mono-, bi-, and tri-valent cations including alkali, alkaline earth metal, heavy and transition metal ions. It can be used as an indicator electrode for the end point determination in the potentiometric titration of cobalt ions against ethylenediaminetetraacetic acid (EDTA) as well as for the determination of cobalt ion concentration in real samples. PMID:19064091

  4. 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. PMID:24191605

  5. Synthesis, characterization and magnetic properties of copper(II) complexes with 4-N-(2‧-pyridylimine)benzoic acid

    NASA Astrophysics Data System (ADS)

    Jiang, Chun-Fang; Liang, Fu-Pei; Li, Yan; Wang, Xiu-Jian; Chen, Zi-Lu; Bian, He-Dong

    2007-10-01

    Four Cu(II) complexes with 4- N-(2'-pyridylimine)benzoic acid ( HL), [Cu(HL) 2] · (ClO 4) 2 ( 1), [Cu(HL) 2(SO 4)] · 3H 2O ( 2), [Cu 2(L) 2Cl 2] n · 3H 2O ( 3), and [Cu 4(L) 2(HL) 2Cl 4] · (CH 3OH) 2 · (ClO 4) 2 ( 4), have been synthesized and structurally characterized by X-ray crystallography. Complexes ( 1) and ( 2) both exhibit a mononuclear structure with a four-coordinated Cu(II) ion by the pyridine- N and imine- N atoms of the ligands for ( 1) and a penta-coordinated Cu(II) ion by pyridine- N, imine- N atoms of the ligands and one oxygen atom of SO42- for ( 2). Complex ( 3) consists of a two-dimensional Cu(II) layer formed by deprotonated HL ligand linking four-membered Cu 2Cl 2 units. Complex ( 4) contains a tetranuclear Cu(II) coordination cation in which the Cu(II) ions are penta-coordinated in square pyramidal geometry by two bridging chloride atoms, two nitrogen atoms of HL ligand with undeprotonated carboxylic group, and one oxygen atom of syn,syn-carboxylato bridge. Magnetic susceptibility data show a weak ferromagnetic coupling between the Cu centers in ( 3) ( J = 4.95 cm -1) and a weak antiferromagnetic interaction in ( 4) ( J = -16.85 cm -1), respectively.

  6. CH 4/N 2/H 2-spark hydrophobic tholins: A systematic approach to the characterisation of tholins. Part II

    NASA Astrophysics Data System (ADS)

    Ruiz-Bermejo, Marta; Menor-Salván, César; de la Fuente, José Luis; Mateo-Martí, Eva; Osuna-Esteban, Susana; Martín-Gago, José Ángel; Veintemillas-Verdaguer, Sabino

    2009-12-01

    Two different simulation experiments of prebiotic synthesis were carried out in a CH 4/N 2/H 2 atmosphere with spark discharge activation of aqueous aerosols and liquid water. In both cases, a hydrophilic tholin and a hydrophobic tholin were obtained. The methodology developed by our group for the characterisation of hydrophilic tholins [Ruiz-Bermejo, M., Menor-Salván, C., Mateo-Martí, E., Osuna-Esteban, S., Martín-Gago, J.A., Veintemillas-Verdaguer, S., 2008. Icarus 198, 232-241] was used in order to study the hydrophobic tholins. The gas precursors of the tholins from mixtures containing CH 4, with and without H 2, were studied. We propose that the formation of the hydrophobic tholins involves the formation of unsaturated oligomeric hydrocarbon chains from vinyl and acetylene monomers, as well as allene derivatives formed in the gas phase after the incorporation of polar groups into these hydrocarbon chains. Finally, we compare our results concerning hydrophobic tholins with HCN polymers, since it is generally suggested that the polymeric material formed in spark experiments are possible oligomers of HCN, and that Titan's tholins could be poly-HCN.

  7. 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.

  8. Optimized deglycosylation of glycoproteins by peptide-N4-(N-acetyl-beta-glucosaminyl)-asparagine amidase from Flavobacterium meningosepticum.

    PubMed

    Nuck, R; Zimmermann, M; Sauvageot, D; Josi D; Reutter, W

    1990-01-01

    Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F(PNGase F) from Flavobacterium meningosepticum is a highly useful enzyme for the structural analysis of N (asparagine)-linked carbohydrate chains derived from glycoproteins. The enzyme was enriched using a published procedure [Tarentino AL, Gomez CM, Plummer TH, Jr (1984) Biochemistry 1985:4665-71; Tarentino AL, Plummer TH, Jr (1987) Methods Enzymol 138:770-78] and further purified by hydrophobic interaction HPLC on a weak hydrophobic TSK-Ether column from which it was eluted by a decreasing gradient of 1.7 M ammonium sulphate in 100 mM sodium phosphate, pH 7.0, containing 5 mM EDTA. To determine the optimal conditions for a complete deglycosylation of glycoproteins by PNGase F, experiments were performed with human alpha 1-acid glycoprotein, because the five complex type carbohydrate chains are quite resistant to enzymic hydrolysis. The influence of different detergents on the enzyme reaction was studied. Complete deglycosylation of human alpha 1-acid glycoprotein was achieved by the use of 60 mU/ml PNGase F in 0.25 M sodium phosphate buffer, pH 8.6, containing 0.2% (w/v) SDS, 20 mM mercaptoethanol and 0.5% Mega-10. PMID:2136346

  9. Enhancing vaccines with immune stimulatory CpG DNA.

    PubMed

    Krieg, A M; Davis, H L

    2001-02-01

    Certain vertebrate immune cells have evolved receptors that detect the presence of pathogen DNA based on its content of unmethylated CpG dinucleotides in particular base contexts. This 'CpG DNA' acts as a 'danger signal', triggering protective innate and acquired immune responses. The activity of CpG DNA can be mimicked with synthetic oligodeoxynucleotides, which when added to a vaccine greatly boost the resulting immune response. PMID:11249727

  10. Detection of sequence variation in parasite ribosomal DNA by electrophoresis in agarose gels supplemented with a DNA-intercalating agent.

    PubMed

    Zhu, X Q; Chilton, N B; Gasser, R B

    1998-05-01

    This study evaluated the use of a commercially available DNA intercalating agent (Resolver Gold) in agarose gels for the direct detection of sequence variation in ribosomal DNA (rDNA). This agent binds preferentially to AT sequence motifs in DNA. Regions of nuclear rDNA, known to provide genetic markers for the identification of species of parasitic ascarid nematodes (order Ascaridida), were amplified by polymerase chain reaction (PCR) and subjected to electrophoresis in standard agarose gels versus gels supplemented with Resolver Gold. Individual taxa examined could not be distinguished reliably based on the size of their amplicons in standard agarose gels, whereas they could be readily delineated based on mobility using Resolver Gold-supplemented gels. The latter was achieved because of differences (approximately 0.1-8.2%) in the AT content of the fragments among different taxa, which were associated with significant interspecific differences (approximately 11-39%) in the rDNA sequences employed. There was a tendency for fragments with higher AT content to migrate slower in supplemented agarose gels compared with those of lower AT content. The results indicate the usefulness of this electrophoretic approach to rapidly screen for sequence variability within or among PCR-amplified rDNA fragments of similar sizes but differing AT contents. Although evaluated on rDNA of parasites, the approach has potential to be applied to a range of genes of different groups of infectious organisms. PMID:9629896

  11. 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.

  12. 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

  13. 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.

  14. Perpendicular magnetic anisotropy in CoxMn4-xN (x = 0 and 0.2) epitaxial films and possibility of tetragonal Mn4N phase

    NASA Astrophysics Data System (ADS)

    Ito, Keita; Yasutomi, Yoko; Kabara, Kazuki; Gushi, Toshiki; Higashikozono, Soma; Toko, Kaoru; Tsunoda, Masakiyo; Suemasu, Takashi

    2016-05-01

    We grow 25-nm-thick Mn4N and Co0.2Mn3.8N epitaxial films on SrTiO3(001) by molecular beam epitaxy. These films show the tetragonal structure with a tetragonal axial ratio c/a of approximately 0.99. Their magnetic properties are measured at 300 K, and perpendicular magnetic anisotropy is confirmed in both films. There is a tendency that as the Co composition increases, an anisotropy field increases, whereas saturation magnetization and uniaxial magnetic anisotropy energy decrease. First-principles calculation predicts the existence of tetragonal Mn4N phase. This explains the c/a ˜ 0.99 in the Mn4N films regardless of their film thickness and lattice mismatch with substrates used.

  15. 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

  16. 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

  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. 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…

  19. 34 CFR Educational - Contents

    Code of Federal Regulations, 2011 CFR

    1997-07-01

    ... 34 Education 2 1997-07-01 1997-07-01 false Contents Educational Local Educational Agency Applications ASSISTANCE TO STATES FOR THE EDUCATION OF CHILDREN WITH DISABILITIES State Plans and Local...) Both. (b) (Authority: 20 U.S.C. 1414(b)(2)) Local Educational Agency Applications—Contents...

  20. Early Learning Content Standards

    ERIC Educational Resources Information Center

    Ohio Department of Education, 2004

    2004-01-01

    The early learning content standards describe essential concepts and skills for young children. Based on research, these achievable indicators emerge as the result of quality early learning experiences regardless of the setting (e.g., nursery school, preschool, family care, etc.). In addition, the early learning content indicators are aligned to…

  1. 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…

  2. 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.

  3. '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

  4. 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'. PMID:16214748

  5. 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

  6. Significance of DNA quantification in testicular germ cell tumors.

    PubMed

    Codesal, J; Paniagua, R; Regadera, J; Fachal, C; Nistal, M

    1991-01-01

    A cytophotometric quantification of DNA in tumor cells was performed in histological sections of orchidectomy specimens from 36 men with testicular germ cell tumors (TGCT), 7 of them showing more than one tumor type. Among the variants of seminoma (classic and spermatocytic) the lowest DNA content were in spermatocytic seminoma. With respect to non-seminomatous tumors (yolk sac tumor, embryonal carcinoma, teratoma, and choriocarcinoma), choriocarcinomas showed the highest DNA content, and the lowest value was found in teratomas. No significant differences were found between the average DNA content of seminomas (all types) and non-seminomatous tumors (all types). Both embryonal carcinoma and yolk sac tumor showed similar DNA content when they were the sole tumor and when they were found associated with other tumors. In this study, except for the 4 cases of teratoma and the case of spermatocytic seminoma, all TGCT examined did not show modal values of DNA content in the diploid range. Such an elevated frequency of aneuploidism in these tumors may be helpful for their diagnosis. PMID:1666273

  7. Variations of atmospheric CH4, N2O and SF6 over Japan and the East China Sea

    NASA Astrophysics Data System (ADS)

    Ishijima, K.; Goto, D.; Ishidoya, S.; Yashiro, H.; Umezawa, T.; Sugawara, S.; Patra, P. K.; Muromachi, A.; Elkins, J. W.; Dutton, G. S.; Dlugokencky, E. J.; Morimoto, S.; Aoki, S.; Nakazawa, T.

    2013-12-01

    East Asia is one of the most important regions for anthropogenic sources of both short-lived air pollutants and long-lived greenhouse gases (GHGs). According to recent estimates from an emission database, China has become the largest emitter of long-lived GHGs. Since Japan and the East China Sea are located at the east end of Eurasia, atmospheric species emitted from the continent are transported over them throughout the year. Particularly in winter to spring, outflow of the emitted species is enhanced over the East China Sea due to the East Asian Monsoon. To monitor temporal and spatial variability of atmospheric GHGs in the East Asian region, we conducted systematic GHG observations during 2003-2012 from flask samples collected onboard four different commercial ferry boats, which connected between Wakkanai and Rishiri islands (WAK ; 45.4°N, 141.5°E), between Sakaiminato and Oki islands (OKI ; 35.8°N, 133.2°E), between Kagoshima and Okinawa islands (RYU ; 30.0°N, 130.0°E), and between Ishigaki and Hateruma islands (HTR ; 24.0°N, 124.0°E). Air samples were collected almost weekly, and they were sent to Tohoku University and analyzed for GHGs and related gases. In this study, we present analyses of observed CH4, N2O and SF6 concentrations in comparison with simulations by the Atmospheric general circulation model-based Chemistry Transport model (ACTM). The observed three species predictably show higher concentrations than those observed at Cape Kumukahi (KUM), which is a NOAA air sampling site located in the Central Pacific, reflecting strong outflow of the species from East Asia. Annual mean latitudinal gradients found from the four locations as well as decrease toward KUM are generally reproduced by the ACTM. This is mostly because of reasonable spatial distributions in GHG emissions given in the ACTM. The three species also show discernible seasonal cycles. ACTM simulates seasonal cycles of CH4 and SF6 relatively well, but not for N2O, suggesting

  8. 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

  9. Missing-Mass Spectroscopy of the 4-Neutron System by Exothermic Double-Charge Exchange Reaction 4He(8He,8Be)4n

    NASA Astrophysics Data System (ADS)

    Kisamori, Keiichi; Shimoura, Susumu; Miya, Hiroyuki; Assie, Marlene; Baba, Hidetada; Baba, Tatsuo; Beaumel, Didier; Dozono, Masanori; Fujii, Toshihiko; Fukuda, Naoki; Go, Shintaro; Hammache, Fariouz; Ideguchi, Eiji; Inabe, Naohiro; Itoh, Masatoshi; Kameda, Daisuke; Kawase, Shoichiro; Kawabata, Takahiro; Kobayashi, Motoki; Kondo, Yosuke; Kubo, Toshiyuki; Kubota, Yuki; Kurata-Nishimura, Mizuki; Lee, CheongSoo; Maeda, Yukie; Matsubara, Hiroaki; Michimasa, Shin'ichiro; Miki, Kenjiro; Nishi, Takahiro; Noji, Shumpei; Ota, Shinsuke; Sakaguchi, Satoshi; Sakai, Hideyuki; Sasamoto, Yoshiko; Sasano, Masaki; Sato, Hiromi; Shimizu, Yohei; Stolz, Andreas; Suzuki, Hiroshi; Takaki, Motonobu; Takeda, Hiroyuki; Takeuchi, Satoshi; Tamii, Atsushi; Tang, Leung; Tokieda, Hiroshi; Tsumura, Miho; Uesaka, Tomohiro; Yako, Kentaro; Yanagisawa, Yoshiyuki; Yokoyama, Rin

    A possible existence of the tetra-neutron system as a resonance state is still an open and fascinating question, while theoretical papers using ab-initio calculation suggests that the bound tetra-neutron does not exist. We have performed a missing-mass spectroscopy of the 4n system via the exothermic double-charge exchange reaction 4He(8He,8Be)4n. The experiment was carried out at the RIBF at RIKEN using the SHARAQ spectrometer. Since the secondary beam, 8He at 190 A MeV, has a large internal energy, it is possible to produce the 4n system with small momentum transfers of less than 20 MeV/c. In the present analysis, a new analytical framework to treat multi-particles under high beam rate condition (2 MHz) was developed for good statistics. At the SHARAQ spectrometer, 8Be can be identified by measuring the invariant mass of the coincident two alpha particles with a good signal-to-noise ratio. About several tens of candidate events are obtained above the 4n threshold.

  10. 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...

  11. 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)

  12. 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)

  13. HPV DNA test

    MedlinePlus

    The HPV DNA test is used to check for high-risk HPV infection in women. HPV infection around the genitals is ... warts spread when you have sex. The HPV-DNA test is generally not recommended for detecting low- ...

  14. 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.

  15. Synthesis and characterization of rhenium(III) organohydrazide compounds. Crystal and molecular structures of [ReCl(PPh{sub 3}){sub 2}(NHNC{sub 5}H{sub 4}N)(HNNC{sub 5}H{sub 4}N)]Cl{sub 2}, [Re{l_brace}2-(Ph{sub 2}P)C{sub 6}H{sub 4}S{r_brace}{l_brace}2-(Ph{sub 2}PO)C{sub 6}H{sub 4}S{r_brace}(NNC{sub 5}H{sub 4}N)(HNNC{sub 5}H{sub 4}N)], and [Re{l_brace}2-(Ph{sub 2}P)C{sub 6}H{sub 4}S{r_brace}{sub 2}(NNC{sub 5}H{sub 4}N)

    SciTech Connect

    Perez-Lourido, P.; Romero, J.; Garcia-Vazquez, J.A.; Sousa, A.; Maresca, K.P.; Zubieta, J.

    1999-04-05

    The reduction of ReO{sub 4}{sup {minus}} with 2-hydrazinopyridine dihydrochloride and PPh{sub 3} gives [ReCl(PPh{sub 3}){sub 2}(NHNC{sub 5}H{sub 4}N)-(HNNC{sub 5}H{sub 4}N)]Cl{sub 2} (2). A similar reaction using 2-hydrazino-2-imidazoline and PPh{sub 3} in methanol hydrochloric acid allows the preparation of [ReCl{sub 3}(PPh{sub 3}){sub 2}(NNC{sub 3}H{sub 4}N{sub 2})] (3). The reaction of the Re(III) complex [ReCl{sub 3}(NNC{sub 5}H{sub 4}NH)(HNNC{sub 5}H{sub 4}N)] (1), with 2-(Ph{sub 2}P)C{sub 6}H{sub 4}SH in methanol yields [Re{l_brace}2-(Ph{sub 2}P)C{sub 6}H{sub 4}S{r_brace}-{l_brace}2-(Ph{sub 2}PO)C{sub 6}H{sub 4}S{r_brace}(NNC{sub 5}H{sub 4}N)(HNNC{sub 5}H{sub 4}N)] (4) and [Re{l_brace}2-(Ph{sub 2}P)C{sub 6}H{sub 4}S{r_brace}{sub 2}(NNC{sub 5}H{sub 4}N)] (5). The same precursor with 2-(Ph{sub 2}PO)-6-(Me{sub 3}Si)C{sub 6}H{sub 3}SH gives [ReCl{l_brace}2-(Ph{sub 2}PO)-6-(Me{sub 3}Si)C{sub 6}H{sub 3}S{r_brace}(NNC{sub 5}H{sub 4}N)(HNNC{sub 5}H{sub 4}N)] (6) and with PhP(C{sub 6}H{sub 4}SH-2){sub 2} yields [Re{l_brace}PhP(C{sub 6}H{sub 4}S-2){sub 2}{r_brace}(NNC{sub 5}H{sub 4}N)(HNNC{sub 5}H{sub 4}N)] (7).

  16. Is DNA a language?

    PubMed

    Tsonis, A A; Elsner, J B; Tsonis, P A

    1997-01-01

    DNA sequences usually involve local construction rules that affect different scales. As such their "dictionary" may not follow Zipf's law (a power law) which is followed in every natural language. Indeed, analysis of many DNA sequences suggests that no linguistics connections to DNA exist and that even though it has structure DNA is not a language. Computer simulations and a biological approach to this problem further support these results. PMID:9039397

  17. 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...

  18. Concentration and content.

    PubMed

    Fuentes-Arderiu, Xavier

    2013-01-01

    One of the more frequent activities in health sciences is the measurement of biological quantities. Frequently, when reading biomedical books and journals some confusion on the metrological meaning of biological quantities related to the concepts 'concentration' and 'content' may be observed. Classically, a concentration is an amount of any type per volume of liquid or gas system, whereas content is an amount of any type per mass of liquid or gas or solid system. However the concepts 'concentration' and 'content' alone are still ambiguous because, depending on the type of amount of the component (analyte) per volume or mass of a system, there are different types of concentrations and contents. This article attempts to give a clarification of these concepts, mainly based on international recommendations about nomenclature and terminology of metrology, chemistry and clinical laboratory sciences. PMID:23894859

  19. 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.

  20. 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. PMID:27285535

  1. DNAzymes in DNA Nanomachines and DNA Analysis

    NASA Astrophysics Data System (ADS)

    He, Yu; Tian, Ye; Chen, Yi; Mao, Chengde

    This chapter discusses our efforts in using DNAzymes in DNA nano-machines and DNA analysis systems. 10-23 DNAzymes can cleave specific phos-phodiester bonds in RNA. We use them to construct an autonomous DNA-RNA chimera nanomotor, which constantly extracts chemical energy from RNA substrates and transduces the energy into a mechanical motion: cycles of contraction and extension. The motor's motion can be reversibly turned on and off by a DNA analogue (brake) of the RNA substrate. Addition and removal of the brake stops and restarts, respectively, the motor's motion. Furthermore, when the RNA substrates are preorganized into a one-dimensional track, a DNAzyme can continuously move along the track so long as there are substrates available ahead. Based on a similar mechanism, a novel DNA detection system has been developed. A target DNA activates a DNAzyme to cleave RNA-containing molecular beacons (MB), which generates an enhanced fluorescence signal. A following work integrates two steps of signal amplifications: a rolling-circle amplification (RCA) to synthesize multiple copies of DNAzymes, and the DNAzymes catalyze a chemical reaction to generate a colorimetric signal. This method allows detection of DNA analytes whose concentration is as low as 1 pM.

  2. 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

  3. 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.

  4. Structural analysis of DNA interaction with retinol and retinoic acid.

    PubMed

    Mandeville, J S; N'soukpoé-Kossi, C N; Neault, J F; Tajmir-Riahi, H A

    2010-06-01

    Dietary constituents of fresh fruits and vegetables may play a relevant role in DNA adduct formation by inhibiting enzymatic activities. Studies have shown the important role of antioxidant vitamins A, C, and E in the protection against cancer and cardiovascular diseases. The antioxidant activity of vitamin A and beta-carotene may consist of scavenging oxygen radicals and preventing DNA damage. This study was designed to examine the interaction of calf-thymus DNA with retinol and retinoic acid in aqueous solution at physiological conditions using a constant DNA concentration and various retinoid contents. Fourier transform infrared (FTIR), circular dichroism (CD), and fluorescence spectroscopic methods were used to determine retinoid binding mode, the binding constant, and the effects of retinol and retinoic acid complexation on DNA conformation and aggregation. Structural analysis showed that retinol and retinoic acid bind DNA via G-C and A-T base pairs and the backbone phosphate groups with overall binding constants of Kret = 3.0 (+/-0.50) x 10(3) (mol.L(-1))(-1) and Kretac = 1.0 (+/-0.20) x 10(4) (mol.L(-1))(-1). The number of bound retinoids per DNA were 0.84 for retinol and 1.3 for retinoic acid. Hydrophobic interactions were also observed at high retinol and retinoic acid contents. At a high retinoid concentration, major DNA aggregation occurred, while DNA remained in the B-family structure. PMID:20555389

  5. Mn(II), Co(II), Zn(II), Fe(III) and U (VI) complexes of 2-acetylpyridine 4N-(2-pyridyl) thiosemicarbazone (HAPT); structural, spectroscopic and biological studies

    NASA Astrophysics Data System (ADS)

    El-Ayaan, Usama; Youssef, Magdy M.; Al-Shihry, Shar

    2009-11-01

    The present work carried out a study on transition metal ion complexes which have been synthesized from 2-acetylpyridine 4N-(2-pyridyl) thiosemicarbazone (HAPT) 1. These complexes namely [Zn(HAPT)Cl 2] 2, [Mn (HAPT)Cl 2] 3, [Co (HAPT)Cl 2] 4, [Fe(APT)Cl 2(H 2O)] 5 and [UO 2(HAPT)(OAc) 2] 6, were characterized by elemental analysis, spectral (IR, 1H NMR and UV-vis) and magnetic moment measurements. 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. The biochemical studies showed that, complexes 3 and 6 have powerful and complete degradation effect on the both DNA and protein. The SOD-like activity exhibited that complex 3 has a strong antioxidative properties. The antibacterial screening demonstrated that, the free ligand (HAPT), complexes 2, 3 and 6 have the maximum and broad activities against Gram-positive and Gram-negative bacterial strains.

  6. 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)

  7. DNA integrity assessment in hemocytes of soft-shell clams (Mya arenaria) in the Saguenay Fjord (Québec, Canada).

    PubMed

    Debenest, T; Gagné, F; Burgeot, T; Blaise, C; Pellerin, J

    2013-02-01

    The purpose of this study was to examine the effects of pollution on DNA integrity in the feral soft-shell clam (Mya arenaria) in the Saguenay Fjord. Intertidal clams were collected downstream and upstream of the fjord at sites under anthropogenic pollution. DNA integrity was assessed by following changes in single- and double-stranded breaks, variation in DNA content and micro-nuclei (MN) incidence in hemocytes. The results revealed that clams collected at polluted sites had reduced DNA strand breaks (lower DNA repair activity), increased DNA content variation and MN frequency in hemocytes. The data revealed that DNA content variation was closely related to MN frequency and negatively with DNA strand breaks formation. Water conductivity was also related to reduced MN frequency and DNA content variation, indicating that, in addition to the effects of pollution, the gradual dilution of saltwater could compromise mussel health. PMID:22744162

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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. PMID:26629954

  14. 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

  15. DNA in Nanoscale Electronics

    NASA Astrophysics Data System (ADS)

    Slinker, Jason

    2012-10-01

    DNA, the quintessential molecule of life, possesses a number of attractive properties for use in nanoscale circuits. Charge transport (CT) through DNA itself is of both fundamental and practical interest. Fundamentally, DNA has a unique configuration of π-stacked bases in a well ordered, double helical structure. Given its unparalleled importance to life processes and its arrangement of conjugated subunits, DNA has been a compelling target of conductivity studies. In addition, further understanding of DNA CT will elucidate the biological implications of this process and advance its use in sensing technologies. We have investigated the fundamentals of DNA CT by measuring the electrochemistry of DNA monolayers under biologically-relevant conditions. We have uncovered both fundamental kinetic parameters to distinguish between competing models of operation as well as the practical implications of DNA CT for sensing. Furthermore, we are leveraging our studies of DNA conductivity for the manufacture of nanoscale circuits. We are investigating the electrical properties and self-assembly of DNA nanowires containing artificial base pair surrogates, which can be prepared through low cost and high throughput automated DNA synthesis. This unique and economically viable approach will establish a new paradigm for the scalable manufacture of nanoscale semiconductor devices.

  16. 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. PMID:25903461

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. Formation of Active Catalysts in the System: Chlorocuprates-CCl4-n-C10H22

    NASA Astrophysics Data System (ADS)

    Golubeva, Elena N.; Kharitonov, Dmitry N.; Kochubey, Dmitry I.; Ikorskii, Vladimir N.; Kriventsov, Vladimir V.; Kokorin, Alexander I.; Stoetsner, Julia; Bahnemann, Detlef W.

    2009-08-01

    Transformations of anionic CuII chlorocomplexes have been studied under conditions of catalytic exchange reactions between carbon tetrachloride and n-alkanes. It was shown that chlorocuprates are just precursors and are easily reduced to the genuine catalysts, that is, to the respective CuI complexes. Both the composition and the geometric structure of the precursor (CuCl42-) and, probably, the active site (CuCl32-) have been investigated by several techniques (UV-vis spectroscopy, electron spin resonance (ESR), extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES), and static magnetic measurements). The dependence of the metathesis velocity on the [Cl-]/[Cu] ratio was found to exhibit a maximum most likely corresponding to the highest content of trichlorocuprite CuCl32-.

  2. 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

  3. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies.

    PubMed

    Alonso, Antonio; Martín, Pablo; Albarrán, Cristina; García, Pilar; García, Oscar; de Simón, Lourdes Fernández; García-Hirschfeld, Julia; Sancho, Manuel; de La Rúa, Concepción; Fernández-Piqueras, Jose

    2004-01-28

    We explore different designs to estimate both nuclear and mitochondrial human DNA (mtDNA) content based on the detection of the 5' nuclease activity of the Taq DNA polymerase using fluorogenic probes and a real-time quantitative PCR detection system. Human mtDNA quantification was accomplished by monitoring the real-time progress of the PCR-amplification of two different fragment sizes (113 and 287 bp) within the hypervariable region I (HV1) of the mtDNA control region, using two fluorogenic probes to specifically determine the mtDNA copy of each fragment size category. This mtDNA real-time PCR design has been used to assess the mtDNA preservation (copy number and degradation state) of DNA samples retrieved from 500 to 1500 years old human remains that showed low copy number and highly degraded mtDNA. The quantification of nuclear DNA was achieved by real-time PCR of a segment of the X-Y homologous amelogenin (AMG) gene that allowed the simultaneous estimation of a Y-specific fragment (AMGY: 112 bp) and a X-specific fragment (AMGX: 106 bp) making possible not only haploid or diploid DNA quantitation but also sex determination. The AMG real-time PCR design has been used to quantify a set of 57 DNA samples from 4-5 years old forensic bone remains with improved sensitivity compared with the slot-blot hybridization method. The potential utility of this technology to improve the quality of some PCR-based forensic and ancient DNA studies (microsatellite typing and mtDNA sequencing) is discussed. PMID:15040907

  4. Differential nuclear and mitochondrial DNA preservation in post-mortem teeth with implications for forensic and ancient DNA studies.

    PubMed

    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. Furthermore 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. 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.

  6. 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.

  7. 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

  8. 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

  9. Forensic DNA analysis.

    PubMed

    McDonald, Jessica; Lehman, Donald C

    2012-01-01

    Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Evaluation of four mathematical models to describe dissipation kinetics of 4-n-nonylphenol and bisphenol-A in groundwater-aquifer material slurry.

    PubMed

    Sarmah, Ajit K; Rohan, Maheswaran

    2011-01-01

    The performance of four mathematical models (hockey stick, biexponential, first-order double exponential decay, and first-order two-compartment) was evaluated to describe the dissipation kinetics for 4-n-nonylphenol (4-n-NP) and bisphenol-A (BPA) in groundwater-aquifer material slurry under aerobic and anaerobic conditions conducted under controlled laboratory conditions. The fit of each model to the measured values under both conditions was tested using an array of statistical indices to judge the model's ability to fit the measured datasets. Corresponding 50% (DT(50)) and 90% (DT(90)) dissipation values for each compound were numerically obtained and compared against each model. The model derived DT(50) values in groundwater-aquifer material ranged from 1.06 to 1.24 (4-n-NP) and 0.341 to 0.568 days (BPA) under aerobic condition, while they were 2- to 4-fold higher under anoxic condition. DT(90) values for 4-n-NP ranged anywhere between 2.3 and 4.45 days under both conditions, while DT(90) values for BPA ranged from around 1 day to as high as 12 days under both conditions tested. A visual examination of the measured and fitted plots as well as the statistical indices showed that, with the exception of the hockey stick model, the models performed satisfactorily. Despite having only 3 parameters, the biexponential model could describe the dissipation kinetics very well and this was supported by the statistical indices generated for each case. PMID:21069247

  15. Pharmacological stress is required for the anti-alcohol effect of the α3β4* nAChR partial agonist AT-1001

    PubMed Central

    Cippitelli, Andrea; Brunori, Gloria; Gaiolini, Kelly A.; Zaveri, Nurulain T.; Toll, Lawrence

    2015-01-01

    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. PMID:25689019

  16. 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. PMID:25689019

  17. Zebrafish lacking functional DNA polymerase gamma survive to juvenile stage, despite rapid and sustained mitochondrial DNA depletion, altered energetics and growth

    PubMed Central

    Rahn, Jennifer J.; Bestman, Jennifer E.; Stackley, Krista D.; Chan, Sherine S.L.

    2015-01-01

    DNA polymerase gamma (POLG) is essential for replication and repair of mitochondrial DNA (mtDNA). Mutations in POLG cause mtDNA instability and a diverse range of poorly understood human diseases. Here, we created a unique Polg animal model, by modifying polg within the critical and highly conserved polymerase domain in zebrafish. polg+/− offspring were indistinguishable from WT siblings in multiple phenotypic and biochemical measures. However, polg−/− mutants developed severe mtDNA depletion by one week post-fertilization (wpf), developed slowly and had regenerative defects, yet surprisingly survived up to 4 wpf. An in vivo mtDNA polymerase activity assay utilizing ethidium bromide (EtBr) to deplete mtDNA, showed that polg+/− and WT zebrafish fully recover mtDNA content two weeks post-EtBr removal. EtBr further reduced already low levels of mtDNA in polg−/− animals, but mtDNA content did not recover following release from EtBr. Despite significantly decreased respiration that corresponded with tissue-specific levels of mtDNA, polg−/− animals had WT levels of ATP and no increase in lactate. This zebrafish model of mitochondrial disease now provides unique opportunities for studying mtDNA instability from multiple angles, as polg−/− mutants can survive to juvenile stage, rather than lose viability in embryogenesis as seen in Polg mutant mice. PMID:26519465

  18. Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA-DNA hybridization.

    PubMed

    Gnat, Sebastian; Małek, Wanda; Oleńska, Ewa; Wdowiak-Wróbel, Sylwia; Kalita, Michał; Rogalski, Jerzy; Wójcik, Magdalena

    2016-04-01

    In this study, the phylogenetic relationship and taxonomic status of six strains, representing different phenons and genomic groups of Astragalus glycyphyllos symbionts, originating from Poland, were established by comparative analysis of five concatenated housekeeping gene sequences (atpD, dnaK, glnA, recA and rpoB), DNA-DNA hybridization and total DNA G+C content. Maximum-likelihood phylogenetic analysis of combined atpD, dnaK, glnA, recA and rpoB sequence data placed the studied bacteria into the clade comprising the genus Mesorhizobium. In the core gene phylograms, four A. glycyphyllos nodule isolates (AG1, AG7, AG15 and AG27) formed a cluster common with Mesorhizobium ciceri, whereas the two other A. glycyphyllos symbionts (AG17 and AG22) were grouped together with Mesorhizobium amorphae and M. septentrionale. The species position of the studied bacteria was clarified by DNA-DNA hybridization. The DNA-DNA relatedness between isolates AG1, AG7, AG15 and AG27 and reference strain M. ciceri USDA 3383T was 76.4-84.2 %, and all these A. glycyphyllos nodulators were defined as members of the genomospecies M. ciceri. DNA-DNA relatedness for isolates AG17 and AG22 and the reference strain M. amorphae ICMP 15022T was 77.5 and 80.1 %, respectively. We propose that the nodule isolates AG17 and AG22 belong to the genomic species M. amorphae. Additionally, it was found that the total DNA G+C content of the six test A. glycyphyllos symbionts was 59.4-62.1 mol%, within the range for species of the genus Mesorhizobium. PMID:26704062

  19. Teaching Content Outrageously

    ERIC Educational Resources Information Center

    Pogrow, Stanley

    2010-01-01

    This article first explores the theoretical bases for why dramatic forms of instruction stimulate student learning and recall. Next, the article considers a practice that systematically applies drama, fun, and fantasy to embed selected content objectives into students' memory. This practical tool, which facilitates instructional reform in the…

  20. Content Management Systems

    ERIC Educational Resources Information Center

    Wisniewski, Jeff; Stenstrom, Cheryl

    2007-01-01

    In this article, the authors provide a guide in acquiring content management system. They conducted a vendor survey that covers four areas: (1) general information about the product (including standards supported); (2) administration of the product; (3) functionality; and (4) contact information for readers who want to know more. A list of product…

  1. Pedagogical Content Knowledge Taxonomies.

    ERIC Educational Resources Information Center

    Veal, William R.; MaKinster, James G.

    1999-01-01

    Presents two taxonomies that offer a relatively comprehensive categorization scheme for future studies of pedagogical content knowledge (PCK) development in teacher education. "The General Taxonomy of PCK" addresses distinctions within and between the knowledge bases of various disciplines, science subjects, and science topics. "The Taxonomy of…

  2. Language, the Forgotten Content.

    ERIC Educational Resources Information Center

    Kelly, Patricia P., Ed.; Small, Robert C., Jr., Ed.

    1987-01-01

    The ways that students can learn about the nature of the English language and develop a sense of excitement about their language are explored in this focused journal issue. The titles of the essays and their authors are as follows: (1) "Language, the Forgotten Content" (R. Small and P. P. Kelly); (2) "What Should English Teachers Know about…

  3. Document image content inventories

    NASA Astrophysics Data System (ADS)

    Baird, Henry S.; Moll, Michael A.; An, Chang; Casey, Matthew R.

    2007-01-01

    We report an investigation into strategies, algorithms, and software tools for document image content extraction and inventory, that is, the location and measurement of regions containing handwriting, machine-printed text, photographs, blank space, etc. We have developed automatically trainable methods, adaptable to many kinds of documents represented as bilevel, greylevel, or color images, that offer a wide range of useful tradeoffs of speed versus accuracy using methods for exact and approximate k-Nearest Neighbor classification. We have adopted a policy of classifying each pixel (rather than regions) by content type: we discuss the motivation and engineering implications of this choice. We describe experiments on a wide variety of document-image and content types, and discuss performance in detail in terms of classification speed, per-pixel classification accuracy, per-page inventory accuracy, and subjective quality of page segmentation. These show that even modest per-pixel classification accuracies (of, e.g., 60-70%) support usefully high recall and precision rates (of, e.g., 80-90%) for retrieval queries of document collections seeking pages that contain a given minimum fraction of a certain type of content.

  4. 59 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    1994-11-09

    ... From the Federal Register Online via the Government Printing Office ] CONTENTS Vol. 59, No. 216 Wednesday, November 9, 1994 Agricultural Marketing Service RULES Peanuts, domestically produced, 55808-55810 Agriculture Department See Agricultural Marketing Service See Forest Service See Rural Telephone Bank...

  5. 59 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    1994-11-30

    ... From the Federal Register Online via the Government Printing Office ] CONTENTS Vol. 59, No. 229 Wednesday, November 30, 1994 Agency for International Development NOTICES Housing guaranty program: South Africa, 61340-61341 Agricultural Marketing Service PROPOSED RULES Potatoes (Irish) grown in-- Idaho...

  6. 59 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    1994-12-28

    ... From the Federal Register Online via the Government Printing Office Editorial note: For the President's letter to Congress transmitting the notice on continuation of the Libyan emergency, see issue 51 of the Weekly Compilation of Presidential Documents. CONTENTS Vol. 59, No. 248 Wednesday, December...

  7. 59 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    1994-10-26

    ... From the Federal Register Online via the Government Printing Office ] CONTENTS Vol. 59, No. 206 Wednesday, October 26, 1994 Agricultural Marketing Service RULES Milk marketing orders: Eastern Ohio-Western Pennsylvania; correction, 53726 Agricultural Research Service NOTICES Patent licenses; non-exclusive,...

  8. 59 FR- CONTENTS

    Code of Federal Regulations, 2010 CFR

    1994-12-07

    ... From the Federal Register Online via the Government Printing Office ] CONTENTS Vol. 59, No. 234 Wednesday, December 7, 1994 Agriculture Department See Forest Service Assassination Records Review Board NOTICES Meetings; Sunshine Act, 63156 Coast Guard RULES Ports and waterways safety: Chesapeake Bay,...

  9. Integrating Language and Content

    ERIC Educational Resources Information Center

    Nordmeyer, Jon, Ed.; Barduhn, Susan, Ed.

    2010-01-01

    The definition of "English language classroom" is changing. When students have the opportunity to learn content and language at the same time, disciplinary boundaries overlap. Teachers are rethinking how they design courses, plan lessons, assess students, and collaborate with colleagues to support student learning and facilitate their own…

  10. Shaping Digital Library Content.

    ERIC Educational Resources Information Center

    Miller, Rush G.

    2002-01-01

    Explores issues related to the selection and purchase of digital content in academic libraries, including commercially-produced databases, electronic journals, and books and other electronic resources that are purchased from vendors; and in-house digitization projects. Considers the degree to which standard collection management principles apply.…

  11. Content Area Vocabulary Learning

    ERIC Educational Resources Information Center

    Fisher, Douglas; Frey, Nancy

    2014-01-01

    Students' vocabulary knowledge is a significant predictor of their overall comprehension. The Common Core State Standards are raising the expectations for word learning and there are now 4 distinct standards related to vocabulary as well as expectations in other standards, including content areas. To address these expectations, teachers need…

  12. LCS Content Document Application

    NASA Technical Reports Server (NTRS)

    Hochstadt, Jake

    2011-01-01

    My project at KSC during my spring 2011 internship was to develop a Ruby on Rails application to manage Content Documents..A Content Document is a collection of documents and information that describes what software is installed on a Launch Control System Computer. It's important for us to make sure the tools we use everyday are secure, up-to-date, and properly licensed. Previously, keeping track of the information was done by Excel and Word files between different personnel. The goal of the new application is to be able to manage and access the Content Documents through a single database backed web application. Our LCS team will benefit greatly with this app. Admin's will be able to login securely to keep track and update the software installed on each computer in a timely manner. We also included exportability such as attaching additional documents that can be downloaded from the web application. The finished application will ease the process of managing Content Documents while streamlining the procedure. Ruby on Rails is a very powerful programming language and I am grateful to have the opportunity to build this application.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Thermodynamic stability, spectroscopic identification, and gas storage capacity of CO2-CH4-N2 mixture gas hydrates: implications for landfill gas hydrates.

    PubMed

    Lee, Hyeong-Hoon; Ahn, Sook-Hyun; Nam, Byong-Uk; Kim, Byeong-Soo; Lee, Gang-Woo; Moon, Donghyun; Shin, Hyung Joon; Han, Kyu Won; Yoon, Ji-Ho

    2012-04-01

    Landfill gas (LFG), which is primarily composed of CH(4), CO(2), and N(2), is produced from the anaerobic digestion of organic materials. To investigate the feasibility of the storage and transportation of LFG via the formation of hydrate, we observed the phase equilibrium behavior of CO(2)-CH(4)-N(2) mixture hydrates. When the specific molar ratio of CO(2)/CH(4) was 40/55, the equilibrium dissociation pressures were gradually shifted to higher pressures and lower temperatures as the mole fraction of N(2) increased. X-ray diffraction revealed that the CO(2)-CH(4)-N(2) mixture hydrate prepared from the CO(2)/CH(4)/N(2) (40/55/5) gas mixture formed a structure I clathrate hydrate. A combination of Raman and solid-state (13)C NMR measurements provided detailed information regarding the cage occupancy of gas molecules trapped in the hydrate frameworks. The gas storage capacity of LFG hydrates was estimated from the experimental results for the hydrate formations under two-phase equilibrium conditions. We also confirmed that trace amounts of nonmethane organic compounds do not affect the cage occupancy of gas molecules or the thermodynamic stability of LFG hydrates. PMID:22380606

  19. Electronic structure, molecular interaction, and stability of the CH4-nH2O complex, for n = 1-21.

    PubMed

    Bravo-Pérez, Graciela; Cruz-Torres, Armando; Romero-Martínez, Ascención

    2008-09-18

    Molecular calculations were carried out with four different methodologies to study the CH 4- nH 2O complex, for n = 1-21. The HF and MP2 methods used considered the O atom with pseudopotential to freeze the 1s shell. The other methodologies applied the Bhandhlyp and B3lyp exchange and correlation functionals. The optimized CH 4- nH 2O structures are reported, specifying the number and type of H 2O subunits (triangle, square, pentagon, etc.) that comprised the nH 2O counterpart cluster or cage, that interacted with the CH 4 molecule, and, in the latter case, that provided its confinement. Results are focused to understand the stability of the CH 4- nH 2O complex. The quality of the electron correlation effect, as well as the size of the nH 2O cage to confine the guest molecule, and the number and type of H 2O subunits comprising the nH 2O cluster or cage are the most important factors to provide the stability of the complex and also dictate the particular n value at which the CH 4 molecule confinement occurs. This number was 14 for the HF, Bhandhlyp, and B3Lyp methods and 16 for the MP2 method. The reported hydrate structures for n < 20 could be predictive for future experiments. PMID:18714955

  20. Effect of prenatal X irradiation on chemical components of DNA and DNA-protein crosslinks in rat cerebrum in the perinatal periods

    SciTech Connect

    Iwasaki, S.; Tanaka, H.; Arima, M.

    1987-04-01

    Wistar rats were X-irradiated in utero with 100 or 200 R on Day 13 of gestation. X Irradiation resulted in decreases not only in cerebral weight up to 15 days old but also in DNA content from Day 19 of gestation to 5 days old, and in a tendency to increase the ratio of protein to DNA in the perinatal period. The DNA contents of the homogenate, isolated nuclei, and chromatin of the cerebrum in the irradiated group were significantly lower than those in the control group. The ratio of protein to DNA at the nuclei, chromatin, and isolated DNA steps increased on irradiation. The total nucleoside content of isolated DNA determined by high-performance liquid chromatography was higher in the irradiated group than that in the control group on Day 21 of gestation but not on Day 19 of gestation. No new peaks were observed and no change in the guanine-cytosine content was seen on irradiation. X Irradiation resulted in decreases in the cytosine and deoxycytidine contents and an increase in the deoxyadenosine content. The formation of DNA-protein crosslinks in the cerebral chromatin as determined by a filter binding assay tended to increase in the irradiated groups.

  1. Quantification of DNA in Biologic Scaffold Materials

    PubMed Central

    Gilbert, Thomas W.; Freund, John; Badylak, Stephen F.

    2009-01-01

    Biologic scaffold materials composed of extracellular matrix (ECM) are routinely used for a variety of clinical applications ranging from the treatment of chronic skin ulcers to hernia repair and orthopaedic soft tissue reconstruction. The tissues and species from which the ECM is harvested vary widely as do the methods used to remove the cellular component of the source tissues. The efficacy of decellularization procedures can be quantified by examination of the DNA that remains in the ECM. The objective of the present study was to determine the DNA content and fragment length in both laboratory produced and commercially available ECM scaffold materials. Results showed that the majority of DNA is removed from ECM devices but that small amounts remained in most tested materials. PMID:18619621

  2. Linear and Nonlinear Statistical Characterization of DNA

    NASA Astrophysics Data System (ADS)

    Norio Oiwa, Nestor; Goldman, Carla; Glazier, James

    2002-03-01

    We find spatial order in the distribution of protein-coding (including RNAs) and control segments of GenBank genomic sequences, irrespective of ATCG content. This is achieved by correlations, histograms, fractal dimensions and singularity spectra. Estimates of these quantities in complete nuclear genome indicate that coding sequences are long-range correlated and their disposition are self-similar (multifractal) for eukaryotes. These characteristics are absent in prokaryotes, where there are few noncoding sequences, suggesting the `junk' DNA play a relevant role to the genome structure and function. Concerning the genetic message of ATCG sequences, we build a random walk (Levy flight), using DNA symmetry arguments, where we associate A, T, C and G as left, right, down and up steps, respectively. Nonlinear analysis of mitochondrial DNA walks reveal multifractal pattern based on palindromic sequences, which fold in hairpins and loops.

  3. 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.

  4. The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding

    PubMed Central

    Keller, Heidi; Kiosze, Kristin; Sachsenweger, Juliane; Haumann, Sebastian; Ohlenschläger, Oliver; Nuutinen, Tarmo; Syväoja, Juhani E.; Görlach, Matthias; Grosse, Frank; Pospiech, Helmut

    2014-01-01

    Human RecQL4 belongs to the ubiquitous RecQ helicase family. Its N-terminal region represents the only homologue of the essential DNA replication initiation factor Sld2 of Saccharomyces cerevisiae, and also participates in the vertebrate initiation of DNA replication. Here, we utilized a random screen to identify N-terminal fragments of human RecQL4 that could be stably expressed in and purified from Escherichia coli. Biophysical characterization of these fragments revealed that the Sld2 homologous RecQL4 N-terminal domain carries large intrinsically disordered regions. The N-terminal fragments were sufficient for the strong annealing activity of RecQL4. Moreover, this activity appeared to be the basis for an ATP-independent strand exchange activity. Both activities relied on multiple DNA-binding sites with affinities to single-stranded, double-stranded and Y-structured DNA. Finally, we found a remarkable affinity of the N-terminus for guanine quadruplex (G4) DNA, exceeding the affinities for other DNA structures by at least 60-fold. Together, these findings suggest that the DNA interactions mediated by the N-terminal region of human RecQL4 represent a central function at the replication fork. The presented data may also provide a mechanistic explanation for the role of elements with a G4-forming propensity identified in the vicinity of vertebrate origins of DNA replication. PMID:25336622

  5. 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. PMID:25391915

  6. 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

  7. 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

  8. 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

  9. Mitochondrial DNA copy number variation across human cancers

    PubMed Central

    Reznik, Ed; Miller, Martin L; Şenbabaoğlu, Yasin; Riaz, Nadeem; Sarungbam, Judy; Tickoo, Satish K; Al-Ahmadie, Hikmat A; Lee, William; Seshan, Venkatraman E; Hakimi, A Ari; Sander, Chris

    2016-01-01

    Mutations, deletions, and changes in copy number of mitochondrial DNA (mtDNA), are observed throughout cancers. Here, we survey mtDNA copy number variation across 22 tumor types profiled by The Cancer Genome Atlas project. We observe a tendency for some cancers, especially of the bladder, breast, and kidney, to be depleted of mtDNA, relative to matched normal tissue. Analysis of genetic context reveals an association between incidence of several somatic alterations, including IDH1 mutations in gliomas, and mtDNA content. In some but not all cancer types, mtDNA content is correlated with the expression of respiratory genes, and anti-correlated to the expression of immune response and cell-cycle genes. In tandem with immunohistochemical evidence, we find that some tumors may compensate for mtDNA depletion to sustain levels of respiratory proteins. Our results highlight the extent of mtDNA copy number variation in tumors and point to related therapeutic opportunities. DOI: http://dx.doi.org/10.7554/eLife.10769.001 PMID:26901439

  10. High resolution analysis of the timing of replication of specific DNA sequences during S phase of mammalian cells.

    PubMed Central

    D'Andrea, A D; Tantravahi, U; Lalande, M; Perle, M A; Latt, S A

    1983-01-01

    A new method, utilizing selective photodegradation of 5-bromo-deoxyuridine (BUdR)-substituted DNA and flow cytometry, has been developed for analyzing the timing of replication of specific DNA sequences. Chemically synchronized Chinese hamster ovary cells were given a pulse of the deoxythymidine analogue, BUdR, at different times during S phase, and flow sorted according to DNA content, before DNA isolation. Newly-replicated, unifilarly BUdR-substituted DNA was selectively degraded by treatment with 33258 Hoechst plus near UV light followed by S1 nuclease digestion; the resistant DNA was analyzed for its content of 18s and 28s rDNA or dihydrofolate reductase (DHFR) sequences via Southern blot analysis. Both the rDNA and DHFR sequences were found to replicate almost entirely during the first quarter of S phase. The approach described should have general utility for analyzing replication kinetics of specific DNA sequences in mammalian cells. Images PMID:6192392

  11. 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 for drug delivery and medical applications. PMID:24647836

  12. In situ labeling of DNA reveals interindividual variation in nuclear DNA breakdown in hair and may be useful to predict success of forensic genotyping of hair.

    PubMed

    Szabo, Sandra; Jaeger, Karin; Fischer, Heinz; Tschachler, Erwin; Parson, Walther; Eckhart, Leopold

    2012-01-01

    Hair fibers are formed by keratinocytes of the hair follicle in a process that involves the breakdown of the nucleus including DNA. Accordingly, DNA can be isolated with high yield from the hair bulb which contains living keratinocytes, whereas it is difficult to prepare from the distal portions of hair fibers and from shed hair. Nevertheless, forensic investigations are successful in a fraction of shed hair samples found at crime scenes. Here, we report that interindividual differences in the completeness of DNA removal from hair corneocytes are major determinants of DNA content and success rates of forensic investigations of hair. Distal hair samples were permeabilized with ammonia and incubated with the DNA-specific dye Hoechst 33258 to label DNA in situ. Residual nuclear DNA was visualized under the fluorescence microscope. Hair from some donors did not contain any stainable nuclei, whereas hair of other donors contained a variable number of DNA-positive nuclear remnants. The number of DNA-containing nuclear remnants per millimeter of hair correlated with the amount of DNA that could be extracted and amplified by quantitative PCR. When individual hairs were investigated, only hairs in which DNA could be labeled in situ gave positive results in short tandem repeat typing. This study reveals that the completeness of DNA degradation during cornification of the hair is a polymorphic trait. Furthermore, our results suggest that in situ labeling of DNA in hair may be useful for predicting the probability of success of forensic analysis of nuclear DNA in shed hair. PMID:21475959

  13. Nuclear DNA Amounts in Macaronesian Angiosperms

    PubMed Central

    SUDA, JAN; KYNCL, TOMÁŠ; FREIOVÁ, RADKA

    2003-01-01

    Nuclear DNA contents for 104 Macaronesian angiosperms, with particular attention on Canary Islands endemics, were analysed using propidium iodide flow cytometry. Prime estimates for more than one‐sixth of the whole Canarian endemic flora (including representatives of 11 endemic genera) were obtained. The resulting 1C DNA values ranged from 0·19 to 7·21 pg for Descurainia bourgeauana and Argyranthemum frutescens, respectively (about 38‐fold difference). The majority of species, however, possessed (very) small genomes, with C‐values <1·6 pg. The tendency towards small nuclear DNA contents and genome sizes was confirmed by comparing average values for Macaronesian and non‐Macaronesian representatives of individual families, genera and major phylogenetic lineages. Our data support the hypothesis that the insular selection pressures in Macaronesia favour small C‐values and genome sizes. Both positive and negative correlations between infrageneric nuclear DNA amount variation and environmental conditions on Tenerife were also found in several genera. PMID:12824074

  14. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  15. Tiny telomere DNA

    PubMed Central

    Ren, Jinsong; Qu, Xiaogang; Trent, John O.; Chaires, Jonathan B.

    2002-01-01

    We describe the design, synthesis and biophysical characterization of a novel DNA construct in which a folded quadruplex structure is joined to a standard double helix. Circular dichroism, gel electrophoresis, three-dimensional UV melting and differential scanning calorimetry were all used to characterize the structure. Rigorous molecular dynamics simulations were used to build a plausible atomic-level structural model of the DNA construct. This novel DNA construct provides a model for the duplex–quadruplex junction region at the end of chromosomal DNA and offers a system for the study of structure-selective ligand binding. PMID:12034817

  16. DNA Damage Response

    PubMed Central

    Giglia-Mari, Giuseppina; Zotter, Angelika; Vermeulen, Wim

    2011-01-01

    Structural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network of DNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance processes, and cell-cycle checkpoints safeguard genomic integrity. Like transcription and replication, DDR is a chromatin-associated process that is generally tightly controlled in time and space. As DNA damage can occur at any time on any genomic location, a specialized spatio-temporal orchestration of this defense apparatus is required. PMID:20980439

  17. Content Maps: A Teaching and Assessment Tool for Content Knowledge

    ERIC Educational Resources Information Center

    Ward, Phillip; Lehwald, Harry; Lee, Yun Soo

    2015-01-01

    Developing content knowledge in teachers presents a constant challenge for teacher educators. This article introduces a teaching and assessment tool called a "content map," which allows teacher educators, teachers, and coaches to conceptualize the scope, sequence, and relational characteristics of the content being taught. Content maps…

  18. 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

  19. 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.

  20. Holographic content addressable storage

    NASA Astrophysics Data System (ADS)

    Chao, Tien-Hsin; Lu, Thomas; Reyes, George

    2015-03-01

    We have developed a Holographic Content Addressable Storage (HCAS) architecture. The HCAS systems consists of a DMD (Digital Micromirror Array) as the input Spatial Light Modulator (SLM), a CMOS (Complementary Metal-oxide Semiconductor) sensor as the output photodetector and a photorefractive crystal as the recording media. The HCAS system is capable of performing optical correlation of an input image/feature against massive reference data set stored in the holographic memory. Detailed system analysis will be reported in this paper.

  1. Replicative DNA polymerases.

    PubMed

    Johansson, Erik; Dixon, Nicholas

    2013-06-01

    In 1959, Arthur Kornberg was awarded the Nobel Prize for his work on the principles by which DNA is duplicated by DNA polymerases. Since then, it has been confirmed in all branches of life that replicative DNA polymerases require a single-stranded template to build a complementary strand, but they cannot start a new DNA strand de novo. Thus, they also depend on a primase, which generally assembles a short RNA primer to provide a 3'-OH that can be extended by the replicative DNA polymerase. The general principles that (1) a helicase unwinds the double-stranded DNA, (2) single-stranded DNA-binding proteins stabilize the single-stranded DNA, (3) a primase builds a short RNA primer, and (4) a clamp loader loads a clamp to (5) facilitate the loading and processivity of the replicative polymerase, are well conserved among all species. Replication of the genome is remarkably robust and is performed with high fidelity even in extreme environments. Work over the last decade or so has confirmed (6) that a common two-metal ion-promoted mechanism exists for the nucleotidyltransferase reaction that builds DNA strands, and (7) that the replicative DNA polymerases always act as a key component of larger multiprotein assemblies, termed replisomes. Furthermore (8), the integrity of replisomes is maintained by multiple protein-protein and protein-DNA interactions, many of which are inherently weak. This enables large conformational changes to occur without dissociation of replisome components, and also means that in general replisomes cannot be isolated intact. PMID:23732474

  2. Many Ways to Loop DNA

    PubMed Central

    Griffith, Jack D.

    2013-01-01

    In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered. PMID:24005675

  3. Determination of Fat Content

    NASA Astrophysics Data System (ADS)

    Carpenter, Charles

    The term "lipid" refers to a group of compounds that are sparingly soluble in water, but show variable solubility in a number of organic solvents (e.g., ethyl ether, petroleum ether, acetone, ethanol, methanol, benzene). The lipid content of a food determined by extraction with one solvent may be quite different from the lipid content as determined with another solvent of different polarity. Fat content is determined often by solvent extraction methods (e.g., Soxhlet, Goldfish, Mojonnier), but it also can be determined by nonsolvent wet extraction methods (e.g., Babcock, Gerber), and by instrumental methods that rely on the physical and chemical properties of lipids (e.g., infrared, density, X-ray absorption). The method of choice depends on a variety of factors, including the nature of the sample (e.g., dry versus moist), the purpose of the analysis (e.g., official nutrition labeling or rapid quality control), and instrumentation available (e.g., Babcock uses simple glassware and equipment; infrared requires an expensive instrument).

  4. Content Documents Management

    NASA Technical Reports Server (NTRS)

    Muniz, R.; Hochstadt, J.; Boelke J.; Dalton, A.

    2011-01-01

    The Content Documents are created and managed under the System Software group with. Launch Control System (LCS) project. The System Software product group is lead by NASA Engineering Control and Data Systems branch (NEC3) at Kennedy Space Center. The team is working on creating Operating System Images (OSI) for different platforms (i.e. AIX, Linux, Solaris and Windows). Before the OSI can be created, the team must create a Content Document which provides the information of a workstation or server, with the list of all the software that is to be installed on it and also the set where the hardware belongs. This can be for example in the LDS, the ADS or the FR-l. The objective of this project is to create a User Interface Web application that can manage the information of the Content Documents, with all the correct validations and filters for administrator purposes. For this project we used one of the most excellent tools in agile development applications called Ruby on Rails. This tool helps pragmatic programmers develop Web applications with Rails framework and Ruby programming language. It is very amazing to see how a student can learn about OOP features with the Ruby language, manage the user interface with HTML and CSS, create associations and queries with gems, manage databases and run a server with MYSQL, run shell commands with command prompt and create Web frameworks with Rails. All of this in a real world project and in just fifteen weeks!

  5. Nanoparticle bridge DNA biosensor

    NASA Astrophysics Data System (ADS)

    Huang, Hong-Wen

    A new DNA sensing method is demonstrated in which DNA hybridization events lead to the formation of nanoparticle satellites that bridge two electrodes and are detected electrically. The hybridization events are exclusively carried out only on specific locations, the surfaces of C-ssDNA modified 50 nm GNPs. The uniqueness of this work is that only a small number of T-ccDNA molecules (<10) is required to form the nanoparticle satellites, allowing ultra-sensitive DNA sensing. The principle of this new DNA sensing technique has been demonstrated using target DNA and three-base-pair-mismatched DNA in 20nM concentrations. Three single-stranded DNA (ssDNA) system is used in our experiment which includes Capture-ssDNA (C-ssDNA), Target-ssDNA (T-ssDNA) and Probe-ssDNA (P-ssDNA). Both C-ssDNA and P-ssDNA are modified by a thiol group and can hybridize with different portions of T-ssDNA. T-ssDNA requires no modification in three ssDNA system, which is beneficial in many applications. C-ssDNA modified 50nm gold nanoparticle (C-50au) and P-ssDNA modified 30nm gold nanoparticle (P-30au) are prepared through the reaction of thiol-gold chemical bonding between thiolated ssDNA and gold nanoparticle (GNP) (C-ssDNA with 50nm GNP, P-ssDNA with 30nm GNP). We controllably place the C-50au only on the SiO2 band surface (˜ 90nm width) between two gold electrodes (source and drain electrodes) by forming positively- and negatively-charged self-assembled monolayers (SAMs) on SiO2 and gold surface, respectively. DNA modified GNP is negatively charged due to ionization of phosphate group on DNA back bone. C-50au therefore is negatively charged and can only be attracted toward SiO2 area (repelled by negatively charged gold electrode surface). The amine group of positively-charged SAMs on SiO2 surface is then passivated by converting to non-polar methyl functional group after C-50au placement. P-30au is first hybridized with T-ssDNA in the solution phase (T-P- 30au formed) and is introduced

  6. Math: Basic Skills Content Standards

    ERIC Educational Resources Information Center

    CASAS - Comprehensive Adult Student Assessment Systems (NJ1), 2008

    2008-01-01

    This document presents content standards tables for math. [CASAS content standards tables are designed for educators at national, state and local levels to inform the alignment of content standards, instruction and assessment. The Content Standards along with the CASAS Competencies form the basis of the CASAS integrated assessment and curriculum…

  7. Curating DNA specimens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA data are used in a variety of ethnobiological disciplines including archaeology, conservation, ecology, medicinal plants and natural products research, taxonomy and systematics, crop evolution and domestication, and genetic diversity. It frequently is convenient to store and share DNA among coop...

  8. Routine DNA testing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your par...

  9. Recombinant DNA for Teachers.

    ERIC Educational Resources Information Center

    Duvall, James G., III

    1992-01-01

    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  10. MICROWAVE RESONANCES IN DNA

    EPA Science Inventory

    This report describes spectroscopic studies of DNA which were undertaken to better understand a physical basis for microwave absorption by this molecule. hree types of studies are described. ) The low frequency scattered light spectrum of DNA was studied by two methods. irst, Ram...

  11. Replicating repetitive DNA.

    PubMed

    Tognetti, Silvia; Speck, Christian

    2016-05-27

    The function and regulation of repetitive DNA, the 'dark matter' of the genome, is still only rudimentarily understood. Now a study investigating DNA replication of repetitive centromeric chromosome segments has started to expose a fascinating replication program that involves suppression of ATR signalling, in particular during replication stress. PMID:27230530

  12. Hydrogels: DNA bulks up

    NASA Astrophysics Data System (ADS)

    Labean, Thom

    2006-10-01

    Since the 1940s DNA has been known as the genetic material connected to heredity, and from the early 1980s it has also been considered as a potential structural material for nanoscale construction. Now, a hydrogel made entirely of DNA brings this molecule into the realm of bulk materials.

  13. Translesion DNA synthesis

    PubMed Central

    Vaisman, Alexandra; McDonald, John P.; Woodgate, Roger

    2014-01-01

    All living organisms are continually exposed to agents that damage their DNA, which threatens the integrity of their genome. As a consequence, cells are equipped with a plethora of DNA repair enzymes to remove the damaged DNA. Unfortunately, situations nevertheless arise where lesions persist, and these lesions block the progression of the cell’s replicase. Under these situations, cells are forced to choose between recombination-mediated “damage avoidance” pathways, or use a specialized DNA polymerase (pol) to traverse the blocking lesion. The latter process is referred to as Translesion DNA Synthesis (TLS). As inferred by its name, TLS not only results in bases being (mis)incorporated opposite DNA lesions, but also downstream of the replicase-blocking lesion, so as to ensure continued genome duplication and cell survival. Escherichia coli and Salmonella typhimurium possess five DNA polymerases, and while all have been shown to facilitate TLS under certain experimental conditions, it is clear that the LexA-regulated and damage-inducible pols II, IV and V perform the vast majority of TLS under physiological conditions. Pol V can traverse a wide range of DNA lesions and performs the bulk of mutagenic TLS, whereas pol II and pol IV appear to be more specialized TLS polymerases. PMID:26442823

  14. DNA-cell conjugates

    DOEpatents

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  15. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms

    PubMed Central

    Padovan-Merhar, Olivia; Nair, Gautham P.; Biaesch, Andrew; Mayer, Andreas; Scarfone, Steven; Foley, Shawn W.; Wu, Angela R.; Churchman, L. Stirling; Singh, Abhyudai; Raj, Arjun

    2015-01-01

    Summary Individual mammalian cells exhibit large variability in cellular volume even with the same absolute DNA content and so must compensate for differences in DNA concentration in order to maintain constant concentration of gene expression products. Using single molecule counting and computational image analysis, we show that transcript abundance correlates with cellular volume at the single cell level due to increased global transcription in larger cells. Cell fusion experiments establish that increased cellular content itself can directly increase transcription. Quantitative analysis shows that this mechanism measures the ratio of cellular volume to DNA content, mostly likely through sequestration of a transcriptional factor to DNA. Analysis of transcriptional bursts reveals a separate mechanism for gene dosage compensation after DNA replication that enables proper transcriptional output during early and late S-phase. Our results provide a framework for quantitatively understanding the relationships between DNA content, cell size and gene expression variability in single cells. PMID:25866248

  16. Premeltons in DNA.

    PubMed

    Sobell, Henry M

    2016-03-01

    Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible--and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions--all readily testable--as will be described in this review

  17. On the molecular mechanism of GC content variation among eubacterial genomes

    PubMed Central

    2012-01-01

    Background As a key parameter of genome sequence variation, the GC content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this GC content variation and its relationship to other fundamental processes. Previously, we classified eubacteria into dnaE-based groups (the dimeric combination of DNA polymerase III alpha subunits), according to a hypothesis where GC content variation is essentially governed by genome replication and DNA repair mechanisms. Further investigation led to the discovery that two major mutator genes, polC and dnaE2, may be responsible for genomic GC content variation. Consequently, an in-depth analysis was conducted to evaluate various potential intrinsic and extrinsic factors in association with GC content variation among eubacterial genomes. Results Mutator genes, especially those with dominant effects on the mutation spectra, are biased towards either GC or AT richness, and they alter genomic GC content in the two opposite directions. Increased bacterial genome size (or gene number) appears to rely on increased genomic GC content; however, it is unclear whether the changes are directly related to certain environmental pressures. Certain environmental and bacteriological features are related to GC content variation, but their trends are more obvious when analyzed under the dnaE-based grouping scheme. Most terrestrial, plant-associated, and nitrogen-fixing bacteria are members of the dnaE1|dnaE2 group, whereas most pathogenic or symbiotic bacteria in insects, and those dwelling in aquatic environments, are largely members of the dnaE1|polV group. Conclusion Our studies provide several lines of evidence indicating that DNA polymerase III α subunit and its isoforms participating in either replication (such as polC) or SOS mutagenesis/translesion synthesis (such as dnaE2), play dominant roles in determining GC variability. Other environmental or bacteriological factors, such

  18. Advances in DNA photonics

    NASA Astrophysics Data System (ADS)

    Heckman, Emily M.; Aga, Roberto S.; Fehrman Cory, Emily M.; Ouchen, Fahima; Lesko, Alyssa; Telek, Brian; Lombardi, Jack; Bartsch, Carrie M.; Grote, James G.

    2012-10-01

    In this paper we present our current research in exploring a DNA biopolymer for photonics applications. A new processing technique has been adopted that employs a modified soxhlet-dialysis (SD) rinsing technique to completely remove excess ionic contaminants from the DNA biopolymer, resulting in a material with greater mechanical stability and enhanced performance reproducibility. This newly processed material has been shown to be an excellent material for cladding layers in poled polymer electro-optic (EO) waveguide modulator applications. Thin film poling results are reported for materials using the DNA biopolymer as a cladding layer, as are results for beam steering devices also using the DNA biopolymer. Finally, progress on fabrication of a Mach Zehnder EO modulator with DNA biopolymer claddings using nanoimprint lithography techniques is reported.

  19. Archaeal DNA replication.

    PubMed

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed. PMID:25421597

  20. DNA with Damage in Both Strands as Affinity Probes and Nucleotide Excision Repair Substrates.

    PubMed

    Lukyanchikova, N V; Petruseva, I O; Evdokimov, A N; Silnikov, V N; Lavrik, O I

    2016-03-01

    Nucleotide excision repair (NER) is a multistep process of recognition and elimination of a wide spectrum of damages that cause significant distortions in DNA structure, such as UV-induced damage and bulky chemical adducts. A series of model DNAs containing new bulky fluoro-azidobenzoyl photoactive lesion dC(FAB) and well-recognized nonnucleoside lesions nFlu and nAnt have been designed and their interaction with repair proteins investigated. We demonstrate that modified DNA duplexes dC(FAB)/dG (probe I), dC(FAB)/nFlu+4 (probe II), and dC(FAB)/nFlu-3 (probe III) have increased (as compared to unmodified DNA, umDNA) structure-dependent affinity for XPC-HR23B (Kdum > KdI > KdII ≈ KdIII) and differentially crosslink to XPC and proteins of NER-competent extracts. The presence of dC(FAB) results in (i) decreased melting temperature (ΔTm = -3°C) and (ii) 12° DNA bending. The extended dC(FAB)/dG-DNA (137 bp) was demonstrated to be an effective NER substrate. Lack of correlation between the affinity to XPC-HR23B and substrate properties of the model DNA suggests a high impact of the verification stage on the overall NER process. In addition, DNAs containing closely positioned, well-recognized lesions in the complementary strands represent hardly repairable (dC(FAB)/nFlu+4, dC(FAB)/nFlu-3) or irreparable (nFlu/nFlu+4, nFlu/nFlu-3, nAnt/nFlu+4, nAnt/nFlu-3) structures. Our data provide evidence that the NER system of higher eukaryotes recognizes and eliminates damaged DNA fragments on a multi-criterion basis. PMID:27262196

  1. DNA Align Editor: DNA Alignment Editor Tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  2. Formation of extrachromosomal circles from telomeric DNA in Xenopus laevis.

    PubMed

    Cohen, Sarit; Méchali, Marcel

    2002-12-01

    Instability and plasticity of telomeric DNA, which includes extrachromosomal DNA, are usually correlated with the absence of telomerase and with abnormal growth of mammalian cells. Here, we show the formation of extrachromosomal circular DNA of telomeric repeats (tel-eccDNA) during the development of Xenopus laevis. Tel-eccDNA is double-stranded relaxed circles composed of the vertebrate consensus telomeric repeats [TTAGGG](n). Its size varies from <2 to >20 kb and it comprises up to 10% of the total cellular telomere content of the early embryo (pre-MBT stage). The amount of tel-eccDNA is reduced in later developmental stages and in adult tissues. Using a cell-free system derived from Xenopus egg extracts, we show that tel-eccDNA can be formed de novo from the telomere chromosomal tracts of sperm nuclei and naked DNA in a replication-independent manner. These results reveal an unusual plasticity of telomeric DNA during normal development of Xenopus. PMID:12446568

  3. Criminal Genomic Pragmatism: Prisoners' Representations of DNA Technology and Biosecurity

    PubMed Central

    Machado, Helena; Silva, Susana

    2012-01-01

    Background. Within the context of the use of DNA technology in crime investigation, biosecurity is perceived by different stakeholders according to their particular rationalities and interests. Very little is known about prisoners' perceptions and assessments of the uses of DNA technology in solving crime. Aim. To propose a conceptual model that serves to analyse and interpret prisoners' representations of DNA technology and biosecurity. Methods. A qualitative study using an interpretative approach based on 31 semi-structured tape-recorded interviews was carried out between May and September 2009, involving male inmates in three prisons located in the north of Portugal. The content analysis focused on the following topics: the meanings attributed to DNA and assessments of the risks and benefits of the uses of DNA technology and databasing in forensic applications. Results. DNA was described as a record of identity, an exceptional material, and a powerful biometric identifier. The interviewees believed that DNA can be planted to incriminate suspects. Convicted offenders argued for the need to extend the criteria for the inclusion of DNA profiles in forensic databases and to restrict the removal of profiles. Conclusions. The conceptual model entitled criminal genomic pragmatism allows for an understanding of the views of prison inmates regarding DNA technology and biosecurity. PMID:22791960

  4. Increased fecal viral content associated with obesity in mice

    PubMed Central

    Yadav, Hariom; Jain, Shalini; Nagpal, Ravinder; Marotta, Francesco

    2016-01-01

    AIM To investigate the presence of total gut viral content in obese mice, and establish correlation with obesity associated metabolic measures and gut microbiome. METHODS Fresh fecal samples were collected from normal and obese (Leptin deficient: Lepob/ob) mice. Total viral DNA and RNA was isolated and quantified for establishing the correlation with metabolic measures and composition of gut bacterial communities. RESULTS In this report, we found that obese mice feces have higher viral contents in terms of total viral DNA and RNA (P < 0.001). Interestingly, these increased viral DNA and RNA content were tightly correlated with metabolic measures, i.e., body weight, fat mass and fasting blood glucose. Total viral content were positively correlated with firmicutes (R2 > 0.6), whilst negatively correlated with bacteroidetes and bifidobacteria. CONCLUSION This study suggests the strong correlation of increased viral population into the gut of obese mice and opens new avenues to explore the role of gut virome in pathophysiology of obesity. PMID:27555892

  5. Studying DNA in the Classroom.

    ERIC Educational Resources Information Center

    Zarins, Silja

    1993-01-01

    Outlines a workshop for teachers that illustrates a method of extracting DNA and provides instructions on how to do some simple work with DNA without sophisticated and expensive equipment. Provides details on viscosity studies and breaking DNA molecules. (DDR)

  6. Simple & Safe Genomic DNA Isolation.

    ERIC Educational Resources Information Center

    Moss, Robert; Solomon, Sondra

    1991-01-01

    A procedure for purifying DNA using either bacteria or rat liver is presented. Directions for doing a qualitative DNA assay using diphenylamine and a quantitative DNA assay using spectroscopy are included. (KR)

  7. Definitive radiotherapy with or without chemotherapy for clinical stage T4N0-1 non-small cell lung cancer

    PubMed Central

    Kim, Yeon Joo; Jeong, Seong-Yun; Kim, Sang We; Lee, Jung-Shin; Kim, Su Ssan; Choi, Wonsik; Choi, Eun Kyung

    2015-01-01

    Purpose To determine failure patterns and survival outcomes of T4N0-1 non-small cell lung cancer (NSCLC) treated with definitive radiotherapy. Materials and Methods Ninety-five patients with T4N0-1 NSCLC who received definitive radiotherapy with or without chemotherapy from May 2003 to October 2014 were retrospectively reviewed. The standard radiotherapy scheme was 66 Gy in 30 fractions. The main concurrent chemotherapy regimen was 50 mg/m2 weekly paclitaxel combined with 20 mg/m2 cisplatin or AUC 2 carboplatin. The primary outcome was overall survival (OS). Secondary outcomes were failure patterns and toxicities. Results The median age was 64 years (range, 34 to 90 years). Eighty-eight percent of patients (n = 84) had an Eastern Cooperative Oncology Group performance status of 0-1, and 42% (n = 40) experienced pretreatment weight loss. Sixty percent of patients (n = 57) had no metastatic regional lymph nodes. The median radiation dose was EQD2 67.1 Gy (range, 56.9 to 83.3 Gy). Seventy-one patients (75%) were treated with concurrent chemotherapy; of these, 13 were also administered neoadjuvant chemotherapy. At a median follow-up of 21 months (range, 1 to 102 months), 3-year OS was 44%. The 3-year cumulative incidences of local recurrence and distant recurrence were 48.8% and 36.3%, respectively. Pretreatment weight loss and combined chemotherapy were significant factors for OS. Acute esophagitis over grade 3 occurred in three patients and grade 3 chronic esophagitis occurred in one patient. There was no grade 3-4 radiation pneumonitis. Conclusion Definitive radiotherapy for T4N0-1 NSCLC results in favorable survival with acceptable toxicity rates. Local recurrence is the major recurrence pattern. Intensity modulated radiotherapy and radio-sensitizing agents would be needed to improve local tumor control. PMID:26756028

  8. Content addressable memory project

    NASA Technical Reports Server (NTRS)

    Hall, J. Storrs; Levy, Saul; Smith, Donald E.; Miyake, Keith M.

    1992-01-01

    A parameterized version of the tree processor was designed and tested (by simulation). The leaf processor design is 90 percent complete. We expect to complete and test a combination of tree and leaf cell designs in the next period. Work is proceeding on algorithms for the computer aided manufacturing (CAM), and once the design is complete we will begin simulating algorithms for large problems. The following topics are covered: (1) the practical implementation of content addressable memory; (2) design of a LEAF cell for the Rutgers CAM architecture; (3) a circuit design tool user's manual; and (4) design and analysis of efficient hierarchical interconnection networks.

  9. Personalized professional content recommendation

    DOEpatents

    Xu, Songhua

    2015-10-27

    A personalized content recommendation system includes a client interface configured to automatically monitor a user's information data stream transmitted on the Internet. A hybrid contextual behavioral and collaborative personal interest inference engine resident to a non-transient media generates automatic predictions about the interests of individual users of the system. A database server retains the user's personal interest profile based on a plurality of monitored information. The system also includes a server programmed to filter items in an incoming information stream with the personal interest profile and is further programmed to identify only those items of the incoming information stream that substantially match the personal interest profile.

  10. Inorganic contents of peats

    SciTech Connect

    Raymond, R. Jr.; Bish, D.L.; Cohen, A.D.

    1988-02-01

    Peat, the precursor of coal, is composed primarily of plant components and secondarily of inorganic matter derived from a variety of sources. The elemental, mineralogic, and petrographic composition of a peat is controlled by a combination of both its botanical and depositional environment. Inorganic contents of peats can vary greatly between geographically separated peat bogs as well as vertially and horizontally within an individual bog. Predicting the form and distribution of inorganic matter in a coal deposit requires understanding the distribution and preservation of inorganic matter in peat-forming environments and diagenetic alterations affecting such material during late-stage peatification and coalification processes. 43 refs., 4 figs., 3 tabs.

  11. 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.

  12. 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.

  13. Synthesis, spectral characteristics, and the crystal and molecular structures of 2,3-dimethyl-1-phenyl-4-( N-phthalimido)pyrazolone-5

    NASA Astrophysics Data System (ADS)

    Sokol, V. I.; Strashnova, S. B.; Kovalchukova, O. V.; Sergienko, V. S.; Davydov, V. V.; Zaĭtsev, B. E.; Evtushenko, Yu. M.

    2008-11-01

    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°. 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.

  14. Fine specificity of domain-I of recombinant tandem-repeat-type galectin-4 from rat gastrointestinal tract (G4-N).

    PubMed Central

    Wu, Albert M; Wu, June H; Tsai, Ming-Sung; Liu, Jia-Hau; André, Sabine; Wasano, Kojiro; Kaltner, Herbert; Gabius, Hans-Joachim

    2002-01-01

    Galectins, a family of beta-galactoside-specific endogenous lectins, are involved in regulating diverse activities such as proliferation/apoptosis, cell-cell (matrix) interaction and cell migration. It is presently unclear to what extent the carbohydrate fine specificities of the combining sites of mammalian galectins overlap. To address this issue, we performed an analysis of the carbohydrate-recognition domain (CRD-I) near the N-terminus of recombinant rat galectin-4 (G4-N) by the biotin/avidin-mediated microtitre plate lectin-binding assay with natural glycoproteins (gps)/polysaccharide and by the inhibition of galectin-glycan interactions with a panel of glycosubstances. Among the 35 glycans tested for lectin binding, G4-N reacted best with human blood group ABH precursor gps, and asialo porcine salivary gps, which contain high densities of the blood group Ii determinants Galbeta1-3GalNAc (the mucin-type sugar sequence on the human erythrocyte membrane) and/or GalNAcalpha1-Ser/Thr ( Tn ), whereas this lectin domain reacted weakly or not at all with most sialylated gps. Among the oligosaccharides tested by the inhibition assay, Galbeta1-3GlcNAcbeta1-3Galbeta1-4Glc was the best. It was 666.7 and 33.3 times more potent than Gal and Galbeta1-3GlcNAc, respectively. G4-N has a preference for the beta-anomer of Gal at the non-reducing ends of oligosaccharides with a Galbeta1-3 linkage, over Galbeta1-4 and Galbeta1-6. The fraction of Tn glycopeptide from asialo ovine submandibular glycoprotein was 8.3 times more active than Galbeta1-3GlcNAc. The overall carbohydrate specificity of G4-N can be defined as Galbeta1-3GlcNAcbeta1-3Galbeta1-4Glc (lacto- N -tetraose)>Galbeta1-4GlcNAcbeta1-3Galbeta1-4Glc (lacto- N -neo-tetraose) and Tn clusters>Galbeta1-4Glc and GalNAcbeta1-3Gal>Galbeta1-3GalNAc>Galbeta1-3GlcNAc>Galbeta1-4GlcNAc>GalNAc>Gal. The definition of this binding profile provides the basis to detect differential binding properties relative to the other galectins with

  15. Extraction of DNA from Forensic Biological Samples for Genotyping.

    PubMed

    Stray, J E; Liu, J Y; Brevnov, M G; Shewale, J G

    2010-07-01

    Biological forensic samples constitute evidence with probative organic matter. Evidence believed to contain DNA is typically processed for extraction and purification of its nucleic acid content. Forensic DNA samples are composed of two things, a tissue and the substrate it resides on. Compositionally, a sample may contain almost anything and for each, the type, integrity, and content of both tissue and substrate will vary, as will the contaminant levels. This fact makes the success of extraction one of the most unpredictable steps in genotypic analysis. The development of robust genotyping systems and analysis platforms for short tandem repeat (STR) and mitochondrial DNA sequencing and the acceptance of results generated by these methods in the court system, resulted in a high demand for DNA testing. The increasing variety of sample submissions created a need to isolate DNA from forensic samples that may be compromised or contain low levels of biological material. In the past decade, several robust chemistries and isolation methods have been developed to safely and reliably recover DNA from a wide array of sample types in high yield and free of PCR inhibitors. In addition, high-throughput automated workflows have been developed to meet the demand for processing increasing numbers of samples. This review summarizes a number of the most widely adopted methods and the best practices for DNA isolation from forensic biological samples, including manual, semiautomated, and fully automated platforms. PMID:26242594

  16. GC-Rich Extracellular DNA Induces Oxidative Stress, Double-Strand DNA Breaks, and DNA Damage Response in Human Adipose-Derived Mesenchymal Stem Cells

    PubMed Central

    Kostyuk, Svetlana; Smirnova, Tatiana; Kameneva, Larisa; Porokhovnik, Lev; Speranskij, Anatolij; Ershova, Elizaveta; Stukalov, Sergey; Izevskaya, Vera; Veiko, Natalia

    2015-01-01

    Background. Cell free DNA (cfDNA) circulates throughout the bloodstream of both healthy people and patients with various diseases. CfDNA is substantially enriched in its GC-content as compared with human genomic DNA. Principal Findings. Exposure of haMSCs to GC-DNA induces short-term oxidative stress (determined with H2DCFH-DA) and results in both single- and double-strand DNA breaks (comet assay and γH2AX, foci). As a result in the cells significantly increases the expression of repair genes (BRCA1 (RT-PCR), PCNA (FACS)) and antiapoptotic genes (BCL2 (RT-PCR and FACS), BCL2A1, BCL2L1, BIRC3, and BIRC2 (RT-PCR)). Under the action of GC-DNA the potential of mitochondria was increased. Here we show that GC-rich extracellular DNA stimulates adipocyte differentiation of human adipose-derived mesenchymal stem cells (haMSCs). Exposure to GC-DNA leads to an increase in the level of RNAPPARG2 and LPL (RT-PCR), in the level of fatty acid binding protein FABP4 (FACS analysis) and in the level of fat (Oil Red O). Conclusions. GC-rich fragments in the pool of cfDNA can potentially induce oxidative stress and DNA damage response and affect the direction of mesenchymal stem cells differentiation in human adipose—derived mesenchymal stem cells. Such a response may be one of the causes of obesity or osteoporosis. PMID:26273425

  17. Quantitive DNA Fiber Mapping

    SciTech Connect

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  18. Reversible DNA compaction.

    PubMed

    González-Pérez, Alfredo

    2014-01-01

    In this review we summarize and discuss the different methods we can use to achieve reversible DNA compaction in vitro. Reversible DNA compaction is a natural process that occurs in living cells and viruses. As a result these process long sequences of DNA can be concentrated in a small volume (compacted) to be decompacted only when the information carried by the DNA is needed. In the current work we review the main artificial compacting agents looking at their suitability for decompaction. The different approaches used for decompaction are strongly influenced by the nature of the compacting agent that determines the mechanism of compaction. We focus our discussion on two main artificial compacting agents: multivalent cations and cationic surfactants that are the best known compacting agents. The reversibility of the process can be achieved by adding chemicals like divalent cations, alcohols, anionic surfactants, cyclodextrins or by changing the chemical nature of the compacting agents via pH modifications, light induced conformation changes or by redox-reactions. We stress the relevance of electrostatic interactions and self-assembly as a main approach in order to tune up the DNA conformation in order to create an on-off switch allowing a transition between coil and compact states. The recent advances to control DNA conformation in vitro, by means of molecular self-assembly, result in a better understanding of the fundamental aspects involved in the DNA behavior in vivo and serve of invaluable inspiration for the development of potential biomedical applications. PMID:24444152

  19. Tracking Mitochondrial DNA In Situ.

    PubMed

    Ligasová, Anna; Koberna, Karel

    2016-01-01

    The methods of the detection of (1) non-labeled and (2) BrdU-labeled mitochondrial DNA (mtDNA) are described. They are based on the production of singlet oxygen by monovalent copper ions and the subsequent induction of DNA gaps. The ends of interrupted DNA serve as origins for the labeling of mtDNA by DNA polymerase I or they are utilized by exonuclease that degrades DNA strands, unmasking BrdU in BrdU-labeled DNA. Both methods are sensitive approaches without the need of additional enhancement of the signal or the use of highly sensitive optical systems. PMID:26530676

  20. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.