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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. Molecular modelling of the interactions of tetra-(4-N-methylpyridyl) porphin with TA and CG sites on DNA.

    PubMed Central

    Ford, K G; Pearl, L H; Neidle, S

    1987-01-01

    The molecular structure of the DNA-intercalating ligand tetra-(4-N-methylpyridyl) porphin has been determined by X-ray crystallography. The porphyrin has a precise centre of symmetry; the central core is planar, with the N-methylpyridyl groups inclined to it at angles of 66-72 degrees. Molecular modelling of this structure into TpA and CpG sites of intercalated DNA, has been performed, and approximate energetics calculated. It has been shown that only the CpG site can have full ligand intercalation, since the thymine methyl group sterically hinders such geometry at TpA sites. Modelling indicates the importance of electrostatic effects in the low-energy forms of intercalated and part-intercalated complexes at both sequences. PMID:3627998

  3. DNA damage following combination of radiation with the bioreductive drug AQ4N: possible selective toxicity to oxic and hypoxic tumour cells.

    PubMed Central

    Hejmadi, M. V.; McKeown, S. R.; Friery, O. P.; McIntyre, I. A.; Patterson, L. H.; Hirst, D. G.

    1996-01-01

    AQ4N (1,4-bis-([2-(dimethylamino-N- oxide)ethyl]amino)5,8-dihydroxyanthracene-9,10-dione) is a novel bioreductive agent that can be reduced to a stable, DNA-affinic compound, AQ4. The alkaline comet assay was used to evaluate DNA damage induced by AQ4N and radiation. Cells prepared from freshly excised T50/80 murine tumours were shown to have the ability to reduce AQ4N to a DNA-damaging agent; this had disappeared within 24 h of excision. When T50/80 tumours implanted in BDF mice were exposed to radiation in vivo a considerable amount of DNA damage was present in tumours excised immediately. Minimal levels of DNA damage were detectable in tumours excised after 2-5 h. AQ4N given 30 min before radiation had no appreciable influence on this effect and AQ4N alone caused only a small amount of damage. When AQ4N and radiation were combined an increasing number of damaged cells were seen in tumours excised 24-96 h after irradiation. This was interpreted as evidence of the continued presence of AQ4, or AQ4-induced damage, which was formed in cells hypoxic at the time of administration of AQ4N. AQ4, a potent topoisomerase II inhibitor, would be capable of damaging cells recruited into the cell cycle following radiation damage to the well-oxygenated cells of the tumour. The kinetics of the expression of the DNA damage is consistent with this hypothesis and shows that AQ4 has persistent activity in vivo. PMID:8595165

  4. Varying the chain length in N4,N9-diacyl spermines: non-viral lipopolyamine vectors for efficient plasmid DNA formulation.

    PubMed

    Ghonaim, Hassan M; Ahmed, Osama A A; Pourzand, Charareh; Blagbrough, Ian S

    2008-01-01

    The aims of this work are to study the effect of varying the chain length in synthesized N4,N9-diacyl spermines on DNA condensation and then to compare their transfection efficiencies in cell lines. The five novel N4,N9-diacyl lipopolyamines: N4,N9-[didecanoyl, dilauroyl, dimyristoyl, dimyristoleoyl, and dipalmitoyl]-1,12-diamino-4,9-diazadodecane were synthesized from the naturally occurring polyamine spermine. The abilities of these novel compounds to condense DNA and to form nanoparticles were studied using ethidium bromide fluorescence quenching and nanoparticle characterization techniques. Transfection efficiency was studied in FEK4 primary skin cells and in an immortalized cancer cell line (HtTA), and compared with a saturated (distearoyl) analogue and also with the non-liposomal transfection formulation Lipogen, N4,N9-dioleoyl-1,12-diamino-4,9-diazadodecane. By incorporating two aliphatic chains and changing their length in a stepwise manner, we show efficient circular plasmid DNA (pEGFP) formulation and transfection of primary skin and cancer cell lines. Two C14 chains (both saturated or both cis-monounsaturated) were efficient transfecting agents, even in the presence of serum, but they were too toxic. N4,N9-Dioleoyl spermine efficiently condenses pDNA and achieves the highest transfection levels with the highest cell viability among the studied lipopolyamines in cultured cells even in the presence of serum.

  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. Repetitive DNA in three Gramineae species with low DNA content.

    PubMed

    Deshpande, V G; Ranjekar, P K

    1980-08-01

    The genomes of three Gramineae species, namely finger millet (Eleusine coracana), pearl millet (Pennisetum americanum) and rice (Oryza sativa) are characterized by studying their DNA denaturation-reassociation properties. The reassociation kinetics measurement of the sonicated DNA (500--700 nucleotide pairs) indicate the presence of a heterogeneous, repetitive DNA fraction accounting for 49--54% of the total DNA in all three species. From the cot 1/2 value of the slow reassociating DNA, the genome size is estimated as 3.0 X 10(8) np in finger millet, 7.8 X 10(8) np in pearl millet and 9.0 X 10(8) np in rice. The melting patterns of the total DNAs reveal Tm value of 88.6 degrees C in the case of pearl millet and 85.0 degrees C in the case of finger millet and rice. Total repetitive and cot 1.0 DNA fractions in all the three species are isolated and their melting properties are compared with those of respective sonicated DNAs. In finger millet, the Tm values of cot 25 and cot 1 fractions are lower by 10.8 degrees C and 12.8 degrees C, respectively, than that of sonicated DNA and thus exhibit the presence of a base pair mismatch in the range of 10.8--12.8%. In rice, the Tm values of the fractions cot 50 and cot 1 are slightly lower than that of sonicated DNA and reveal a nucleotide mismatching of only 1.8--3.8%. In the case of pearl millet cot 10 DNA fraction a high-melting DNA component (Tm = 92 degrees C) representing 12% of the total cot 10 DNA and a low-melting component with a Tm of 78 degrees C are present. In cot 1 DNA fraction of pearl millet the proportion of the high-melting component is 35% and it has a Tm or 94.8 degrees C. Optical reassociation studies of cot 1.0 DNA fractions have revealed the presence of two kinetically distinct components, namely minor fast-reassociating and major slow-reassociating, having complexities in the range of 330--390 np and 1.28 X 10(5)--6.0 X 10(5) np, respectively in pearl millet and rice and only one DNA fraction with an

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

    PubMed

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

    2012-02-28

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

  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

    2016-06-01

    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.

  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. 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.

  12. Influence of light on DNA content of Helianthus annuus Linnaeus.

    PubMed

    Price, H J; Johnston, J S

    1996-10-01

    Mean nuclear 2C DNA content (C equaling haploid DNA per nucleus) of the first leaf of the sunflower, Helianthus annuus L., is influenced by the quality and the quantity of light. Seedlings of two inbred lines, RHA 299 and RHA 271 were germinated and grown in controlled environmental conditions. Lighting was adjusted to provide different combinations of photon flux densities and red to far red (R:FR) ratios. At R:FR = 5.8 and photon flux densities of 170 mumol.m-2.s-1, 200 mumol.m-2.s-1, and 230 mumol.m-2.s-1, DNA content remained high and relatively constant (x = 6.97 pg for RHA 271 and x = 7.32 pg for RHA 299). When the photon flux density range (R:FR = 5.8) was elevated to 350 mumol.m-2.s-1, 410 mumol.m-2.s-1, and 470 mumol.m-2.s-1, mean DNA content was reduced to 6.23 pg (RHA 271) and 6.46 pg (RHA 299). At R:FR = 1.5, mean DNA content was consistently high (7.2-7.9 pg) only at the lowest photon flux density of 170 mumol.m-2.s-1. Significant decreases in DNA content (< or = 12%) were observed at photon flux densities of 200 mumol.m-2.s-1 and 230 mumol.m-2.s-1. At the higher photon flux densities (350 mumol.m-2.s-1, 410 mumol.m-2.s-1, and 470 mumol.m-2.s-1) and R:RF = 1.5, the plants had extremely low DNA contents (mean x = 3.36 pg for RHA 271 and 3.41 pg for RHA 299) and high between-plant variance. The instability of DNA content, particularly for plants grown under light that is far red rich, suggests that phytochromes may be involved in regulating DNA content of the sunflower.

  13. 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

  14. 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.

  15. 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

  16. DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses.

    PubMed

    Acosta, Sharlene; Carela, Miguelina; Garcia-Gonzalez, Aurian; Gines, Mariela; Vicens, Luis; Cruet, Ricardo; Massey, Steven E

    2015-01-01

    The concept of a "proteomic constraint" proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes.

  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. Nuclear DNA content variation and evolution in liverworts.

    PubMed

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

    2013-09-01

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

  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. [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.

  3. Nuclear DNA content analysis of plant seeds by flow cytometry.

    PubMed

    Sliwinska, Elwira

    2006-02-01

    Procedures describing the utilization of seeds or their parts for flow cytometric determination of plant ploidy and endopolyploidy, genome size, and cell cycle activity are presented. The methods have been developed for a single-fluorescence-parameter flow cytometer, equipped with light sources for 488-nm and UV-light illumination. The procedures presented in this unit utilize the two most widely used fluorochromes for plant DNA content analysis, propidium iodide (PI) and 4',6-diamidino-2-phenylindole (DAPI). These methods provide an alternative to estimation of DNA content based on the fluorescence of DNA in cell nuclei isolated from plant leaves. In some instances seeds are more suitable for analysis than leaves, e.g., when plant material must be transported for a long distances or stored for prolonged periods before flow cytometric analysis, or when leaves contain fluorochrome-staining inhibitors. In addition, flow cytometric determination of nuclear replication stages in seeds gives information about their physiological status (e.g., maturity, advancement of germination), which is valuable to seed producers and technologists.

  4. Relationship between DAPI-fluorescence fading and nuclear DNA content: An alternative method to DNA quantification?

    PubMed

    Gallardo-Escárate, Cristian; Alvarez-Borrego, Josué; Von Brand, Elisabeth; Dupré, Enrique; Del Río-Portilla, Miguel Angel

    2007-01-01

    In observations by confocal or conventional fluorescence microscopy, important factors should be considered in order to obtain accurate images. One of them, such as the fluorescence bleaching from highest intensity to lowest signal of fluorescence is a common problem with several DNA fluorochromes and especially for DAPI stain. The fluorescence of DAPI fades rapidly when it is exposed to UV light, under optimal conditions of observation. Although the fading process can be retarded using a mounting medium with antifading reagents, the photochemical process underlying the fluorescence decay has not yet been fully explained. In addition, no relationship between fluorescence fading and nuclear DNA content has been tested. In order to test this relationship, we measured by means of image analysis the DAPI-fluorescence intensity in several cellular types (spermatozoa, erythrocytes and haemocytes) during their fluorescence bleaching. An algorithm specifically built in MATLAB software was used for this approach. The correlation coefficient between nuclear DNA content and DAPI-fluorescence fading was found equal to 99%. This study demonstrates the feasibility to measure nuclear DNA content by fluorescence fading quantification, as an alternative method concurrently with image analysis procedures.

  5. 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.

  6. DNA content and chromosomal composition of malignant human gliomas.

    PubMed

    Bigner, S H; Bjerkvig, R; Laerum, O D

    1985-11-01

    A short review is given on DNA aberrations and chromosomal composition of malignant human gliomas. By flow cytometric DNA analysis, a wide range of different ploidies has been reported in biopsied gliomas, from diploid to strongly aneuploid nuclear DNA. However, with the preparation and analysis methods used so far, no clear relationship between the type of ploidy and histology or prognosis has been established. A high proportion of glioblastomas is near-diploid, indicating a high degree of biologic malignancy is not necessarily connected to aberration of the nuclear DNA content. It is possible that improved methods giving a higher degree of resolution will allow separation of the near-diploid populations of malignant human gliomas from normal diploid cells and permit the detection of subpopulations with small differences from the dominant DNA mode. Chromosomal studies of malignant gliomas have confirmed that the majority of them have near-diploid stemlines. These populations are seldom normal diploid, however, as both numerical and structural abnormalities are usually present. In addition, chromosomal analyses have shown that when gliomas are bimodal, the polyploid populations are usually doubled versions of the near-diploid ones. In contrast to the near-diploid populations that characterize biopsied malignant gliomas, both FCM studies and karyotyping have demonstrated that permanent cultured cell lines derived from malignant gliomas are usually near-triploid or near-tetraploid. Sequential karyotypic studies of these tumors from biopsy through establishment in vitro have shown an evolutionary pattern consisting of doubling of the original stemline, followed by gains or losses of individual chromosomes with new marker formation in late culture. Evaluation of biopsied malignant gliomas by karyotyping has also demonstrated that subgroups of them are characterized by specific numerical and structural deviations. These groupings may prove useful in predicting prognosis

  7. 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.

  8. Influence of the thermodynamic parameters on the temper embrittlement of SA508 Gr.4N Ni-Cr-Mo low alloy steel with variation of Ni, Cr and Mn contents

    NASA Astrophysics Data System (ADS)

    Park, Sang-Gyu; Lee, Ki-Hyoung; Min, Ki-Deuk; Kim, Min-Chul; Lee, Bong-Sang

    2012-07-01

    It is well known that SA508 Gr.4N low alloy steel offers improved fracture toughness and strength compared to commercial low alloy steels such as SA508 Gr.3 Mn-Mo-Ni low alloy steel. In this study, the effects of Cr, Mn, and Ni on temper embrittlement in SA508 Gr.4N low alloy steel were evaluated from the viewpoint of thermodynamic parameters such as P diffusivity and C activity. The changes of the ductile-brittle transition temperatures before and after aging were correlated with varying alloying element content, and the diffusivity of P and the activity of C were calculated and correlated with the transition behaviors. The addition of Ni, Cr, and Mn reduce the resistance to temper embrittlement, showing increased Transition-Temperature Shift (TTS) and an increased fraction of intergranular fracture. Although the diffusivity of P is changed by the addition of alloying elements, it does not considerably affect the temper embrittlement. The Mn and Cr content in the matrix significantly reduce the C activity, with showing an inversely proportional relationship to TTS. The change of susceptibility to temper embrittlement caused by Cr and Mn addition could be explained by the variation of C activity. Unlike Cr and Mn, Ni has little effect on the temper embrittlement and C activity.

  9. 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

  10. 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

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

    PubMed

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

    2005-10-01

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

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

    PubMed

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

    2014-07-01

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

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

    PubMed Central

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

    1982-01-01

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

  14. 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.

  15. Mitochondrial DNA content, an inaccurate biomarker of mitochondrial alteration in human immunodeficiency virus-related lipodystrophy.

    PubMed

    Kim, Min Ji; Jardel, Claude; Barthélémy, Cyrille; Jan, Véronique; Bastard, Jean Philippe; Fillaut-Chapin, Sandrine; Houry, Sydney; Capeau, Jacqueline; Lombès, Anne

    2008-05-01

    Lipoatrophy is a prevalent side effect of antiretroviral treatment of human immunodeficiency virus (HIV) infection. Its mechanisms are still disputed but include mitochondrial toxicity and, in particular, mitochondrial DNA (mtDNA) depletion induced by nucleoside reverse transcriptase inhibitors. To obtain an integrated evaluation of the mitochondrial alteration in lipoatrophy, we investigated the DNA, RNA, and protein levels in 15 samples of abdominal subcutaneous adipose tissue from HIV-infected patients with peripheral lipoatrophy and compared the results with those for 15 samples from age- and body mass index-matched controls. The DNA and RNA analyses used PCR-based techniques, while proteins were quantified with enzyme-linked immunosorbent assay and measurement of activities with spectrophotometric assays. Depletion of mtDNA and mtDNA-encoded MT-CO2 mRNA was present, but normal levels of mtDNA-dependent activity (cytochrome c oxidase) and protein (MT-CO2p) showed that it was compensated for. An increase in nuclear-DNA-dependent mitochondrial activities (citrate synthase and malate dehydrogenase) and protein (COX4I1p), as well as transcriptional up-regulation of nuclear-DNA-encoded mitochondrial genes (COX4I1 and UCP2), demonstrated increased mitochondrial biogenesis. However, the expression of the known transcription factors of mitochondrial biogenesis (TFAM, NRF1, GABPA, PPARGC1A, PPARGC1B, and PPRC1) was normal or decreased. Increased amounts of activated caspase 3 and of DDIT3 mRNA showed the induction of apoptosis and oxidative stress, respectively. The mtDNA content did not correlate with any other mitochondrial parameter. In conclusion, mtDNA content does not appear to be an accurate biomarker of mitochondrial alteration in lipoatrophic adipose tissue. The preservation of mtDNA-dependent mitochondrial functions occurred despite severe mtDNA depletion. The presence of significant oxidative stress and apoptosis did not correlate with the mtDNA content.

  16. Mitochondrial DNA Content, an Inaccurate Biomarker of Mitochondrial Alteration in Human Immunodeficiency Virus-Related Lipodystrophy▿

    PubMed Central

    Kim, Min Ji; Jardel, Claude; Barthélémy, Cyrille; Jan, Véronique; Bastard, Jean Philippe; Fillaut-Chapin, Sandrine; Houry, Sydney; Capeau, Jacqueline; Lombès, Anne

    2008-01-01

    Lipoatrophy is a prevalent side effect of antiretroviral treatment of human immunodeficiency virus (HIV) infection. Its mechanisms are still disputed but include mitochondrial toxicity and, in particular, mitochondrial DNA (mtDNA) depletion induced by nucleoside reverse transcriptase inhibitors. To obtain an integrated evaluation of the mitochondrial alteration in lipoatrophy, we investigated the DNA, RNA, and protein levels in 15 samples of abdominal subcutaneous adipose tissue from HIV-infected patients with peripheral lipoatrophy and compared the results with those for 15 samples from age- and body mass index-matched controls. The DNA and RNA analyses used PCR-based techniques, while proteins were quantified with enzyme-linked immunosorbent assay and measurement of activities with spectrophotometric assays. Depletion of mtDNA and mtDNA-encoded MT-CO2 mRNA was present, but normal levels of mtDNA-dependent activity (cytochrome c oxidase) and protein (MT-CO2p) showed that it was compensated for. An increase in nuclear-DNA-dependent mitochondrial activities (citrate synthase and malate dehydrogenase) and protein (COX4I1p), as well as transcriptional up-regulation of nuclear-DNA-encoded mitochondrial genes (COX4I1 and UCP2), demonstrated increased mitochondrial biogenesis. However, the expression of the known transcription factors of mitochondrial biogenesis (TFAM, NRF1, GABPA, PPARGC1A, PPARGC1B, and PPRC1) was normal or decreased. Increased amounts of activated caspase 3 and of DDIT3 mRNA showed the induction of apoptosis and oxidative stress, respectively. The mtDNA content did not correlate with any other mitochondrial parameter. In conclusion, mtDNA content does not appear to be an accurate biomarker of mitochondrial alteration in lipoatrophic adipose tissue. The preservation of mtDNA-dependent mitochondrial functions occurred despite severe mtDNA depletion. The presence of significant oxidative stress and apoptosis did not correlate with the mtDNA content. PMID

  17. Nuclear DNA contents of Echinchloa crus-galli and its Gaussian relationships with environments

    NASA Astrophysics Data System (ADS)

    Li, Dan-Dan; Lu, Yong-Liang; Guo, Shui-Liang; Yin, Li-Ping; Zhou, Ping; Lou, Yu-Xia

    2017-02-01

    Previous studies on plant nuclear DNA content variation and its relationships with environmental gradients produced conflicting results. We speculated that the relationships between nuclear DNA content of a widely-distributed species and its environmental gradients might be non-linear if it was sampled in a large geographical gradient. Echinochloa crus-galli (L.) P. Beauv. is a worldwide species, but without documents on its intraspecific variation of nuclear DNA content. Our objectives are: 1) to detect intraspecific variation scope of E. crus-galli in its nuclear DNA content, and 2) to testify whether nuclear DNA content of the species changes with environmental gradients following Gaussian models if its populations were sampled in a large geographical gradient. We collected seeds of 36 Chinese populations of E. crus-galli across a wide geographical gradient, and sowed them in a homogeneous field to get their offspring to determine their nuclear DNA content. We analyzed the relationships of nuclear DNA content of these populations with latitude, longitude, and nineteen bioclimatic variables by using Gaussian and linear models. (1) Nuclear DNA content varied from 2.113 to 2.410 pg among 36 Chinese populations of E. crus-galli, with a mean value of 2.256 pg. (2) Gaussian correlations of nuclear DNA content (y) with geographical gradients were detected, with latitude (x) following y = 2.2923*e -(x - 24.9360)2/2*63.79452 (r = 0.546, P < 0.001), and with longitude (x) following y = 2.2933*e -(x - 116.1801)2/2*44.74502 (r = 0.672, P < 0.001). (3) Among the nineteen bioclimatic variables, except temperature isothermality, precipitations of the wettest month, the wettest quarter and the warmest quarter, the others could be better fit with nuclear DNA content by using Gaussian models than by linear models. There exists intra-specific variation among 36 Chinese populations of E. crus-galli, Gaussian models could be applied to fit the correlations of its Nuclear DNA content

  18. 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

  19. Flow cytometric analysis of DNA content differences in blood samples obtained by leucoconcentration.

    PubMed

    Pierrez, J; Guerci, A; Guerci, O

    1988-07-01

    The leucoconcentration technique allows rapid obtainment of cellular suspensions from total blood or bone marrow for flow cytometric analysis. The technique is based on picric acid in ethyl alcohol fixation and saponin red cell lysis, followed by mithramycin staining for DNA. It gives a good resolution of DNA distributions that allow detection of slight variations in DNA content. These results were obtained with cellular suspensions differing only in one X or Y chromosome (male, female, Klinefelter and Turner syndromes). In these studies the ratio of the DNA content of X and Y chromosomes agrees with the chromosomal mass ratio already reported by other authors, but the "absolute values" are 10-fold more compared to these same works. Our conclusion is that leucoconcentration technique followed by DNA staining with mithramycin increases the difference in the dye's penetration and binding between X and Y chromosomes.

  20. Specific melanin content in human hairs and mitochondrial DNA typing success.

    PubMed

    Linch, Charles A; Champagne, Jarrod R; Bonnette, Michelle D; Dawson Cruz, Tracey

    2009-06-01

    This study investigated whether a difference exists in the ability to obtain quality mitochondrial DNA (mtDNA) sequence data from hair shafts due to specific melanin content differences. Eumelanin, the pigment in darker hairs, protects nuclear DNA in the skin by absorbing and scattering UV radiation. In contrast, sensitized pheomelanin, the predominate melanin in red hairs and some blond hairs, is unable to prevent DNA damage in skin upon exposure to UV radiation. It has been reported in the literature that darker hairs (predominate eumelanin content) have a higher mtDNA sequencing success rate than lighter colored hairs. However, others have reported to the contrary when different methodologies are used. In this study, 2-cm hair fragments were cut from dark brown, red, and gray white hairs and typed using standard casework mtDNA sequence analysis methods. All 30 hair fragments produced quality mtDNA sequence data on first attempt from the second half of hypervariable region 1. These results are likely due to the apparent shielding of mtDNA by the hard protein of the hair shaft fiber from radiation-induced damage, regardless of melanin type, after 10-months minimal solar exposure. Nonetheless, this study may serve as a guide for future quantitative studies that investigate hair mtDNA photodamage in circumstances of increased solar, chemical, environmental, or mechanical damage.

  1. Cloning of a chicken liver cDNA encoding 5-aminoimidazole ribonucleotide carboxylase and 5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase by functional complementation of Escherichia coli pur mutants.

    PubMed Central

    Chen, Z D; Dixon, J E; Zalkin, H

    1990-01-01

    We have used functional complementation of Escherichia coli pur mutants to clone avian cDNA encoding 5-aminoimidazole ribonucleotide (AIR) carboxylase-5-aminoimidazole-4-N-succinocarboxamide ribonucleotide (SAICAR) synthetase, the bifunctional enzyme catalyzing steps 6 and 7 in the pathway for de novo purine nucleotide synthesis. Mutational analyses have been used to establish the structure-function relationship: NH2-SAICAR synthetase-AIR carboxylase-COOH. The amino acid sequence of the SAICAR synthetase domain is homologous to that of bacterial purC-encoded enzymes, and the sequence of the following AIR carboxylase domain is homologous to that of bacterial purE-encoded enzymes. In E. coli, AIR carboxylase is the product of genes purEK with the purK subunit postulated to have a role in CO2 binding. The avian enzyme lacks sequences corresponding to purK yet functions in E. coli. Functional complementation of E. coli pur mutants can be used to clone additional avian cDNAs for de novo purine nucleotide synthesis. Images PMID:1691501

  2. Whole-Mount DAPI Staining and Measurement of DNA Content in Plant Cells.

    PubMed

    Schnittger, Arp; Hülskamp, Martin

    2007-01-01

    INTRODUCTIONDuring development, many plant cells undergo endoreduplication, whereby ploidy increases to a multiple of the normal 2C content. For example, trichome development is accompanied by an increase in ploidy to 32C, indicating that trichome cells undergo four rounds of endoreduplication. In the protocol described here, DNA levels, and hence developmental progress in the corresponding cells, are measured by staining the DNA with a fluorescent marker and then quantifying the fluorescence of individual nuclei.

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    Trifa, Youssef; Zhang, David

    2004-03-10

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

  7. 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)

  8. Increased 8-hydroxyguanine content of chloroplast DNA from ozone-treated plants

    SciTech Connect

    Floyd, R.A.; West, M.S. ); Hogsett, W.E.; Tingey, D.T. )

    1989-10-01

    The mechanism of ozone-mediated plant injury is not known 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 electrochemical detection, the 8-hydroxy-2-{prime}-deoxyguanosine (8-OHdG) content of a DNA enzymatic digest can be sensitively quantitated. Beans (Phaseolus vulgaris L.) and peas (Pisum sativum L.) were treated with an ozone regime that caused acute injury. Chloroplast DNA was obtained from plants harvested either immediately after ozone treatment or 24 hours later. Ozone-exposed plants in general had nearly two-fold higher levels of 8-OHdG as compared to control plants. In vitro treatment of DNA in buffer solution with ozone did not cause formation of 8-OHdG in DNA, even though ozone did react directly with the macromolecule per se. Exposure of isolated, illuminated chloroplasts to ozone caused nearly a seven-fold increase in the amount of 8-OHdG in the chloroplast DNA as compared to none-ozone-exposed chloroplasts. These results suggest that ozone exposure to plants causes formation of enhanced levels of oxygen free radicals, thus mediating formation of 8-OHdG in chloroplast DNA. The reaction of ozone with DNA per se did not cause formation of 8-OHdG. Therefore, it is the interaction of ozone with plant cells and isolated chloroplasts which mediates oxygen free radical formation.

  9. 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.

  10. 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)

  11. Identification of human remains by DNA analysis of the gastrointestinal contents of fly larvae.

    PubMed

    de Lourdes Chávez-Briones, María; Hernández-Cortés, Raquel; Díaz-Torres, Porfirio; Niderhauser-García, Alberto; Ancer-Rodríguez, Jesús; Jaramillo-Rangel, Gilberto; Ortega-Martínez, Marta

    2013-01-01

    Dipterous fly larvae (maggots) are frequently collected from a corpse during a criminal investigation. Previous studies showed that DNA analysis of the gastrointestinal contents of maggots might be used to reveal the identity of a victim. However, this approach has not been used to date in legal investigations, and thus its practical usefulness is unknown. A badly burned body was discovered with its face and neck colonized by fly larvae. Given the condition of the body, identification was not possible. Short tandem repeat (STR) typing was performed using the gastrointestinal contents of maggots collected from the victim and was compared to STR profiles obtained from the alleged father. The probability of paternity was 99.685%. Thus, this comparative DNA test enabled the conclusive identification of the remains. This is the first reported case of analysis of human DNA isolated from the gastrointestinal tract of maggots used to identify a victim in a criminal case.

  12. 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

  13. 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.

  14. 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.

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

    PubMed

    Luz, Anthony L; Meyer, Joel N

    2016-09-01

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

  16. 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

  17. Intraspecific DNA Content Variability in Festuca pallens on Different Geographical Scales and Ploidy Levels

    PubMed Central

    ŠMARDA, PETR; BUREŠ, PETR

    2006-01-01

    • Background and Aims Intraspecific genome size variability of Festuca pallens occurring on relict rocky steppes in Central Europe was studied on two ploidy levels and three geographical scales: (1) local scale of 24 populations, (2) landscape scale of three transects in river canyons or hill systems, and (3) global scale of 160 samples covering the whole distribution area. • Methods DAPI flow cytometry of homogeneously cultivated samples (≥1 year), measured randomly with two internal standards, Lycopersicon esculentum and Pisum sativum. Differences in DNA content were confirmed (1) by the double peaks of simultaneously measured samples, (2) based on measurements carried out in different seasons, and (3) by additional measurements with propidium iodide. • Key Results On a global scale, the relative DNA content ranged between 1·170-fold in diploids and 1·164-fold in tetraploids. A maximum difference of 1·088-fold between the mean relative DNA content of nearby populations was found. In 16 of 24 populations significant variability was shown (P < 0·001, 1·121-fold as maximum). For both ploidy levels, the relative genome size had the same range and geographical pattern, correlated with geographical coordinates (P < 0·01). Diploids with larger genomes occur on relict habitats (P < 0·01), and in areas of periglacial steppes (20 000 years ago; P < 0·02). In tetraploids, the relative DNA content differs among the three previously recognized geographical types (Alpine, Pannonian and Scabrifolia, P < 0·001). Tetraploids have a relative DNA content smaller than twice that of the diploids (P < 0·001). An influence of microhabitat on DNA content variation was not confirmed. • Conclusions Genome size variability occurs over all spatial scales: intrapopulation, landscape and global. Correlation between geographical coordinates and palaeovegetation type, concomitant with diploids and tetraploids, and no influence of microhabitat were found. Genome size

  18. Genetic stock assessment of spawning arctic cisco (Coregonus autumnalis) populations by flow cytometric determination of DNA content.

    PubMed

    Lockwood, S F; Bickham, J W

    1991-01-01

    Intraspecific variation in cellular DNA content was measured in five Coregonus autumnalis spawning populations from the Mackenzie River drainage, Canada, using flow cytometry. The rivers assayed were the Peel, Arctic Red, Mountain, Carcajou, and Liard rivers. DNA content was determined from whole blood preparations of fish from all rivers except the Carcajou, for which kidney tissue was used. DNA content measurements of kidney and blood preparations of the same fish from the Mountain River revealed statistically indistinguishable results. Mosaicism was found in blood preparations from the Peel, Arctic Red, Mountain, and Liard rivers, but was not observed in kidney tissue preparations from the Mountain or Carcajou rivers. The Liard River sample had significantly elevated mean DNA content relative to the other four samples; all other samples were statistically indistinguishable. Significant differences in mean DNA content among spawning stocks of a single species reinforces the need for adequate sample sizes of both individuals and populations when reporting "C" values for a particular species.

  19. 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.

  20. 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

  1. Karyotype analysis, DNA content and molecular screening in Lippia alba (Verbenaceae).

    PubMed

    Pierre, Patrícia M O; Sousa, Saulo M; Davide, Lisete C; Machado, Marco A; Viccini, Lyderson F

    2011-09-01

    Cytogenetic analyses, of pollen viability, nuclear DNA content and RAPD markers were employed to study three chemotypes of Lippia alba (Mill.) (Verbenaceae) in order to understand the genetic variation among them. Different ploidy levels and mixoploid individuals were observed. This work comprises the first report of different chromosome numbers (cytotypes) in L. alba. The chromosome numbers of La2-carvone and La3-linalool chemotypes suggested that they are polyploids. Flow cytometric analysis showed an increase of nuclear DNA content that was not directly proportional to ploidy level variation. A cluster analysis based on RAPD markers revealed that La3-linalool shares genetic markers with La1-citral and La2-carvone. The analysis showed that the majority of genetic variation of La3-linalool could be a consequence of ixoploidy. ur data indicates that sexual reproduction aong those three chemotypes is unlikely and suggests the beginning of reproductive isolation. The results demonstrated that chromosome analysis, nuclear DNA content estimation and RAPD markers constitute excellent tools for detecting genetic variation among L. alba chemotypes.

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

    PubMed Central

    Akashi, Motohiro; Yoshikawa, Hirofumi

    2013-01-01

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

  3. 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

  4. 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.

  5. Chemical mapping of DNA and counter-ion content inside phage by energy-filtered TEM.

    PubMed

    Nevsten, Pernilla; Evilevitch, Alex; Wallenberg, Reine

    2012-03-01

    Double-stranded DNA in many bacterial viruses (phage) is strongly confined, which results in internal genome pressures of tens of atmospheres. This pressure is strongly dependent on local ion concentration and distribution within the viral capsid. Here, we have used electron energy loss spectroscopy (EELS), energy-filtered TEM (EFTEM) and X-ray energy dispersive spectroscopy to provide such chemical information from the capsid and the phage tail through which DNA is injected into the cell. To achieve this, we have developed a method to prepare thin monolayers of self-supporting virus/buffer films, suitable for EELS and EFTEM analysis. The method is based on entrapment of virus particles at air-liquid interfaces; thus, the commonly used method of staining by heavy metal salts can be avoided, eliminating the risk for chemical artifacts. We found that Mg(2 + ) concentration was approximately 2-4 times higher in the DNA-filled capsid than in the surrounding TM buffer (containing 10 mM Mg(2 + )). Furthermore, we also analyzed the DNA content inside the phage tail by mapping phosphorus and magnesium.

  6. Nuclear DNA content and base composition in 28 taxa of Musa.

    PubMed

    Kamaté, K; Brown, S; Durand, P; Bureau, J M; De Nay, D; Trinh, T H

    2001-08-01

    The nuclear DNA content of 28 taxa of Musa was assessed by flow cytometry, using line PxPC6 of Petunia hybrida as an internal standard. The 2C DNA value of Musa balbisiana (BB genome) was 1.16 pg, whereas Musa acuminata (AA genome) had an average 2C DNA value of 1.27 pg, with a difference of 11% between its subspecies. The two haploid (IC) genomes, A and B, comprising most of the edible bananas, are therefore of similar size, 0.63 pg (610 million bp) and 0.58 pg (560 million bp), respectively. The genome of diploid Musa is thus threefold that of Arabidopsis thaliana. The genome sizes in a set of triploid Musa cultivars or clones were quite different, with 2C DNA values ranging from 1.61 to 2.23 pg. Likewise, the genome sizes of tetraploid cultivars ranged from 1.94 to 2.37 pg (2C). Apparently, tetraploids (for instance, accession I.C.2) can have a genome size that falls within the range of triploid genome sizes, and vice versa (as in the case of accession Simili Radjah). The 2C values estimated for organs such as leaf, leaf sheath, rhizome, and flower were consistent, whereas root material gave atypical results, owing to browning. The genomic base composition of these Musa taxa had a median value of 40.8% GC (SD = 0.43%).

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

    PubMed Central

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

    2016-01-01

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

  8. Cutaneous photoprotection and melanoma susceptibility: reaching beyond melanin content to the frontiers of DNA repair.

    PubMed

    Kadekaro, Ana Luisa; Wakamatsu, Kazumasa; Ito, Shosuke; Abdel-Malek, Zalfa A

    2006-09-01

    Melanoma is the most devastating form of skin cancer. The steady increase in the incidence of melanoma, its resistance to chemotherapy, together with its high potential to metastasize, have emphasized the importance of its prevention. It is becoming clear that solar ultraviolet radiation is a main culprit in the etiology of melanoma, the same as in basal and squamous cell carcinomas. It is commonly accepted that skin pigmentation and melanin content are principal determinants of the susceptibility to melanoma and other sun-induced skin cancers. Although this is generally true, however, prediction of melanoma risk based solely on pigmentary phenotype is not always precise and fails to identify high-risk individuals with dark skin color. Other important risk factors need to be considered and better defined, particularly DNA repair capacity. Emerging studies have revealed the role of melanoma susceptibility genes in regulating DNA repair, and indicated that melanoma patients have a lower DNA repair capacity than the general population. As the response of human melanocytes to ultraviolet radiation is modulated by an array of paracrine factors, we have focused our investigation on the role of melanocortins and the melanocortin 1 receptor, as well as endothelin-1, in this response. We have discovered novel roles for melanocortins and endothelin-1 as survival factors that rescue human melanocytes from ultraviolet radiation-induced apoptosis, and importantly enhance repair of DNA photoproducts and reduce the release of hydrogen peroxide that can cause oxidative stress. Our findings, together with epidemiological data showing that loss-of-function mutations in the melanocortin-1 receptor gene increase the risk of melanoma, substantiate the role of DNA repair in melanoma genesis, and suggest that responsiveness to melanocortins and endothelin-1 is important for melanoma prevention.

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

    PubMed

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

    2015-03-01

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

  10. Chromosome numbers and DNA content in some species of Mecardonia (Gratiolae, Plantaginaceae)

    PubMed Central

    Sosa, María M.; Angulo, María B.; Greppi, Julián A.; Bugallo, Verónica

    2016-01-01

    Abstract Cytogenetic characterization and determination of DNA content by flow cytometry of five species of Mecardonia Ruiz et Pavon, 1798 (Gratiolae, Plantaginaceae) was performed. This is the first study of nuclear DNA content carried out in the genus. Mitotic analysis revealed a base chromosome number x = 11 for all entities and different ploidy levels, ranging from diploid (2n = 2x = 22) to hexaploid (2n = 6x = 66). The results include the first report of the chromosome numbers for Mecardonia flagellaris (Chamisso & Schlechtendal, 1827) (2n = 22), Mecardonia grandiflora (Bentham) Pennell, 1946 (2n = 22), Mecardonia kamogawae Greppi & Hagiwara, 2011 (2n = 66), and Mecardonia sp. (2n = 44). The three ploidy levels here reported suggest that polyploidy is common in Mecardonia and appear to be an important factor in the evolution of this genus. The 2C- and 1Cx-values were also estimated in all the species. The 2C-values ranged from 1.91 to 5.29 pg. The 1Cx-values ranged from 0.88 to 1.03 pg. The general tendency indicated a decrease in the 1Cx-value with increasing ploidy level. The significance of the results is discussed in relation to taxonomy of the genus. PMID:28123693

  11. High-content fluorescent-based assay for screening activators of DNA damage checkpoint pathways.

    PubMed

    Bin Zhang; Xiubin Gu; Uppalapati, Uma; Ashwell, Mark A; Leggett, David S; Li, Chiang J

    2008-07-01

    Activation of DNA damage checkpoint pathways, including Chk2, serves as an anticancer barrier in precancerous lesions. In an effort to identify small-molecule activators of Chk2, the authors developed a quantitative cell-based assay using a high-content analysis (HCA) platform. Induction of phosphorylated Chk2 was evaluated using several different parameters, including fold induction, Kolmogorov-Smirnov score, and percentage of positively stained cells. These measurements were highly correlated and provided an accurate method for compound ranking/binning, structure-activity relationship studies, and lead identification. Screening for Chk2 activators was undertaken with a target-focused library and a diversified library from ArQule chemical space. Several compounds exhibited submicromolar EC( 50) values for phosphorylated Chk2 induction. These compounds were further analyzed for Chk2-dependent cytotoxicity, as assessed through a high-content cell death assay in combination with siRNA silencing of Chk2 expression. Several compounds were identified and showed specific inhibition or lethality in a target-dependent manner. Therefore, identification of DNA damage checkpoint pathway activators by HCA is an attractive approach for discovering the next generation of targeted cancer therapeutics.

  12. Polyploidization in the trophoblast and uterine glandular epithelium of the endotheliochorial placenta of silver fox (Vulpes fulvus Desm.), as revealed by the DNA content.

    PubMed

    Zybina, T G; Zybina, E V; Kiknadze, I I; Zhelezova, A I

    2001-05-01

    Dynamics of genome multiplication during establishment of interrelations between trophoblast and glandular epithelium of the endometrium has been studied in the course of formation of placenta in the silver fox. During formation of the placenta, penetration of the trophoblast into the zone of the endometrial glandular epithelium and of endometrial blood vessels into the zone of expanding trophoblast occurs. The trophoblast, which gradually replaces epithelium and a part of the stroma of the endometrium, closely adjoins endometrial vessels but does not disrupt them, thereby the endotheliochorial placenta is formed. Cytophotometric measurements of the DNA content in trophoblast nuclei have shown that most of them are polyploid: predominantly 4-64c, occasionally 128c and 256c. Polyploidy of the trophoblast may be a consequence of various types of polyploidizing mitoses. Cytophotometric measurements of the DNA content in mitotic figures have revealed the presence of mitoses of diploid cells, i.e. with the DNA amount of 4c (2n), and polyploid cells, i.e. 8c (4n), and 16c (8n), therefore trophoblast cells in the silver fox placenta are able to enter mitosis up to the octaploid level. Higher degrees of polyploidy in the trophoblast cells seem to be achieved by endoreduplication. Polyploidization of the uterine glandular epithelial cells during placentation in the silver fox occurs until the level of 8c. Thus, the tissue-specific response of the uterus to the implanting embryo consists of active proliferation and polyploidization of the glandular epithelium, which may compensate formation of prominent population of decidual cells (i.e., connective tissue cells). In the endotheliochorial placenta of the silver fox the regularity is confirmed that cells of both maternal and fetal origin are, as a rule, polyploid in sites of their contact in placenta, which may be of protective significance in the contact of allogenic organisms.

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

    PubMed

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

    2011-08-01

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

  14. Fragile sites, telomeric DNA sequences, B chromosomes, and DNA content in raccoon dogs, Nyctereutes procyonoides, with comparative notes on foxes, coyote, wolf, and raccoon.

    PubMed

    Wurster-Hill, D H; Ward, O G; Davis, B H; Park, J P; Moyzis, R K; Meyne, J

    1988-01-01

    Earlier studies of the genus Nyctereutes disclosed two subspecies of differing chromosome numbers accompanied by B chromosomes. To further define the relationship of these subspecies to each other, and to other carnivores, and to learn more about the structure and function of their chromosomes, we characterized and compared the genomes in terms of DNA content by flow cytometry, fragile sites induced by aphidicolin, and telomere sequences using biotinylated DNA probes detected with fluorescence. We also characterized the B chromosomes of these two subspecies.

  15. 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.

  16. 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

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

    PubMed

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

    2016-03-01

    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 μm(2)) 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.

  18. 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

  19. New reports of nuclear DNA content for 407 vascular plant taxa from the United States

    PubMed Central

    Bai, Chengke; Alverson, William S.; Follansbee, Aaron; Waller, Donald M.

    2012-01-01

    Background and Aims The amount of DNA in an unreplicated haploid nuclear genome (C-value) ranges over several orders of magnitude among plant species and represents a key metric for comparing plant genomes. To extend previously published datasets on plant nuclear content and to characterize the DNA content of many species present in one region of North America, flow cytometry was used to estimate C-values of woody and herbaceous species collected in Wisconsin and the Upper Peninsula of Michigan, USA. Methods A total of 674 samples and vouchers were collected from locations across Wisconsin and Michigan, USA. From these, C-value estimates were obtained for 514 species, subspecies and varieties of vascular plants. Nuclei were extracted from samples of these species in one of two buffers, stained with the fluorochrome propidium iodide, and an Accuri C-6 flow cytometer was used to measure fluorescence peaks relative to those of an internal standard. Replicate extractions, coefficients of variation and comparisons to published C-values in the same and related species were used to confirm the accuracy and reliability of our results. Key Results and Conclusions Prime C-values for 407 taxa are provided for which no published data exist, including 390 angiosperms, two gymnosperms, ten monilophytes and five lycophytes. Non-prime reports for 107 additional taxa are also provided. The prime values represent new reports for 129 genera and five families (of 303 genera and 97 families sampled). New family C-value maxima or minima are reported for Betulaceae, Ericaceae, Ranunculaceae and Sapindaceae. These data provide the basis for phylogenetic analyses of C-value variation and future analyses of how C-values covary with other functional traits. PMID:23100602

  20. 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.

  1. Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes.

    PubMed

    Kim, Mincheol; Park, Sang-Cheol; Baek, Inwoo; Chun, Jongsik

    2015-03-01

    Historically, DNA G+C content has played a critical role in the description of bacterial and archaeal species. Despite its importance in prokaryote taxonomy, its accuracy has been questioned due to methodological heterogeneity and measurement errors of conventional methods. Here we investigated the extent of accuracy of experimentally determined DNA G+C contents by comparing the reference values calculated from whole genome sequences. The large-scale comparison revealed that G+C contents determined by high-performance liquid chromatography and buoyant density centrifugation methods were more similar to the genome-derived reference values than those generated by thermal denaturation method. However, there was a substantial degree of discrepancy in DNA G+C contents between values obtained by conventional methods and genome-derived reference values. The majority of the differences between them fell out of the acceptable range (i.e. 1 mol% G+C content difference) for species delimitation of prokaryotes. In contrast, when average nucleotide identity (ANI) was correlated to G+C difference among genomes, most G+C difference was confined to less than 1% within species. Therefore, erroneous conventional methods are not meaningful in the description of bacterial and archaeal species. For taxonomic purposes, DNA G+C content should be determined by calculating directly from high-quality genome sequences with at least 16× or higher sequencing depth of coverage.

  2. 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

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

    PubMed

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

    2007-04-01

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

  4. Novel DNA damage checkpoint in mitosis: Mitotic DNA damage induces re-replication without cell division in various cancer cells.

    PubMed

    Hyun, Sun-Yi; Rosen, Eliot M; Jang, Young-Joo

    2012-07-06

    DNA damage induces multiple checkpoint pathways to arrest cell cycle progression until damage is repaired. In our previous reports, when DNA damage occurred in prometaphase, cells were accumulated in 4 N-DNA G1 phase, and mitosis-specific kinases were inactivated in dependent on ATM/Chk1 after a short incubation for repair. We investigated whether or not mitotic DNA damage causes cells to skip-over late mitotic periods under prolonged incubation in a time-lapse study. 4 N-DNA-damaged cells re-replicated without cell division and accumulated in 8 N-DNA content, and the activities of apoptotic factors were increased. The inhibition of DNA replication reduced the 8 N-DNA cell population dramatically. Induction of replication without cell division was not observed upon depletion of Chk1 or ATM. Finally, mitotic DNA damage induces mitotic slippage and that cells enter G1 phase with 4 N-DNA content and then DNA replication is occurred to 8 N-DNA content before completion of mitosis in the ATM/Chk1-dependent manner, followed by caspase-dependent apoptosis during long-term repair.

  5. Screening for Methylated Poly(l-histidine) with Various Dimethylimidazolium/Methylimidazole/Imidazole Contents as DNA Carrier.

    PubMed

    Asayama, Shoichiro; Kumagai, Takao; Kawakami, Hiroyoshi

    2015-08-25

    : Methylated poly(l-histidine) (PLH-Me), our original polypeptide, has controlled the contents of dimethylimidazolium, τ/π-methylimidazole and imidazole groups for efficient gene delivery. The screening for the PLH-Me as DNA carrier has been carried out by use of the PLH with 25 mol% (τ-methyl, 16 mol%; π-methyl, 17 mol%; deprotonated imidazole, 41 mol%), 68 mol% (τ-methyl, 16 mol%; π-methyl, 8 mol%; deprotonated imidazole, 8 mol%) and 87 mol% (τ-methyl, 7 mol%; π-methyl, 4 mol%; deprotonated imidazole, 2 mol%) dimethylimidazolium groups, that is, PLH-Me(25), PLH-Me(68) and PLH-Me(87), respectively. The screening of the chemical structure of PLH-Me has been carried out for DNA carrier properties, which are the stability of its DNA polyion complexes and gene expression. The DNA complexes with the 25 mol% and 68 mol% dimethylated PLH-Me possessed almost same ability to retain DNA, as compared with the 87 mol% dimethylated PLH-Me, which was examined by competitive exchange with dextran sulfate. From the gene transfection experiment against HepG2 cells, human hepatoma cell line, the PLH-Me(25)/DNA complex was revealed to mediate highest gene expression. These results suggest that the dimethyl-imidazolium/methylimidazole/imidazole balance of the PLH-Me is important for DNA carrier design.

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

    PubMed

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

    2014-04-01

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

  7. Cross-species analysis of genic GC3 content and DNA methylation patterns.

    PubMed

    Tatarinova, Tatiana; Elhaik, Eran; Pellegrini, Matteo

    2013-01-01

    The GC content in the third codon position (GC(3)) exhibits a unimodal distribution in many plant and animal genomes. Interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. High GC(3) was previously found to be associated with variable expression, higher frequency of upstream TATA boxes, and an increase of GC(3) from 5' to 3'. Moreover, GC(3)-rich genes are predominant in certain gene classes and are enriched in CpG dinucleotides that are potential targets for methylation. Based on the GC(3) bimodal distribution we hypothesize that GC(3) has a regulatory role involving methylation and gene expression. To test that hypothesis, we selected diverse taxa (rice, thale cress, bee, and human) that varied in the modality of their GC(3) distribution and tested the association between GC(3), DNA methylation, and gene expression. We examine the relationship between cytosine methylation levels and GC(3), gene expression, genome signature, gene length, and other gene compositional features. We find a strong negative correlation (Pearson's correlation coefficient r = -0.67, P value < 0.0001) between GC(3) and genic CpG methylation. The comparison between 5'-3' gradients of CG(3)-skew and genic methylation for the taxa in the study suggests interplay between gene-body methylation and transcription-coupled cytosine deamination effect. Compositional features are correlated with methylation levels of genes in rice, thale cress, human, bee, and fruit fly (which acts as an unmethylated control). These patterns allow us to generate evolutionary hypotheses about the relationships between GC(3) and methylation and how these affect expression patterns. Specifically, we propose that the opposite effects of methylation and compositional gradients along coding regions of GC(3)-poor and GC(3)-rich genes are the products of several competing processes.

  8. Cross-Species Analysis of Genic GC3 Content and DNA Methylation Patterns

    PubMed Central

    Tatarinova, Tatiana; Elhaik, Eran; Pellegrini, Matteo

    2013-01-01

    The GC content in the third codon position (GC3) exhibits a unimodal distribution in many plant and animal genomes. Interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. High GC3 was previously found to be associated with variable expression, higher frequency of upstream TATA boxes, and an increase of GC3 from 5′ to 3′. Moreover, GC3-rich genes are predominant in certain gene classes and are enriched in CpG dinucleotides that are potential targets for methylation. Based on the GC3 bimodal distribution we hypothesize that GC3 has a regulatory role involving methylation and gene expression. To test that hypothesis, we selected diverse taxa (rice, thale cress, bee, and human) that varied in the modality of their GC3 distribution and tested the association between GC3, DNA methylation, and gene expression. We examine the relationship between cytosine methylation levels and GC3, gene expression, genome signature, gene length, and other gene compositional features. We find a strong negative correlation (Pearson’s correlation coefficient r = −0.67, P value < 0.0001) between GC3 and genic CpG methylation. The comparison between 5′-3′ gradients of CG3-skew and genic methylation for the taxa in the study suggests interplay between gene-body methylation and transcription-coupled cytosine deamination effect. Compositional features are correlated with methylation levels of genes in rice, thale cress, human, bee, and fruit fly (which acts as an unmethylated control). These patterns allow us to generate evolutionary hypotheses about the relationships between GC3 and methylation and how these affect expression patterns. Specifically, we propose that the opposite effects of methylation and compositional gradients along coding regions of GC3-poor and GC3-rich genes are the products of several competing processes. PMID:23833164

  9. 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

  10. Group-specific primers for DNA-based detection of springtails (Hexapoda: Collembola) within predator gut contents.

    PubMed

    Kuusk, A K; Agustí, N

    2008-05-01

    Group-specific, degenerate polymerase chain reaction primers for DNA-based detection of springtails (Hexapoda: Collembola) within predator gut contents have been developed for the first time. Primers were designed from 18S rDNA and amplified fragments of 272 bp and 177 bp from 17 springtail species collected in agricultural habitats. Specificity tests against 41 nontarget species revealed no cross-reactivity. Group-specific polymerase chain reaction is advantageous when working in species-rich habitats and these primers could facilitate studies of trophic links between springtails and generalist arthropod predators worldwide.

  11. Information content and complexity in the high-order organization of DNA.

    PubMed

    Minsky, Abraham

    2004-01-01

    Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.

  12. An association analysis between mitochondrial DNA content, G10398A polymorphism, HPV infection, and the prognosis of cervical cancer in the Chinese Han population.

    PubMed

    Feng, Dali; Xu, Hui; Li, Xin; Wei, Yuehua; Jiang, Huangang; Xu, Hong; Luo, Aihua; Zhou, Fuxiang

    2016-04-01

    The aim was to analyze quantitative (mitochondrial DNA (mtDNA) content) and qualitative (G10398A polymorphism) mtDNA alterations as well as human papillomavirus (HPV) infection in cervical cancer prognosis. One hundred and twenty-two cases of formalin-fixed paraffin-embedded cervical carcinoma specimens were collected from the Yichang Tumor Hospital and Zhongnan Hospital of Wuhan University in the recent 10 years together with medical records. A quantitative real-time PCR (RT-PCR) was used to determine the copy number of the mitochondrial DNA and HPV expression levels. G10398A polymorphism was determined by PCR-RFLP assay. The overall survival of patients with higher mtDNA content was significantly reduced compared with lower mtDNA content patients (P = 0.029). But there was no difference of prognosis between the mtDNA 10398 A allele and G allele. However, the Kaplan-Meier survival curve illustrated a significantly reduced overall survival in the patients with 10398A plus high mtDNA copy number compared with the other groups (P < 0.05). Although no association between HPV expression level and cervical cancer prognosis was observed, 10398A got increased mtDNA content compared with 10398G (P < 0.05) and 10398G displayed an increased HPV-positive rate compared with 10398A. Furthermore, HPV-18 and mtDNA content were positively related in the younger subgroup (≤45 years) (correlation coefficient = 0.456, P = 0.022). This study indicated that mtDNA content and HPV infection status are associated with cervical cancer prognosis. High mitochondrial DNA content plus 10398 A may be a marker of poor prognosis in cervical cancer. And mtDNA variation may potentially influence the predisposition to HPV infection and cervical carcinogenesis.

  13. 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.

  14. 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.

  15. Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates.

    PubMed

    Biller, Steven J; McDaniel, Lauren D; Breitbart, Mya; Rogers, Everett; Paul, John H; Chisholm, Sallie W

    2017-02-01

    Diverse microbes release membrane-bound extracellular vesicles from their outer surfaces into the surrounding environment. Vesicles are found in numerous habitats including the oceans, where they likely have a variety of functional roles in microbial ecosystems. Extracellular vesicles are known to contain a range of biomolecules including DNA, but the frequency with which DNA is packaged in vesicles is unknown. Here, we examine the quantity and distribution of DNA associated with vesicles released from five different bacteria. The average quantity of double-stranded DNA and size distribution of DNA fragments released within vesicles varies among different taxa. Although some vesicles contain sufficient DNA to be visible following staining with the SYBR fluorescent DNA dyes typically used to enumerate viruses, this represents only a small proportion (<0.01-1%) of vesicles. Thus DNA is packaged heterogeneously within vesicle populations, and it appears that vesicles are likely to be a minor component of SYBR-visible particles in natural sea water compared with viruses. Consistent with this hypothesis, chloroform treatment of coastal and offshore seawater samples reveals that vesicles increase epifluorescence-based particle (viral) counts by less than an order of magnitude and their impact is variable in space and time.

  16. Arbitrary single primer amplification of trace DNA substrates yields sequence content profiles that are discriminatory and reproducible.

    PubMed

    Waters, James M; Eariss, Graham; Yeadon, P Jane; Kirkbride, K Paul; Burgoyne, Leigh A; Catcheside, David E A

    2012-02-01

    Single primer amplification is shown to yield a DNA profile that is reproducible when based on the sequence content of the amplicons rather than on the pattern of length polymorphism. The sequence-based profile increases in reliability with increasing numbers of cycles of amplification. This process uses an arbitrarily chosen primer and a low initial annealing temperature in order to amplify sequences from the whole metagenome present in a sample that may contain only trace DNA, and a large number of cycles to select subsets of sequences based on variable amplification efficiency. Using arrays, we demonstrate the utility and limitations of this approach for profiling the large metagenomes typical of soils and the trace DNA present in drug seizures. We suggest that this type of profiling will be most effective once next-generation sequencing and advanced sequence analysis becomes routine.

  17. Renin–angiotensin system inhibitors protect against age-related changes in rat liver mitochondrial DNA content and gene expression

    PubMed Central

    de Cavanagh, Elena M.V.; Flores, Idhaliz; Ferder, Marcelo; Inserra, Felipe; Ferder, León

    2016-01-01

    Chronic renin–angiotensin system inhibition protects against liver fibrosis, ameliorates age-associated mitochondrial dysfunction and increases rodent lifespan. We hypothesized that life-long angiotensin-II-mediated stimulation of oxidant generation might participate in mitochondrial DNA “common deletion” formation, and the resulting impairment of bioenergetic capacity. Enalapril (10 mg/kg/d) or losartan (30 mg/kg/d) administered during 16.5 months were unable to prevent the age-dependent accumulation of rat liver mitochondrial DNA “common deletion”, but attenuated the decrease of mitochondrial DNA content. This evidence – together with the enhancement of NRF-1 and PGC-1 mRNA contents – seems to explain why enalapril and losartan improved mitochondrial functioning and lowered oxidant production, since both the absolute number of mtDNA molecules and increased NRF-1 and PGC-1 transcription are positively related to mitochondrial respiratory capacity, and PGC-1 protects against increases in ROS production and damage. Oxidative stress evoked by abnormal respiratory function contributes to the pathophysiology of mitochondrial disease and human aging. If the present mitochondrial actions of renin–angiotensin system inhibitors are confirmed in humans they may modify the therapeutic significance of that strategy. PMID:18765277

  18. Chromosomal instability, aneuploidy and routine high-resolution DNA content analysis in oral cancer risk evaluation.

    PubMed

    Giaretti, Walter; Pentenero, Monica; Gandolfo, Sergio; Castagnola, Patrizio

    2012-10-01

    Carcinogen exposure of the oral cavity is thought to create an extensive 'field cancerization'. According to this model, a very early precursor of oral cancer is a patch of normal-appearing mucosa in which stem cells share genetic/genomic aberrations. These precancerous fields then become clinically visible as white and red lesions (leuko- and erythro-plakias), which represent the vast majority of the oral potentially malignant disorders. This review focuses on aneuploidy (where it is from) and on biomarkers associated with DNA aneuploidy in oral mucosa and oral potentially malignant disorders, as detected by DNA image and flow cytometry. Data from the literature strongly support the association of DNA ploidy with dysplasia. However, work is still needed to prove the clinical value of DNA ploidy in large-scale prospective studies. Using high-resolution DNA flow cytometry with fresh/frozen material and the degree of DNA aneuploidy (DNA Index) might improve the prediction of risk of oral cancer development.

  19. 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

  20. Relationship between radiation-induced aberrations in individual chromosomes and their DNA content: effects of interaction distance

    NASA Technical Reports Server (NTRS)

    Wu, H.; Durante, M.; Lucas, J. N.

    2001-01-01

    PURPOSE: To study the effect of the interaction distance on the frequency of inter- and intrachromosome exchanges in individual chromosomes with respect to their DNA content. Assumptions: Chromosome exchanges are formed by misrejoining of two DNA double-strand breaks (DSB) induced within an interaction distance, d. It is assumed that chromosomes in G(0)/G(1) phase of the cell cycle occupy a spherical domain in a cell nucleus, with no spatial overlap between individual chromosome domains. RESULTS: Formulae are derived for the probability of formation of inter-, as well as intra-, chromosome exchanges relating to the DNA content of the chromosome for a given interaction distance. For interaction distances <1 microm, the relative frequency of interchromosome exchanges predicted by the present model is similar to that by Cigarran et al. (1998) based on the assumption that the probability of interchromosome exchanges is proportional to the "surface area" of the chromosome territory. The "surface area" assumption is shown to be a limiting case of d-->0 in the present model. The present model also predicts that the probability of intrachromosome exchanges occurring in individual chromosomes is proportional to their DNA content with correction terms. CONCLUSION: When the interaction distance is small, the "surface area" distribution for chromosome participation in interchromosome exchanges has been expected. However, the present model shows that for the interaction distance as large as 1 microm, the predicted probability of interchromosome exchange formation is still close to the surface area distribution. Therefore, this distribution does not necessarily rule out the formation of complex chromosomal aberrations by long-range misrejoining of DSB.

  1. 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

  2. Phylogenetic information content of Copepoda ribosomal DNA repeat units: ITS1 and ITS2 impact.

    PubMed

    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.

  3. 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.

  4. 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

  5. Measuring the DNA Content of Cells in Apoptosis and at Different Cell-Cycle Stages by Propidium Iodide Staining and Flow Cytometry.

    PubMed

    Crowley, Lisa C; Chojnowski, Grace; Waterhouse, Nigel J

    2016-10-03

    All cells are created from preexisting cells. This involves complete duplication of the parent cell to create two daughter cells by a process known as the cell cycle. For this process to be successful, the DNA of the parent cell must be faithfully replicated so that each daughter cell receives a full copy of the genetic information. During the cell cycle, the DNA content of the parent cell increases as new DNA is synthesized (S phase). When there are two full copies of the DNA (G2/M phase), the cell splits to form two new cells (G0/G1 phase). As such, cells in different stages of the cell cycle have different DNA contents. The cell cycle is tightly regulated to safeguard the integrity of the cell and any cell that is defective or unable to complete the cell cycle is programmed to die by apoptosis. When this occurs, the DNA is fragmented into oligonucleosomal-sized fragments that are disposed of when the dead cell is removed by phagocytosis. Consequently apoptotic cells have reduced DNA content compared with living cells. This can be measured by staining cells with propidium iodide (PI), a fluorescent molecule that intercalates with DNA at a specific ratio. The level of PI fluorescence in a cell is, therefore, directly proportional to the DNA content of that cell. This protocol describes the use of PI staining to determine the percentage of cells in each phase of the cell cycle and the percentage of apoptotic cells in a sample.

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

    SciTech Connect

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

    1994-02-01

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

  7. DNA repeat lengths of erythrocyte chromatins differing in content of histones H1 and H5.

    PubMed Central

    Miki, B L; Neelin, J M

    1980-01-01

    Among the erythrocytes of chicken, trout, carp, and sucker, the relative proportion of the lysine-rich histone H5 varied from 20 to 0% of the total histones. Following digestion of nuclear chromatin with micrococcal nuclease, each of them displayed a longer DNA repeat length and greater repeat length heterogeneity than found in liver chromatin. Fish erythrocytes possessed similar repeat lengths of 207-209 base pairs which was 10-12 base pairs shorter than in chicken erythrocyte chromatin and approximately 10 base pairs longer than in liver chromatin. No correlation existed between the DNA repeat length or repeat length heterogeneity and the relative proportion of H5. Images PMID:6777761

  8. 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.

  9. Flow cytometric analysis of DNA content of living and fixed cells: a comparative study using various fixatives.

    PubMed

    Rousselle, C; Robert-Nicoud, M; Ronot, X

    1998-11-01

    The majority of studies dealing with DNA analyses are made on fixed cells. In this context, the efficiency as fixatives of ethanol, methanol, acetone, Carnoy, Boehm-Sprenger and aldehydes was determined using two different DNA fluorescent probes, Hoechst 33342 and propidium iodide. The purpose of our study was to find the fixative that would provide the best results with respect to the following parameters: aggregates, cell size and granularity, and DNA staining analysis. Using murine fibroblasts, we found that 68% ethanol, 85% methanol and aldehydes did not increase aggregate formation, whereas Carnoy, acetone or Boehm-Sprenger fixatives did. The results show that aldehydes seem to alter cell size least. All fixatives induce an increase in cell granularity, which is very pronounced with alcohols, but aldehydes alter morphology less than alcohols. We observed that the fixatives giving the best resolution with Hoechst 33342 staining lead to a lower measurement variability than with propidium iodide staining. This study leads us to conclude that 68% ethanol and 85% methanol can be considered as appropriate fixatives for flow cytometry studies of DNA content.

  10. DNA G+C content of the third codon position and codon usage biases of human genes.

    PubMed

    Sueoka, N; Kawanishi, Y

    2000-12-30

    The human genome, as in other eukaryotes, has a wide heterogeneity in the DNA base composition. The evolutionary basis for this heterogeneity has been unknown. A previous study of the human genome (846 genes analyzed) has shown that, in the major range of the G+C content in the third codon position (0.25-0.75), biases from the Parity Rule 2 (PR2) among the synonymous codons of the four-codon amino acids are similar except in the highest G+C range (Sueoka, N., 1999. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58.). PR2 is an intra-strand rule where A=T and G=C are expected when there are no biases between the two complementary strands of DNA in mutation and selection rates (substitution rates). In this study, 14,026 human genes were analyzed. In addition, the third codon positions of two-codon amino acids were analyzed. New results show the following: (a) The G+C contents of the third codon position of human genes are scattered in the G+C range of 0.22-0.96 in the third codon position. (b) The PR2 biases are similar in the range of 0.25-0.75, whereas, in the high G+C range (0.75-0.96; 13% of the genes), the PR2-bias fingerprints are different from those of the major range. (c) Unlike the PR2 biases, the G+C contents of the third codon position for both four-codon and two-codon amino acids are all correlated almost perfectly with the G+C content of the third codon position over the total G+C ranges. These results support the notion that the directional mutation pressure, rather than the directional selection pressure, is mainly responsible for the heterogeneity of the G+C content of the third codon position.

  11. The Clinical Value of Flow Cytometric DNA Content Analysis in Patients with Soft Tissue Sarcomas

    PubMed Central

    Samur, Mustafa; Pamir, Ali; Erekul, Selim; Sağlik, Yener; Yildiz, Yusuf; Dinçol, Dilek; Içli, Fikri

    1999-01-01

    Purpose. The purpose of this study was to evaluate: (1) the correlation between grade and ploidy or S-phase fraction (SPF), (2) the prognostic value of DNA flow cytometric study in soft tissue sarcomas. Patients /Methods. In all, 47 tissue samples from soft tissue sarcoma patients, surgically treated in the same center, were included. Flow cytometric analyses were performed according to a modified version of the original method of Hedley et al. Results. DNA ploidy status could be determined in 44 samples out of 47 (success rate 94%). Of these 44, S-phase fraction could be calculated in 34 samples (77%). In the study group as a whole, aneuploidy was significantly correlated with high grade. Survival analyses were carried out in 21 patients with soft tissue sarcoma, all surgically treated in the same center, without chemotherapy or radiotherapy. In univariate analyses, DNA ploidy was found to be a significant factor for overall survival (OAS) and metastasis-free survival MFS. Mean OAS for aneuploid tumors and diploid tumors were 35 and 65 months (p=0.034), and mean MFS 23 and 61 months, respectively (p=0.005) . Discussion.There is a relation between histological grade and ploidy in soft tissue sarcomas. It appears that low-grade tumors are generally diploid, whereas high-grade tumors tend to be aneuploid. In a subgroup of patients treated only with surgery, DNA ploidy was found to be an important factor for predicting OAS and MFS. PMID:18521281

  12. 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...

  13. 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.

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

    PubMed

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

    2016-06-01

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

  15. 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...

  16. 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...

  17. Correlation of Inter-Locus Polyglutamine Toxicity with CAG•CTG Triplet Repeat Expandability and Flanking Genomic DNA GC Content

    PubMed Central

    Nestor, Colm E.; Monckton, Darren G.

    2011-01-01

    Dynamic expansions of toxic polyglutamine (polyQ)-encoding CAG repeats in ubiquitously expressed, but otherwise unrelated, genes cause a number of late-onset progressive neurodegenerative disorders, including Huntington disease and the spinocerebellar ataxias. As polyQ toxicity in these disorders increases with repeat length, the intergenerational expansion of unstable CAG repeats leads to anticipation, an earlier age-at-onset in successive generations. Crucially, disease associated alleles are also somatically unstable and continue to expand throughout the lifetime of the individual. Interestingly, the inherited polyQ length mediating a specific age-at-onset of symptoms varies markedly between disorders. It is widely assumed that these inter-locus differences in polyQ toxicity are mediated by protein context effects. Previously, we demonstrated that the tendency of expanded CAG•CTG repeats to undergo further intergenerational expansion (their ‘expandability’) also differs between disorders and these effects are strongly correlated with the GC content of the genomic flanking DNA. Here we show that the inter-locus toxicity of the expanded polyQ tracts of these disorders also correlates with both the expandability of the underlying CAG repeat and the GC content of the genomic DNA flanking sequences. Inter-locus polyQ toxicity does not correlate with properties of the mRNA or protein sequences, with polyQ location within the gene or protein, or steady state transcript levels in the brain. These data suggest that the observed inter-locus differences in polyQ toxicity are not mediated solely by protein context effects, but that genomic context is also important, an effect that may be mediated by modifying the rate at which somatic expansion of the DNA delivers proteins to their cytotoxic state. PMID:22163004

  18. Metallic ion content and damage to the DNA in oral mucosa cells patients treated dental implants.

    PubMed

    López-Jornet, Pía; Perrez, Francisco Parra; Calvo-Guirado, José Luis; Ros-Llor, Irene; LLor-Ros, Irene; Ramírez-Fernández, Piedad

    2014-07-01

    The aim of this study was to assess the potential genotoxicity of dental implants, evaluating biomarkers of DNA damage (micronuclei and/or nuclear buds), cytokinetic defects (binucleated cells) and the presence of trace metals in gingival cells of patients with implants, comparing these with a control group. A total of 60 healthy adults (30 patients with dental implants and 30 control patients without) were included in the study. Medical and dental histories were made for each including life-style factors. Genotoxicity effects were assessed by micronucleus assays in the gingival epithelial cells of each patient; 1,000 epithelial cells were analyzed, evaluating the frequency of micronucleated cells and other nuclear anomalies. The concentration of metals (Al(27), Ag(107), Co (59), Cr (52), Cu(63), Fe(56), Sn(118), Mn(55), Mo(92), Ni(60), Pb(208), Ti(47)) were assayed by means of coupled plasma-mass spectrophotometry (ICP-MS). The frequency of micronuclei in the patient group with implants was higher than in the control group but without statistically significant differences (P > 0.05). Similar results were found for binucleated cells and nuclear buds (P > 0.05). For metals assayed by ICP-MS, significant differences were found for Ti(47) (P ≤ 0.045). Univariate analysis identified a significant association between the presence of micronuclei and age. Dental implants do not induce DNA damage in gingival cells, the slight effects observed cannot be indicated as biologically relevant.

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

    PubMed

    Inaba, Satomi; Fukada, Harumi; Oda, Masayuki

    2016-01-01

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

  20. Cryopreservation by encapsulation of Gentiana spp cell suspensions maintains regrowth, embryogenic competence and DNA content.

    PubMed

    Mikula, Anna; Olas, Marta; Sliwinska, Elwira; Rybczynski, Jan J

    2008-01-01

    A reliable technique for cryopreservation by encapsulation was developed for two suspension cultures of gentian species (Gentiana tibetica and G. cruciata) of different ages and embryogenic potential. The effect of water content, aggregate size and the subculture time on viability was determined by the 2,3,5-triphenyltetrazolium chloride (TTC) test. Regrowth of a proembryogenic mass (PEM) on agar, liquid or agar/liquid media was assayed by measuring the increase in biomass. A water content of 24-30% (fresh weight basis) after 5-6 h dehydration of encapsulated cells of gentians yielded the highest survival (68% for G. tibetica and 83% for G. cruciata) after cryopreservation. Regardless of species, aggregate size and subculture time, the lowest PEM survival was 44%. These parameters did not influence the survival of G. tibetica PEM, but the survival of G. cruciata was higher when the smaller aggregates were cryopreserved on the 5th day of culture. Agar/liquid culture caused the greatest biomass increase. Cryopreservation did not affect the characteristics of suspension cultures and their regrowth after thawing, nor the number and dynamics of somatic embryos formed. Flow cytometry showed that cryopreservation did not change the genome size of the PEMs or regenerants.

  1. Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A = T and G = C.

    PubMed

    Sueoka, N

    1999-07-01

    The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon position from Parity Rule 2 (PR2), where A = T and G = C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available, it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition, PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint.

  2. Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content.

    PubMed

    Houben, Andreas; Demidov, Dmitri; Gernand, Dorota; Meister, Armin; Leach, Carolyn R; Schubert, Ingo

    2003-03-01

    Strong methylation of lysine 4 (K4) and low methylation of lysine 9 (K9) have been proposed as modifications of histone H3, typical for transcriptionally active euchromatin and the opposite for inactive heterochromatin. We have analysed the correlation between the global distribution of histone H3, methylated at either lysine 4 or lysine 9, and of microscopically detectable euchromatic or heterochromatic regions in relation to genome size for 24 plant species. Two different distribution patterns of methylated (K9)H3 (Met(K9)H3) were found that depend on genome size. For most species with small genomes (1C <500 Mbp), including Arabidopsis thaliana, strong methylation of (K9)H3 was restricted to constitutive heterochromatin. Species with larger genomes showed a uniform distribution of Met(K9)H3. Contrary to this and regardless of the genome size, methylated (K4)H3 (Met(K4)H3) was found to be enriched within the euchromatin of all species. Transcriptionally less active B chromosomes showed the same patterns as basic A chromosomes. We thus propose that large genomes with high amounts of dispersed repetitive sequences (mainly retroelements) have to silence these sequences and therefore display epigenetic modifications such as methylation of DNA and (K9)H3 also within euchromatic regions.

  3. 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.

  4. 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.

  5. 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.

  6. Novel alterations in CDK1/cyclin B1 kinase complex formation occur during the acquisition of a polyploid DNA content.

    PubMed Central

    Datta, N S; Williams, J L; Caldwell, J; Curry, A M; Ashcraft, E K; Long, M W

    1996-01-01

    The pathways that regulate the S-phase events associated with the control of DNA replication are poorly understood. The bone marrow megakaryocytes are unique in that they leave the diploid (2C) state to differentiate, synthesizing 4 to 64 times the normal DNA content within a single nucleus, a process known as endomitosis. Human erythroleukemia (HEL) cells model this process, becoming polyploid during phorbol diester-induced megakaryocyte differentiation. The mitotic arrest occurring in these polyploid cells involves novel alterations in the cdk1/cyclin B1 complex: a marked reduction in cdk1 protein levels, and an elevated and sustained expression of cyclin B1. Endomitotic cells thus lack cdk1/cyclin B1-associated H1-histone kinase activity. Constitutive over-expression of cdk1 in endomitotic cells failed to re-initiate normal mitotic events even though cdk1 was present in a 10-fold excess. This was due to an inability of cyclin-B1 to physically associate with cdk1. Nonetheless, endomitotic cyclin B1 possesses immunoprecipitable H1-histone kinase activity, and specifically translocates to the nucleus. We conclude that mitosis is abrogated during endomitosis due to the absence of cdk1 and the failure to form M-phase promoting factor, resulting in a disassociation of mitosis from the completion of S-phase. Further studies on cyclin and its interacting proteins should be informative in understanding endomitosis and cell cycle control. Images PMID:8688553

  7. Bivariate flow cytometric analysis of DNA content versus immunopositivity for ribonucleotide reductase M1 subunit in the cell cycle.

    PubMed

    Mangiarotti, R; Bottone, M G; Danova, M; Pellicciari, C

    1998-06-01

    Ribonucleotide reductase (RR) is a cytoplasmatic enzyme catalyzing the reduction of all four ribonucleotides to their corresponding deoxyribonucleotides. Its activity strongly correlates to the rate of DNA synthesis. By using a specific monoclonal antibody against the large M1 subunit of RR, we assessed the expression of M1-RR versus DNA content by dual-parameter flow cytometry. The aim of this paper was to compare the variations in the immunopositivity for M1-RR during the cell cycle to the positivity for other cell cycle markers identifying either proliferating cells (Ki-67 and PCNA) or quiescent cells (statin). To do this, normal human embryonic fibroblasts in different growth conditions as well as several other mammalian cell lines (rat C6 glioma cells; mouse 3T3 fibroblasts and B16 melanoma cells; human epithelial EUE cells and mammary carcinoma MCF-7 cells) were used. The expression of M1-RR antigen was found to correlate positively with the expression of Ki-67 and PCNA, and negatively with the expression of statin. During early G1 phase, M1-RR becomes detectable by specific antibodies relatively later compared to PCNA and Ki-67; therefore, the lack of immunopositivity for M1-RR cannot be taken as an absolute indication of cell quiescence in G0.

  8. 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)

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

    PubMed

    Zaitlin, David; Pierce, Andrew J

    2010-12-01

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

  10. Nuclear DNA content of Vitis vinifera cultivars and ploidy level analyses of somatic embryo-derived plants obtained from anther culture.

    PubMed

    Leal, F; Loureiro, J; Rodriguez, E; Pais, M S; Santos, C; Pinto-Carnide, O

    2006-09-01

    Flow cytometry was employed to determine the ploidy level of Vitis vinifera L. somatic embryo-derived plants obtained from anther culture. Only one among the 41 analysed plants (2.4%) presented somaclonal variation (tetraploidy); the other plants were diploid. No significant differences (PDNA content of nine V. vinifera cultivars was also estimated using flow cytometry. A non-significant variation was found among the cultivars, with DNA content ranging from 1.17 pg/2C (cv. 'Tinta Barroca' and 'Viosinho') to 1.26 pg/2C (cv. 'Cabernet Sauvignon'). These results and previous studies on other Vitis species suggest that Vitis genome is stable with regard to nuclear DNA content.

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

    PubMed

    Tinti, F; Scali, V

    1992-11-01

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

  12. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position.

    PubMed

    Sueoka, N

    1999-09-30

    The genome of higher eukaryotes consists of genes having a widely heterogeneous base composition at the third codon position. Ubiquitous variability of the DNA base composition has the following two aspects: intragenomic heterogeneity of the G+C content and the amino-acid-specific translation-coupled biases from the Parity Rule 2 (PR2). PR2 is an intrastrand rule where A = T and G = C are expected if there is no bias in mutation and selection between the two complementary strands of DNA. To examine whether or not the biases from PR2 are responsible for the wide heterogeneity of the DNA G+C content in human, the third codon position of 846 human genes was analyzed. Genes were separated into six groups according to their G+C content of the third codon position, and each group was examined for the translation-coupled PR2 biases in the nucleotide composition of the third codon position for two- and four-codon amino acids. The results show that genes in the different G+C content groups have similar PR2 biases, indicating that the intragenomic heterogeneity of the G+C content is not correlated with translation-coupled biases from the PR2. Therefore, the heterogeneity of the G+C content is likely to be determined by some other mechanism (e.g. locally variable directional mutation pressures) than amino-acid-specific selections for the codon preference.

  13. Analysis of the polycyclic aromatic hydrocarbon content of petrol and diesel engine lubricating oils and determination of DNA adducts in topically treated mice by 32P-postlabelling.

    PubMed

    Carmichael, P L; Jacob, J; Grimmer, G; Phillips, D H

    1990-11-01

    Engine lubricating oils are known to accumulate carcinogenic polycyclic aromatic hydrocarbons (PAHs) during engine running. Oils from nine petrol-powered and 11 diesel-powered vehicles, in addition to samples of unused oil, were analysed for PAH content and ability to form DNA adducts when applied topically to mouse skin. The levels of 19 PAHs, determined by GC, were in total, approximately 22 times higher in used oils from petrol engines than in oils from diesel engines. Male Parkes mice were treated with 50 microliters of oil daily for 4 days before they were killed and DNA isolated from skin and lung tissue. DNA samples were analysed by nuclease P1-enhanced 32P-postlabelling. Used oils from both diesel and petrol engines showed several adduct spots on PEI-cellulose plates at total adduct levels of up to 0.57 fmol/microgram DNA [approximately 60 times greater than in experiments with samples of unused oil in which adduct levels (0.01-0.02 fmol adducts/microgram DNA) were close to the limit of detection]. Higher adduct levels were generally formed by petrol engine oils than by diesel engine oils. Lung DNA contained similar total adduct levels to those in skin although the adduct maps were less complex. Total adduct levels correlated with extent of oil use in the engine, the total PAH concentration in oils and with the concentrations of certain individual PAHs present in the oils. An adduct spot that co-eluted with that of the major benzo[a]pyrene-DNA adduct accounted for 9-26% of the total adducts in skin DNA, and approximately 8% of the adducts in lung DNA, of mice treated with petrol engine oils. A major, and as yet unidentified, adduct spot comprised up to 30% of the total adducts in skin DNA, and up to 89% of the total adducts in lung DNA, of these animals.

  14. Detection of rare circulating breast cancer cells by filtration cytometry and identification by DNA content: sensitivity in an experimental model.

    PubMed

    Rostagno, P; Moll, J L; Bisconte, J C; Caldani, C

    1997-01-01

    Current methods of detecting micrometastases in breast cancer fail in a large proportion of patients. Therefore an improved method for detection of metastases in blood samples could be of great clinical interest both for prognosis and selection of patients for adjuvant systemic therapy. We have developed a new non-invasive method which associates immuno-magnetic separation and filtration cytometry. The sensitivity of our procedure was evaluated in a model system using a mixture from a human breast cancer cell line (MCF-7) and a normal human blood sample. The identification of tumoral cells was achieved by measuring DNA content in comparison with standard cells. The lowest concentration of MCF-7 detected was 1 tumoral cell in 500,000 white blood cells. In addition, filtration cytometry provides a visual control of nuclei permitting the elimination of all doubtful cases and an automatic count of tumoral cells directly per ml of blood, which may be an independent predictor of early relapse. This new method may avoid unnecessary axillary lymph node dissection in patients with negative nodes. Our procedure seems suitable for the detection of rare circulating cells in routine laboratory testing and could be used in other applications.

  15. 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)

  16. 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.

  17. 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.

  18. 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.

  19. Quantification of meat proportions by measuring DNA contents in raw and boiled sausages using matrix-adapted calibrators and multiplex real-time PCR.

    PubMed

    Köppel, René; Eugster, Albert; Ruf, Jürg; Rentsch, Jürg

    2012-01-01

    The quantification of meat proportions in raw and boiled sausage according to the recipe was evaluated using three different calibrators. To measure the DNA contents from beef, pork, sheep (mutton), and horse, a tetraplex real-time PCR method was applied. Nineteen laboratories analyzed four meat products each made of different proportions of beef, pork, sheep, and horse meat. Three kinds of calibrators were used: raw and boiled sausages of known proportions ranging from 1 to 55% of meat, and a dilution series of DNA from muscle tissue. In general, results generated using calibration sausages were more accurate than those resulting from the use of DNA from muscle tissue, and exhibited smaller measurement uncertainties. Although differences between uses of raw and boiled calibration sausages were small, the most precise and accurate results were obtained by calibration with fine-textured boiled reference sausages.

  20. 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...

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

    PubMed

    Wisedchanwet, Trong; Wongphatcharachai, Manoosak; Boonyapisitsopa, Supanat; Bunpapong, Napawan; Kitikoon, Pravina; Amonsin, Alongkorn

    2011-03-21

    : 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 were characterized by whole genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis of all eight viral genes showed that the viruses clustered in the Eurasian lineage of influenza A viruses. Genetic analysis showed that H4N6 and H4N9 viruses display low pathogenic avian influenza characteristics. The HA cleavage site and receptor binding sites were conserved and resembled to LPAI viruses. This study is the first to report isolation of H4N6 and H4N9 viruses from birds in LBM in Thailand and shows the genetic diversity of the viruses circulating in the LBM. In addition, co-infection of H4N6 and H4N9 in the same Muscovy duck was observed.

  2. ProPSA and Diagnostic Biopsy Tissue DNA Content Combination Improves Accuracy to Predict Need for Prostate Cancer Treatment Among Men Enrolled in an Active Surveillance Program

    PubMed Central

    Isharwal, Sumit; Makarov, Danil V.; Sokoll, Lori J.; Landis, Patricia; Marlow, Cameron; Epstein, Jonathan I.; Partin, Alan W.; Carter, H. Ballentine; Veltri, Robert W.

    2015-01-01

    OBJECTIVES To assess a novel application of the Prostate Health Index (phi) and biopsy tissue DNA content in benign-adjacent and cancer areas to predict which patients would eventually require treatment of prostate cancer in the Proactive Surveillance cohort. METHODS We identified 71 men who had had serum and biopsy tissue from their diagnosis banked and available for the present study. Of the 71 patients, 39 had developed unfavorable biopsy findings and 32 had maintained favorable biopsy status during surveillance. The serum total prostate-specific antigen (tPSA), free PSA (fPSA) and [−2]proPSA were measured using the Beckman Coulter immunoassay. The DNA content measurements of Feulgen-stained biopsy sections were performed using the AutoCyte imaging system. RESULTS The ratio of phi was significantly greater (37.23 ± 15.76 vs 30.60 ± 12.28; P = .03) in men who ultimately had unfavorable biopsy findings. The serum phi ratio (P = .003), [−2]proPSA/%fPSA (P = .004), biopsy tissue DNA content (ie, benign-adjacent excess of optical density, P = .019; and cancer area standard deviation of optical density, P = .002) were significant predictors of unfavorable biopsy conversion on Cox regression analysis. However, phi and [−2]proPSA/%fPSA showed a highly significant correlation (rho = 0.927, P < .0001) and no difference in accuracy (c-index, 0.6247 vs 0.6158; P = .704) for unfavorable biopsy conversion prediction. Furthermore, phi and [−2]proPSA/%fPSA remained significant (P = .047 and P = .036, respectively) in the multivariate models and, combined with the biopsy tissue DNA content, showed improvement in the predictive accuracy (c-index, 0.6908 and 0.6884, respectively) for unfavorable biopsy conversion. CONCLUSIONS The Prostate Health Index to proPSA/%fPSA, combined with biopsy tissue DNA content, improved the accuracy to about 70% to predict unfavorable biopsy conversion at the annual surveillance biopsy examination among men enrolled in an Active

  3. 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.

  4. 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.

  5. 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

  6. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

    PubMed Central

    Kalinka, Anna; Poter, Paulina

    2017-01-01

    Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue. PMID:28149679

  7. Comparison Between Dust Particle Generation In CH4 or CH4/N2 Mixing RF Plasmas

    SciTech Connect

    Pereira, Jeremy; Massereau-Guilbaud, Veronique; Geraud-Grenier, Isabelle; Plain, Andre

    2005-10-31

    Dust particles have been spontaneously generated either in pure CH4 or in CH4/N2 r.f. plasmas. The dust particle formation results from homogeneous nucleation in the plasma and is detected by laser light scattering (Ar+, {lambda} = 514.5 nm). The temporal and spatial behaviour of dust particles is studied. In pure methane gas, particles are trapped in well defined clouds at the plasma sheath boundaries. In a CH4/N2 mixture, the nitrogen addition leads to an expansion of the clouds. For nitrogen contents higher than 50%, the space between the electrodes is nearly completely filled with dust particles leading to plasma instabilities and a void appears in the center of the discharge. The particles are spherical with diameters in the range 0.8-2 {mu}m. For nitrogen-rich plasmas, the particles growth is improved and leads to a rough shape with an orange-peel-type surface texture.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    1995-01-01

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

  11. Pyrroloquinoline quinone nutritional status alters lysine metabolism and modulates mitochondrial DNA content in the mouse and rat.

    PubMed

    Bauerly, K A; Storms, D H; Harris, C B; Hajizadeh, S; Sun, M Y; Cheung, C P; Satre, M A; Fascetti, A J; Tchaparian, E; Rucker, R B

    2006-11-01

    Pyrroloquinoline quinone (PQQ) added to purified diets devoid of PQQ improves indices of perinatal development in rats and mice. Herein, PQQ nutritional status and lysine metabolism are described, prompted by a report that PQQ functions as a vitamin-like enzymatic cofactor important in lysine metabolism (Nature 422 [2003] 832). Alternatively, we propose that PQQ influences lysine metabolism, but by mechanisms that more likely involve changes in mitochondrial content. PQQ deprivation in both rats and mice resulted in a decrease in mitochondrial content. In rats, alpha-aminoadipic acid (alphaAA), which is derived from alpha-aminoadipic semialdehyde (alphaAAS) and made from lysine in mitochondria, and the plasma levels of amino acids known to be oxidized in mitochondria (e.g., Thr, Ser, and Gly) were correlated with changes in the liver mitochondrial content of PQQ-deprived rats, but not PQQ-supplemented rats. In contrast, the levels of NAD dependent alpha-aminoadipate-delta-semialdehyde dehydrogenase (AASDH), a cytosolic enzyme important to alphaAA production from alphaAAS, was not influenced by PQQ dietary status. Moreover, the levels of U26 mRNA were not significantly changed even when diets differed markedly in PQQ and dietary lysine content. U26 mRNA levels were measured, because of U26's proposed, albeit questionable role as a PQQ-dependent enzyme involved in alphaAA formation.

  12. 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...

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  15. Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: substitutional bias and information content of transitions relative to transversions.

    PubMed

    Reeder, T W

    1995-06-01

    The phylogenetic relationships among 40 species, representing all genera, within the North American lizard family Phrynosomatidae were inferred from mitochondrial ribosomal RNA gene sequences. Cladistic analysis of the DNA sequence data (779 bp; 162 informative characters) supported the monophyly of the sand lizards (Callisaurus, Cophosaurus, Holbrookia, and Uma), Petrosaurus, Phrynosoma, Urosaurus, and Uta. All the species of Sceloporus, except S. variabilis and S. chrysostictus, formed a clade. Except for a sand lizard + Phrynosoma clade, the intergeneric relationships inferred from the mtDNA were largely incongruent with recent cladistic analyses based on morphology. Sceloporus group monophyly was not supported, with Petrosaurus being a member of a clade containing Sator, Sceloporus, and Urosaurus, to the exclusion of Uta. The phylogenetic placement of Uta was ambiguous. The substitutional bias in the phrynosomatid mitochondrial rDNA sequences was examined, as well as the phylogenetic information content of transitions relative to transversions. There appeared to be a lower transition bias than observed in other vertebrate sequences, with some classes of transversions occurring as frequently as G <-> A transitions. Transitions were no less informative for phylogeny reconstruction than transversions. Therefore, transitions should not be down-weighted in phylogenetic analysis, as is often done.

  16. 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.

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

    PubMed

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

    2012-07-01

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

  18. Simultaneous analysis of mitochondrial activity and DNA content in Ehrlich ascites tumor cells by dual parameter flow cytometry.

    PubMed

    Hämmerle, T; Löffler, M

    1989-01-01

    Ehrlich ascites tumor cells were permeabilized using low concentrations of digitonin, 8 micrograms/10(6) cells. Permeabilization was monitored by the assay of lactate dehydrogenase released into the incubation medium and of hexokinase partially bound to mitochondria. Integrity of the cellular organelles was unaffected as determined by assay of the mitochondrial enzyme glutamate dehydrogenase. Cells were stained with rhodamine 123 as a mitochondrial specific dye and propidium iodide/mithramycin as DNA specific dyes. The green fluorescence of bound rhodamine 123 versus red fluorescence of DNA in individual cells was analysed by dual parameter flow cytometry. Incubation of cells with inhibitors of mitochondrial energy metabolism, such as, potassium cyanide and carbonyl cyanide m-chlorophenylhydrazone abolished binding of rhodamine 123. Flow cytometric data allowed a correlation between cell position in the mitotic cycle with total mitochondrial activity. In addition, comparison of the characteristics of propidium iodide and ethidium bromide staining further elucidated the molecular basis of the staining with the positively-charged fluorescent dye rhodamine 123.

  19. Intraguild Predation Among Three Common Coccinellids (Coleoptera: Coccinellidae) in China: Detection Using DNA-Based Gut-Content Analysis.

    PubMed

    Yang, Fan; Wang, Qian; Wang, Dongmei; Xu, Bin; Xu, Jianxiang; Lu, Yanhui; Harwood, James D

    2016-12-26

    The ubiquity of intraguild predation (IGP) has been widely recognized for predatory coccinellids (Coleoptera: Coccinellidae). In Chinese agroecosystems, three species (Coccinella septempunctata L., Harmonia axyridis (Pallas), and Propylea japonica (Thunberg)) are particularly common, but there is little information of interactions occurring between them. In no-choice laboratory feeding trials, differential directional predation was observed between species: C. septempunctata preyed on eggs of P. japonica more than H. axyridis and H. axyridis consumed eggs of C. septempunctata and P. japonica equally, whereas P. japonica had a very low predation rate on eggs of the other two species. In choice trials, C. septempunctata and P. japonica larvae preyed less on H. axyridis eggs than those of P. japonica and C. septempunctata, respectively, contrasting with H. axyridis larvae, which showed similar preference for both species. Species-specific primers were developed for each coccinellid and used to determine the relative frequency of prey consumption in the field. Prior to field-based analysis, primer specificity was confirmed and consumption of prey elicited a positive reaction success, and detection time varied between different predator-prey combinations. Predators were then collected from cotton agroecosystems and, interestingly, no DNA of C. septempunctata was found in P. japonica, but all other predator-prey combinations yielded positive documentation of IGP in the field, with the greatest rate of 9% of C. septempunctata testing positive for H. axyridis DNA. This study confirmed the frequency of IGP among three common coccinellids in Chinese agroecosystems and the likelihood for interference to the biological control services provided by these important natural enemies.

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

    PubMed

    De Weert, Jasperien P A; Viñas, Marc; Grotenhuis, Tim; Rijnaarts, Huub H M; Langenhoff, Alette A M

    2011-02-01

    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.

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

    PubMed

    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

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

    DOE PAGES

    Georgescu, Walter; Osseiran, Alma; Rojec, Maria; ...

    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

  3. 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

  4. 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

  5. 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.

  6. Consequences of stoichiometric error on nuclear DNA content evaluation in Coffea liberica var. dewevrei using DAPI and propidium iodide.

    PubMed

    Noirot, Michel; Barre, Philippe; Louarn, Jacques; Duperray, Christophe; Hamon, Serge

    2002-04-01

    The genome size of coffee trees (Coffea sp.) was assessed using flow cytometry. Nuclear DNA was stained with two dyes [4',6-diamino-2-phenylindole dihydrochloride hydrate (DAPI) and propidium iodide (PI)]. Fluorescence in coffee tree nuclei (C-PI or C-DAPI) was compared with that of the standard, petunia (P-PI or P-DAPI). If there is no stoichiometric error, then the ratio between fluorescence of the target nuclei and that of the standard nuclei (R-PI or R-DAPI) is expected to be proportional to the genome size. Between-tree differences in target : standard fluorescence ratios were noted in Coffea liberica var. dewevrei using propidium iodide and DAPI. For both dyes, between-tree differences were due to a lack of proportionality when comparing locations of the coffee peak and the petunia peak. Intraspecific genome size variations clearly cannot explain variations in the target : standard fluorescence ratio. The origin of the lack of proportionality between target and standard fluorescences differed for the two dyes. With propidium iodide, there was a regression line convergence point, and no between-tree differences were noted in this respect, whereas there was no such convergence with DAPI. An accurate estimate of genome size can thus be obtained with PI. Implications with respect to accessibility and binding mode are discussed.

  7. Consequences of Stoichiometric Error on Nuclear DNA Content Evaluation in Coffea liberica var. dewevrei using DAPI and Propidium Iodide

    PubMed Central

    NOIROT, MICHEL; BARRE, PHILIPPE; LOUARN, JACQUES; DUPERRAY, CHRISTOPHE; HAMON, SERGE

    2002-01-01

    The genome size of coffee trees (Coffea sp.) was assessed using flow cytometry. Nuclear DNA was stained with two dyes [4′,6‐diamino‐2‐phenylindole dihydrochloride hydrate (DAPI) and propidium iodide (PI)]. Fluorescence in coffee tree nuclei (C‐PI or C‐DAPI) was compared with that of the standard, petunia (P‐PI or P‐DAPI). If there is no stoichiometric error, then the ratio between fluorescence of the target nuclei and that of the standard nuclei (R‐PI or R‐DAPI) is expected to be proportional to the genome size. Between‐tree differences in target : standard fluorescence ratios were noted in Coffea liberica var. dewevrei using propidium iodide and DAPI. For both dyes, between‐tree differences were due to a lack of proportionality when comparing locations of the coffee peak and the petunia peak. Intraspecific genome size variations clearly cannot explain variations in the target : standard fluorescence ratio. The origin of the lack of proportionality between target and standard fluorescences differed for the two dyes. With propidium iodide, there was a regression line convergence point, and no between‐tree differences were noted in this respect, whereas there was no such convergence with DAPI. An accurate estimate of genome size can thus be obtained with PI. Implications with respect to accessibility and binding mode are discussed. PMID:12096798

  8. Air pollution particles mediated oxidative DNA base damage in a cell free system and in human airway epithelial cells in relation to particulate metal content and bioreactivity.

    PubMed

    Prahalad, A K; Inmon, J; Dailey, L A; Madden, M C; Ghio, A J; Gallagher, J E

    2001-07-01

    Epidemiological studies demonstrate an association between increased human morbidity and mortality with exposure to air pollution particulate matter. We hypothesized that such effects may be associated with the ability of the particles to mediate generation of reactive oxygen species (ROS), either directly, via interaction with ambient oxygen or indirectly through initiation of an oxidative burst in phagocytes. To test this hypothesis, we determined 8-oxo-dG formation as a measure of direct generation of ROS, in response to particulate exposures to 2'-deoxyguanosine (dG), free and in calf thymus DNA in aerated solutions as the target molecule and cell culture, to assess the relationship between induction of oxidative damage, particulate metal content and metal bioreactivity. The HPLC-ECD technique was employed for separation and quantification of 8-oxo-dG, the most widely recognized marker of DNA oxidation. Particles used in this study include: Arizona desert dust (AZDD), coal fly ash (CFA and ECFA), oil fly ash (OFA and ROFA), and ambient air [SRM 1649 and Dusseldorf (DUSS), Germany]. The major difference between these particles is the concentration of water-soluble metals. The fly ash particulates OFA and ROFA showed a significant dose-dependent increase in dG hydroxylation to 8-oxo-dG formation over the control dG (p < 0.05), with yields 0.03 and 1.25% at the highest particulate concentration (1 mg/mL). Metal ion chelators and DMSO, a hydroxyl radical scavenger, inhibited this hydroxylation. In contrast, desert dust, coal fly ash and urban air particles induced 8-oxo-dG with yields ranging from 0.003 to 0.006%, respectively, with levels unaffected by pretreatment of the particles with metal ion chelators or addition of DMSO to the incubation mixture. When calf thymus DNA was used as a substrate, all the particles induced 8-oxo-dG in a pattern similar to that observed for dG hydroxylation, but with relatively less yield. Treatment of the particles with metal ion

  9. [Cell kinetic analysis of human brain tumors by bivariate flow cytometric measurement of cellular DNA content and amount of incorporated bromodeoxyuridine].

    PubMed

    Okuda, Y; Taomoto, K; Saya, H; Ijichi, A; Kudo, H; Kokunai, T; Tamaki, N; Matsumoto, S

    1989-04-01

    Cell kinetics of 91 human brain tumors obtained from 88 patients were analyzed with the following two methods, 1) bivariate (two-color) flow cytometric measurement of cellular DNA content and amount of bromodeoxyuridine (BrdU) incorporated into cellular DNA, in 66 specimens, 2) immunohistochemical detection of BrdU incorporated S-phase cells, in 34 specimens. Patients were given an intravenous 1 hour infusion of 200 mg/sq. m. of BrdU 1-2 hours before the surgical removal. The excised tumor specimen was divided into several portions. One was fixed with 70% ethanol and embedded in paraffin, and another was digested mechanically and/or chemically to obtain a single cell suspension, and fixed in 70% ethanol. Paraffin-embedded tissue sections were stained by the peroxidase-antiperoxidase immunohistochemical method using anti-BrdU monoclonal antibody (MoAb). Single cell suspensions were reacted with fluorescein isothiocyanate (FITC) conjugated anti-BrdU MoAb, or anti-BrdU MoAb and FITC-conjugated second antibody successively by the staining with propidium iodide, for flow cytometry (FCM). Rates of S-phase fraction in single cell suspensions calculated by bivariate FCM were correlated well with labeling indexes (LI, i.e. the percentage of BrdU incorporated cells) calculated in tissue sections, but not with the result of analysis of DNA histogram by Dean's method. This discrepancy is probably due to large coefficient value in several samples. Histological malignancy of the tumors was reflected both in the proliferating index (PI, i.e. % S+G2M phase) calculated by bivariate FCM and the LI by immunohistochemical method. PI tended to be high in primitive neuroectodermal tumors and metastatic carcinomas, moderately high in gliomas, and low in benign tumor groups.(ABSTRACT TRUNCATED AT 250 WORDS)

  10. Assessment of polyphenolic content, antioxidant activity, protection against ROS-induced DNA damage and anticancer activity of Vitis vinifera stem extracts.

    PubMed

    Apostolou, Anna; Stagos, Dimitrios; Galitsiou, Elissavet; Spyrou, Argiris; Haroutounian, Serko; Portesis, Nikolaos; Trizoglou, Ioanna; Wallace Hayes, A; Tsatsakis, Aristides M; Kouretas, Dimitrios

    2013-11-01

    Grape extracts and wine have been studied widely due to their beneficial effects on human health. However, there are only few studies from grape stems extracts. Therefore, the main objective of the present study was the assessment in stem extracts from Greek Vitis vinifera varieties of the total polyphenolic content (TPC), the identification of the polyphenols present in them, and the evaluation of their antioxidant activity, protection against ROS-induced DNA damage and inhibition of liver (HepG2) and cervical (HeLa) cancer cell growth. The range of the TPC in grape stem extracts was from 345 to 584 mg GAE/g dry weight. Moreover, stem extracts contained different classes of polyphenols as flavonols, flavanols, procyanidins, phenolic acids and stilbenes. In DPPH and ABTS assays, the IC50 values of the stem extracts had an average of 7.8 ± 2.8 and 5.4 ± 2.6 μg/mL respectively. Also, all stem extracts inhibited OH- and ROO-induced DNA damage dose dependent with average IC50 values of 478 ± 217 and 1.15 ± 0.85 μg/mL respectively. Furthermore, stem extracts inhibited at low concentrations the growth of HepG2 and HeLa cancer cells with average IC50 values of 50 ± 12 and 32 ± 16 μg/mL respectively. The above activities of grape stem extracts were comparable to those of seed extracts.

  11. Tertiary amine N-oxides as bioreductive drugs: DACA N-oxide, nitracrine N-oxide and AQ4N.

    PubMed Central

    Wilson, W. R.; Denny, W. A.; Pullen, S. M.; Thompson, K. M.; Li, A. E.; Patterson, L. H.; Lee, H. H.

    1996-01-01

    Tertiary amine N-oxides of DNA intercalators with alkylamino sidechains are a new class of bioreductive drugs. N-oxidation masks the cationic charge of the amines, forming prodrugs with low DNA binding affinity and low toxicity which can be activated selectively by metabolic reduction under hypoxic conditions. This study compares three intercalator N-oxides (NC-NO, DACA-NO and AQ4N), which, respectively, give nitracrine (NC), DACA and AQ4 on reduction. In aerobic cell culture all three N-oxide were much less toxic than the corresponding amines, and showed large increases in cytotoxicity under hypoxia. The topoisomerase poisons DACA and AQ4 (and their N-oxides) were less active against non-cycling than cycling cells. However, only AQ4N was active against the mouse mammary tumour MDAH-MCa-4. This dialkylaminoanthraquinone-di-N-oxide has activity at least as great as the reference bioreductive drug RB 6145 against this tumour, both with and without radiation and when combined with the tumour blood flow inhibitor 5,6-dimethylxanthenone-4-acetic acid (DMXAA). It is suggested that the high in vivo activity of AQ4N relative to the other topoisomerase-targeted N-oxide, DACA-NO, may be in part due to release in hypoxic cells of an intracalator with sufficiently high DNA binding affinity that it is retained long enough to kill non-cycling cells when they eventually re-enter the cell cycle. PMID:8763844

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

    NASA Astrophysics Data System (ADS)

    Li, Wentian; Holste, Dirk

    2005-04-01

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

  13. 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.

  14. DNA content, chromatin supraorganization, nuclear glycoproteins and RNA amounts in hepatocytes of mice expressing insulin-dependent diabetes.

    PubMed

    Mello, Maria Luiza S; Aldrovani, Marcela; Moraes, Alberto Silva; Guaraldo, Ana Maria Aparecida; Vidal, Benedicto de Campos

    2009-01-01

    Chromatin supraorganization and extensibility and nuclear glycoprotein content have been reported to change in hepatocytes from mice during development and aging, as well as under starvation and refeeding conditions. In non-obese diabetic (NOD) mice, the expression of insulin-dependent diabetes may be accompanied by metabolic changes in the liver. These changes are likely to be similar to those involved in the aging processes of non-diabetic animals. Therefore, we hypothesized that the chromatin organization, as well as the physical properties and compositions of hepatocyte nuclei would also be affected in NOD mice in the same way as those in aged non-diabetic mice. Nuclear image parameters were evaluated by image analysis of Feulgen-stained preparations. Chromatin extensibility in response to gravity was observed with polarized light after lysis and toluidine blue staining. The Con-A response of nuclear glycoproteins was evaluated with scanning microspectrophotometry. These characteristics were assessed using hepatocyte imprints from female NOD mice after a 28-day period of diabetes expression. Observations and measurements were made in comparison to healthy BALB/c mice. Total RNA amounts were determined for livers of NOD and BALB/c mice. Enhanced polyploidy levels, a decrease in chromatin higher-order packing states, an increased frequency of extended chromatin fiber formation, and deeper Con-A-responsive chromatin areas were observed in the hepatocytes of the NOD mice expressing insulin-dependent diabetes. Reduced amounts of total RNA were also found in the livers of these mice. Our findings for NOD mice expressing insulin-dependent diabetes are consistent with previously reported data for old-aged mice of the inbred strain A/Uni and may reflect changes in transcriptional activities associated with the stressful physiological demands on the liver during the expression of diabetes.

  15. Stereoselective Synthesis of α- and β-l-Ara4N Glycosyl H-Phosphonates and a Neoglycoconjugate Comprising Glycosyl Phosphodiester Linked β-l-Ara4N

    PubMed Central

    2016-01-01

    Stereoselective synthesis of variably protected α- and β-l-Ara4N glycosyl H-phosphonates as key intermediates in the syntheses of β-l-Ara4N-modified LPS structures and α-l-Ara4N-containing biosynthetic precursors is reported. A facile one-pot approach toward β-l-Ara4N glycosyl H-phosphonates includes anomeric deallylation of protected 4-azido β-l-Ara4N via terminal olefin isomerization followed by ozonolysis and methanolysis of formyl groups to furnish exclusively β-configured lactols that are phosphitylated with retention of configuration. The carbohydrate epitope of β-l-Ara4N-modified Lipid A, βGlcN(1→6)αGlcN(1→P←1)β-l-Ara4N, was stereoselectively synthesized and linked to maleimide-activated bovine serum albumin. PMID:28009171

  16. 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

  17. Cholera toxin treatment of vascular smooth muscle cells decreases smooth muscle α-actin content and abolishes the platelet-derived growth factor-BB-stimulated DNA synthesis

    PubMed Central

    Sachinidis, Agapios; Seul, Claudia; Gouni-Berthold, Ioanna; Seewald, Stefan; Ko, Yon; Vetter, Hans; Fingerle, Jürgen; Hoppe, Jürgen

    2000-01-01

    The second messenger cyclic AMP regulates diverse biological processes such as cell morphology and cell growth. We examined the role of the second messenger cyclic AMP on rat aortic vascular smooth muscle cell (VSMC) morphology and the intracellular transduction pathway mediated by platelet-derived growth factor β-receptor (PDGF-Rβ). The effect of PDGF-BB on VSMCs growth was assessed by [3H]-thymidine incorporation. Tyrosine phosphorylation of PDGF-Rβ, PLC-γ1, ERK1 and ERK2, p125FAK and paxillin as well as Sm α-actin was examined by the chemiluminescence Western blotting method. Actin mRNA level was quantitated by Northern blotting. Visualization of Sm α-actin filaments, paxillin and PDGF-Rβ was performed by immunfluorescence microscopy. Cholera toxin (CTX; 10 nM) treatment lead to a large and sustained increase in the cyclic AMP concentration after 2 h which correlated with change of VSMC morphology including complete disruption of the Sm α-actin filament array and loss of focal adhesions. Treatment of VSMCs with CTX did not influence tyrosine phosphorylation of p125FAK and paxillin but decreased the content of a Sm α-actin protein. Maximal decrease of 70% was observed after 24 h of treatment. CTX also caused a 90% decrease of the actin mRNA level. CTX treatment completely abolished PDGF-BB stimulated DNA-synthesis although PDGF-Rβ level and subcellular distribution and translocation was not altered. Furthermore CTX attenuated the PDGF-BB-induced tyrosine phosphorylation of the PDGF-Rβ, PI 3′-K, PLC-γ1 and ERK1/2 indicating an action of cyclic AMP on PDGF-β receptor. We conclude that although cyclic AMP attenuates the PDGF-Rβ mediated intracellular transduction pathway, an intact actin filament may be required for the PDGF-BB-induced DNA synthesis in VSMCs. PMID:10928958

  18. 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.

  19. 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

  20. 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

  1. Changes in nucleus, nucleolus and cell size accompanying somatic embryogenesis of Theobroma cacao L. I. Relationship between DNA and total protein content and size of nucleus, nucleolus and cell.

    PubMed

    Kononowicz, H; Janick, J

    1988-01-01

    There was a linear relation between an increase in DNA content and size of nuclei, nucleoli and cells in callus and proembryos (Theobroma cacao L.). In callus the increase of DNA content was accompanied by proportional increase in nuclear size whereas in proembryos the increase in nuclear size did not match the increasing amount of DNA. The stimulation of embryogenesis by 10(-2) mg/l 2,4-D was associated with increase in nuclear and nucleolar size and with decrease in cell sizes. Inhibition of embryogenesis by 1.0 mg/l 2,4-D+10% coconut water did not change nuclear size, but increased cell size in relation to the control. The process of embryo formation was accompanied by changes in relationship between nuclear, nucleolar and cell size and the total (DNFB-stained) proteins content. In callus as well as in proembryo the increase in total protein content in nucleus was not equivalent to the increasing sizes of nuclei which leads to the decrease in nuclear protein concentration. Similar situation was observed for nucleoli. Differences were found in the concentration of cytoplasmic proteins between the callus and proembryo cells. The stimulation of embryogenesis by low concentration of 2,4-D resulted in decrease in concentration of total proteins in nuclei and nucleoli and the increase in cytoplasm.

  2. Effect of CoCl₂ on the content of different metals and a relative activity of DNA-hydrolyzing abzymes in the blood plasma of mice.

    PubMed

    Legostaeva, Galina A; Zaksas, Nataliya P; Gluhcheva, Yordanka G; Sedykh, Sergey E; Madzharova, Maria E; Atanassova, Nina N; Buneva, Valentina N; Nevinsky, Georgy A

    2013-01-01

    Cobalt is a transition metal and an essential trace element that is required for vitamin B₁₂ biosynthesis, enzyme activation, and so on but is toxic in high concentrations. It was shown that the content of different elements in the plasma of 2-month-old BALB/c mice (control group) decreased in the following order: Ca > Mg > Si > Fe > Zn > Cu ≥ Al ≥ B. The treatment of mice with CoCl₂ did not appreciably change the relative content of Ca, Cu, and Zn, but a significant increase in the content of B (2.3-fold), Mg (1.5-fold), Al and Fe (2.1-fold), and Si (3.4-fold) was found. The treatment of mice led to a 2.2-fold decrease in the concentration of the total blood protein and a 1.7 ± 0.2-fold decrease of total immunoglobulin Gs (IgGs). Deoxyribonuclease IgGs corresponding to mice treated (t-IgGs) and non-treated (nt-IgGs) with CoCl₂ contained intrinsically bound metal ions; these IgGs hydrolyzed DNA with very low activity but were not active in the presence of ethylenediaminetetraacetic acid or after Ab dialysis against ethylenediaminetetraacetic acid. The average RAs of deoxyribonuclease nt-IgGs increased after addition of external metal ions in the following order: Zn²⁺< Ca²⁺ < Cu²⁺ < Fe²⁺ < Mn²⁺ < Mg²⁺ < Co²⁺ < Ni²⁺. Interestingly, t-IgGs demonstrated lower activities than those for nt-IgGs either in the absence of external metal ions (2.7-fold) or in the presence of Cu²⁺ (9.5-fold) > Co²⁺ (5.6-fold) > Zn²⁺ (5.1-fold) > Mg²⁺ (4.1-fold) > Ca²⁺ (3.0-fold) > Fe²⁺ (1.3-fold). However, the RAs of t-IgGs were remarkably more active than nt-IgGs in the presence of best activators of t-IgGs Ni²⁺ (1.4-fold) and especially Mn²⁺ (2.2-fold). The data may be useful for an understanding of Co toxicity, its effect on the concentration of other metal ions, and a change of metal-dependent specificity of Abzs.

  3. DNA systematics. Volume II

    SciTech Connect

    Dutta, S.K.

    1986-01-01

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

  4. Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail

    PubMed Central

    Ludwigsen, Johanna; Pfennig, Sabrina; Singh, Ashish K; Schindler, Christina; Harrer, Nadine; Forné, Ignasi; Zacharias, Martin; Mueller-Planitz, Felix

    2017-01-01

    ISWI-family nucleosome remodeling enzymes need the histone H4 N-terminal tail to mobilize nucleosomes. Here we mapped the H4-tail binding pocket of ISWI. Surprisingly the binding site was adjacent to but not overlapping with the docking site of an auto-regulatory motif, AutoN, in the N-terminal region (NTR) of ISWI, indicating that AutoN does not act as a simple pseudosubstrate as suggested previously. Rather, AutoN cooperated with a hitherto uncharacterized motif, termed AcidicN, to confer H4-tail sensitivity and discriminate between DNA and nucleosomes. A third motif in the NTR, ppHSA, was functionally required in vivo and provided structural stability by clamping the NTR to Lobe 2 of the ATPase domain. This configuration is reminiscent of Chd1 even though Chd1 contains an unrelated NTR. Our results shed light on the intricate structural and functional regulation of ISWI by the NTR and uncover surprising parallels with Chd1. DOI: http://dx.doi.org/10.7554/eLife.21477.001 PMID:28109157

  5. [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.

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

    PubMed

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

    2011-08-01

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

  7. An improved, non-isotopic method of screening cells from patients with abnormalities of sexual differentiation for Y chromosomal DNA content.

    PubMed Central

    Witt, M; Michalczak, K; Latos-Bielenska, A; Jaruzelska, J; Kuczora, I; Lopez, M

    1993-01-01

    The detection of 45,X/46,XY mosaicism in patients with abnormalities of sexual differentiation is of crucial diagnostic importance. Here we present application of a PCR based method of detection of alphoid repeats of Y chromosomal origin. The method detects 0.01% of male DNA on a female DNA background. Out of 28 patients studied, in all cases where the Y chromosome or a part of it containing centromeric sequences was present, a positive amplification signal of Y chromosomal alphoid repeats was detected. In five cases the Y origin of marker chromosomes was diagnosed. The pattern of amplification signal distribution of the SRY gene was identical to that of Y specific alphoid primers, which confirms applicability of this method in the molecular diagnostic laboratory. The other diagnostic advantage is the ability to use dried blood specimens as an easy to handle and efficient source of DNA. Images PMID:8487276

  8. An improved, non-isotopic method of screening cells from patients with abnormalities of sexual differentiation for Y chromosomal DNA content.

    PubMed

    Witt, M; Michalczak, K; Latos-Bielenska, A; Jaruzelska, J; Kuczora, I; Lopez, M

    1993-04-01

    The detection of 45,X/46,XY mosaicism in patients with abnormalities of sexual differentiation is of crucial diagnostic importance. Here we present application of a PCR based method of detection of alphoid repeats of Y chromosomal origin. The method detects 0.01% of male DNA on a female DNA background. Out of 28 patients studied, in all cases where the Y chromosome or a part of it containing centromeric sequences was present, a positive amplification signal of Y chromosomal alphoid repeats was detected. In five cases the Y origin of marker chromosomes was diagnosed. The pattern of amplification signal distribution of the SRY gene was identical to that of Y specific alphoid primers, which confirms applicability of this method in the molecular diagnostic laboratory. The other diagnostic advantage is the ability to use dried blood specimens as an easy to handle and efficient source of DNA.

  9. Fate of tetraploid cells in 4n<-->2n chimeric mouse blastocysts.

    PubMed

    Mackay, Gillian E; West, John D

    2005-12-01

    Previous studies have shown that tetraploid (4n) cells rarely contribute to the derivatives of the epiblast lineage of mid-gestation 4n<-->2n mouse chimeras. The aim of the present study was to determine when and how 4n cells were excluded from the epiblast lineage of such chimeras. The contributions of GFP-positive cells to different tissues of 4n<-->2n chimeric blastocysts labelled with tauGFP were analysed at E3.5 and E4.5 using confocal microscopy. More advanced E5.5 and E7.5 chimeric blastocysts were analysed after a period of diapause to allow further growth without implantation. Tetraploid cells were not initially excluded from the epiblast in 4n<-->2n chimeric blastocysts and they contributed to all four blastocyst tissues at all of the blastocyst stages examined. Four steps affected the allocation and fate of 4n cells in chimeras, resulting in their exclusion from the epiblast lineage by mid-gestation. (1) Fewer 4n cells were allocated to the inner cell mass than trophectoderm. (2) The blastocyst cavity tended to form among the 4n cells, causing more 4n cells to be allocated to the hypoblast and mural trophectoderm than the epiblast and polar trophectoderm, respectively. (3) 4n cells were depleted from the hypoblast and mural trophectoderm, where initially they were relatively enriched. (4) After implantation 4n cells must be lost preferentially from the epiblast lineage. Relevance of these results to the aetiology of human confined placental mosaicism and possible implications for the interpretation of mouse tetraploid complementation studies of the site of gene action are discussed.

  10. Different rates of DNA replication at early versus late S-phase sections: multiscale modeling of stochastic events related to DNA content/EdU (5-ethynyl-2'deoxyuridine) incorporation distributions.

    PubMed

    Li, Biao; Zhao, Hong; Rybak, Paulina; Dobrucki, Jurek W; Darzynkiewicz, Zbigniew; Kimmel, Marek

    2014-09-01

    Mathematical modeling allows relating molecular events to single-cell characteristics assessed by multiparameter cytometry. In the present study we labeled newly synthesized DNA in A549 human lung carcinoma cells with 15-120 min pulses of EdU. All DNA was stained with DAPI and cellular fluorescence was measured by laser scanning cytometry. The frequency of cells in the ascending (left) side of the "horseshoe"-shaped EdU/DAPI bivariate distributions reports the rate of DNA replication at the time of entrance to S phase while their frequency in the descending (right) side is a marker of DNA replication rate at the time of transition from S to G2 phase. To understand the connection between molecular-scale events and scatterplot asymmetry, we developed a multiscale stochastic model, which simulates DNA replication and cell cycle progression of individual cells and produces in silico EdU/DAPI scatterplots. For each S-phase cell the time points at which replication origins are fired are modeled by a non-homogeneous Poisson Process (NHPP). Shifted gamma distributions are assumed for durations of cell cycle phases (G1, S and G2 M), Depending on the rate of DNA synthesis being an increasing or decreasing function, simulated EdU/DAPI bivariate graphs show predominance of cells in left (early-S) or right (late-S) side of the horseshoe distribution. Assuming NHPP rate estimated from independent experiments, simulated EdU/DAPI graphs are nearly indistinguishable from those experimentally observed. This finding proves consistency between the S-phase DNA-replication rate based on molecular-scale analyses, and cell population kinetics ascertained from EdU/DAPI scatterplots and demonstrates that DNA replication rate at entrance to S is relatively slow compared with its rather abrupt termination during S to G2 transition. Our approach opens a possibility of similar modeling to study the effect of anticancer drugs on DNA replication/cell cycle progression and also to quantify other

  11. Why are [P(C6H5)4](+)N3- and [As(C6H5)4](+)N3- ionic salts and Sb(C6H5)4N3 and Bi(C6H5)4N3 covalent solids? A theoretical study provides an unexpected answer.

    PubMed

    Christe, Karl O; Haiges, Ralf; Boatz, Jerry A; Jenkins, H Donald Brooke; Garner, Edward B; Dixon, David A

    2011-04-18

    A recent crystallographic study has shown that, in the solid state, P(C(6)H(5))(4)N(3) and As(C(6)H(5))(4)N(3) have ionic [M(C(6)H(5))(4)](+)N(3)(-)-type structures, whereas Sb(C(6)H(5))(4)N(3) exists as a pentacoordinated covalent solid. Using the results from density functional theory, lattice energy (VBT) calculations, sublimation energy estimates, and Born-Fajans-Haber cycles, it is shown that the maximum coordination numbers of the central atom M, the lattice energies of the ionic solids, and the sublimation energies of the covalent solids have no or little influence on the nature of the solids. Unexpectedly, the main factor determining whether the covalent or ionic structures are energetically favored is the first ionization potential of [M(C(6)H(5))(4)]. The calculations show that at ambient temperature the ionic structure is favored for P(C(6)H(5))(4)N(3) and the covalent structures are favored for Sb(C(6)H(5))(4)N(3) and Bi(C(6)H(5))(4)N(3), while As(C(6)H(5))(4)N(3) presents a borderline case.

  12. 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.

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

    PubMed Central

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

    2015-01-01

    The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k (‘k-mers’). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. PMID:25378322

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

    PubMed

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

    2015-01-01

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

  15. Internal validation of the DNAscan/ANDE™ Rapid DNA Analysis™ platform and its associated PowerPlex(®) 16 high content DNA biochip cassette for use as an expert system with reference buccal swabs.

    PubMed

    Moreno, Lilliana I; Brown, Alice L; Callaghan, Thomas F

    2017-03-31

    Rapid DNA platforms are fully integrated systems capable of producing and analyzing short tandem repeat (STR) profiles from reference sample buccal swabs in less than two hours. The technology requires minimal user interaction and experience making it possible for high quality profiles to be generated outside an accredited laboratory. The automated production of point of collection reference STR profiles could eliminate the time delay for shipment and analysis of arrestee samples at centralized laboratories. Furthermore, point of collection analysis would allow searching against profiles from unsolved crimes during the normal booking process once the infrastructure to immediately search the Combined DNA Index System (CODIS) database from the booking station is established. The DNAscan/ANDE™ Rapid DNA Analysis™ System developed by Network Biosystems was evaluated for robustness and reliability in the production of high quality reference STR profiles for database enrollment and searching applications. A total of 193 reference samples were assessed for concordance of the CODIS 13 loci. Studies to evaluate contamination, reproducibility, precision, stutter, peak height ratio, noise and sensitivity were also performed. The system proved to be robust, consistent and dependable. Results indicated an overall success rate of 75% for the 13 CODIS core loci and more importantly no incorrect calls were identified. The DNAscan/ANDE™ could be confidently used without human interaction in both laboratory and non-laboratory settings to generate reference profiles.

  16. 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.

  17. Prevention of mammalian DNA reduplication, following the release from the mitotic spindle checkpoint, requires p53 protein, but not p53-mediated transcriptional activity.

    PubMed

    Notterman, D; Young, S; Wainger, B; Levine, A J

    1998-11-26

    The tumor suppressor p53 has been identified as a component of a mitotic spindle checkpoint. When exposed to a spindle-disrupting drug such as nocodazole, fibroblasts derived from mice having wild-type p53 are blocked with a 4N content of DNA. Conversely, fibroblasts from p53-deficient mice become polyploid. To learn if transcriptional activation of downstream genes by p53 plays a role in this putative checkpoint, three cell lines were exposed to nocodazole. In one line, p53 protein is not expressed, while the other two cell lines over-express p53. In one of these two lines, the N-terminal transactivation domain is wild-type and in the second, this region contains a mutation that eliminates the ability of the protein to act as a transcription factor. Incubation with nocodazole of cells containing wild-type p53 results in accumulation of both 2N and 4N populations of cells. Under the same conditions, cells containing a transactivation-deficient mutant of p53 accumulate a 4N population of cells, but not a 2N population of cells. Cells entirely deficient in p53 protein become hyperdiploid, and display 8N to 16N DNA content. In all three cell lines, nocodazole elicited an initial increase in mitotic cells, but within 24 h the mitotic index returned to baseline. Expression patterns of cyclins B and D indicated that following entry into mitosis, the cells returned to a G1 state but with 4N DNA content. Subsequent re-duplication of DNA beyond 4N is prevented in cells containing either wild-type or transcriptionally inactive p53 protein. In cells entirely lacking p53 protein, DNA is re-duplicated (without an intervening mitosis) and the cells become hyperdiploid. These experiments indicate that p53 does not participate in the transient mitotic arrest that follows spindle disruption, but is essential to prevent subsequent reduplication of DNA and the resulting hyperdiploid state. This function is intact in a mutant that is transcriptionally inactive.

  18. Fatty acid 16:4(n-3) stimulates a GPR120-induced signaling cascade in splenic macrophages to promote chemotherapy resistance

    PubMed Central

    Houthuijzen, Julia M.; Oosterom, Ilse; Hudson, Brian D.; Hirasawa, Akira; Daenen, Laura G. M.; McLean, Chelsea M.; Hansen, Steffen V. F.; van Jaarsveld, Marijn T. M.; Peeper, Daniel S.; Jafari Sadatmand, Sahar; Roodhart, Jeanine M. L.; van de Lest, Chris H. A.; Ulven, Trond; Ishihara, Kenji; Milligan, Graeme; Voest, Emile E.

    2017-01-01

    Although chemotherapy is designed to eradicate tumor cells, it also has significant effects on normal tissues. The platinum-induced fatty acid 16:4(n-3) (hexadeca-4,7,10,13-tetraenoic acid) induces systemic resistance to a broad range of DNA-damaging chemotherapeutics. We show that 16:4(n-3) exerts its effect by activating splenic F4/80+/CD11blow macrophages, which results in production of chemoprotective lysophosphatidylcholines (LPCs). Pharmacologic studies, together with analysis of expression patterns, identified GPR120 on F4/80+/CD11blow macrophages as the relevant receptor for 16:4(n-3). Studies that used splenocytes from GPR120-deficient mice have confirmed this conclusion. Activation of the 16:4(n-3)-GPR120 axis led to enhanced cPLA2 activity in these splenic macrophages and secretion of the resistance-inducing lipid mediator, lysophosphatidylcholine(24:1). These studies identify a novel and unexpected function for GPR120 and suggest that antagonists of this receptor might be effective agents to limit development of chemotherapy resistance.—Houthuijzen, J. M., Oosterom, I., Hudson, B. D., Hirasawa, A., Daenen, L. G. M., McLean, C. M., Hansen, S. V. F., van Jaarsveld, M. T. M., Peeper, D. S., Jafari Sadatmand, S., Roodhart, J. M. L., van de Lest, C. H. A., Ulven, T., Ishihara, K., Milligan, G., Voest, E. E. Fatty acid 16:4(n-3) stimulates a GPR120-induced signaling cascade in splenic macrophages to promote chemotherapy resistance.

  19. Unusual DNA structures

    SciTech Connect

    Wells, R.D.; Harvey, S.C.

    1988-01-01

    The contents of this book are: Unusual DNS Structures and the Probes Used for Their Detection; The Specificity of Single Strand Specific Endonucleases; Chromatin STructure and DNA Structure at the hsp 26 Locus of Drosophilia; Cruciform Extrusion in Supercoiled DNA-Mechanisms and Contextual Influence; Torsional Stress, Unusual DNA Structures, and Eukaryotic Gene Expression; DNA Sequence and Structure: Bending to Biology. Cruciform Transitions Assayed Using a Psoralen Cross-linking Method: Applications to Measurements of DNA Torisonal Tension; NMR-Distance Geometry Studies of Helical Errors and Sequence Dependent Conformations of DNA in Solution; Hyperreactivity of the B-Z Junctions Probed by Two Aromatic Chemical Carcinogens; Inherently Curved DNA and Its Structural Elements; and DNA Flexibility Under Control: The Juma Algorithm and its Application to BZ Junctions.

  20. 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

  1. 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.

  2. 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.

  3. Niobium Nitride Nb4N5 as a New High‐Performance Electrode Material for Supercapacitors

    PubMed Central

    Cui, Houlei; Zhu, Guilian; Liu, Xiangye; Liu, Fengxin; Xie, Yian; Yang, Chongyin; Lin, Tianquan; Gu, Hui

    2015-01-01

    Supercapacitors suffer either from low capacitance for carbon or derivate electrodes or from poor electrical conductivity and electrochemical stability for metal oxide or conducting polymer electrodes. Transition metal nitrides possess fair electrical conductivity but superior chemical stability, which may be desirable candidates for supercapacitors. Herein, niobium nitride, Nb4N5, is explored to be an excellent capacitive material for the first time. An areal capacitance of 225.8 mF cm−2, with a reasonable rate capability (60.8% retention from 0.5 to 10 mA cm−2) and cycling stability (70.9% retention after 2000 cycles), is achieved in Nb4N5 nanochannels electrode with prominent electrical conductivity and electrochemical activity. Faradaic pseudocapacitance is confirmed by the mechanistic studies, deriving from the proton incorporation/chemisorption reaction owing to the copious +5 valence Nb ions in Nb4N5. Moreover, this Nb4N5 nanochannels electrode with an ultrathin carbon coating exhibits nearly 100% capacitance retention after 2000 CV cycles, which is an excellent cycling stability for metal nitride materials. Thus, the Nb4N5 nanochannels are qualified for a candidate for supercapacitors and other energy storage applications. PMID:27980920

  4. Optimization of a flow cytometric method for the simultaneous measurement of cell surface antigen, DNA content, and in vitro BrdUrd incorporation into normal and malignant hematopoietic cells.

    PubMed

    Holm, M; Thomsen, M; Høyer, M; Hokland, P

    1998-05-01

    We have designed an assay for the simultaneous measurement of cell surface phenotype, S-phase fraction, and DNA content by single laser instrumentation for the purpose of determining the labeling index (LI), duration of S-phase (Ts), and the potential doubling time (Tpot) of leukocyte subpopulations. The procedure was optimized with regard to: mode of bromodeoxyuridine (BrdUrd) incorporation, selection of suitable leukocyte differentiation antigens (LDAs) as well as PE-conjugated monoclonal antibodies (MoAbs) against myeloid cells, overnight permeabilization and fixation (paraformaldehyde 1% and 0.05% Nonidet P40), DNase I treatment (250 Kunitz units), concentration of FITC-conjugated anti-BrdUrd MoAb (dilution 1:5), and DNA staining with 7-amino-actinomycin (7-AAD) (10 microg/ml). We validated this assay by measuring LI, Ts, and Tpot repeatedly in four leukemic cell lines and found these to be stable (coefficients of variation (CV): 0.06, 0.13, and 0.08, respectively). Finally, we employed the assay on different leukocyte preparations from normal donors (including purified CD34 + cells) and patients with malignant myeloid disorders, and we concluded that it will yield valuable data regarding the cell cycle kinetics of subsets of leukocytes in heterogeneous mixtures of hematopoietic cells.

  5. 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.

  6. The chemopotentiation of cisplatin by the novel bioreductive drug AQ4N

    PubMed Central

    Gallagher, R; Hughes, C M; Murray, M M; Friery, O P; Patterson, L H; Hirst, D G; McKeown, S R

    2001-01-01

    AQ4N is a bioreductive drug that can significantly enhance the anti-tumour effect of radiation and cyclophosphamide. The aim of this study was to examine the ability of AQ4N to potentiate the anti-tumour effect of cisplatin and to compare it to the chemopotentiation effect of tirapazamine. In the T50/80 murine tumour model, AQ4N (50–100 mg/kg) was administered 30 min, 2.5 or 6 h prior to cisplatin (4 mg/kg or 8 mg/kg); this produced an anti-tumour effect that was approximately 1.5 to 2 times greater than that achieved by a single 4 or 8 mg/kg dose of cisplatin. Tirapazamine (25 mg/kg) administered 2.5 h prior to cisplatin (4 mg/kg) resulted in a small increase in anti-tumour efficacy. AQ4N was also successful in enhancing the anti-tumour effect of cisplatin in the SCCVII and RIF-1 murine tumour models. This resulted in an increased cell kill of greater than 3 logs in both models; this was a greater cell kill than that observed for tirapazamine with cisplatin. Combination of cisplatin with AQ4N or tirapazamine resulted in no additional bone marrow toxicity compared to cisplatin administered alone. In conclusion, AQ4N has the potential to improve the clinical efficacy of cisplatin. © 2001 Cancer Research Campaign http://www.bjcancer.com PMID:11506506

  7. Spin Polarization Inversion at Benzene-Absorbed Fe4N Surface.

    PubMed

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

    2015-05-27

    We report a first-principle study on electronic structure and simulation of the spin-polarized scanning tunneling microscopy graphic of a benzene/Fe(4)N interface. Fe(4)N 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 p(z) and the out-of-plane d orbitals of Fe atom.

  8. 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

  9. Reconstructing species phylogeny of the carabid beetles Ohomopterus using multiple nuclear DNA sequences: heterogeneous information content and the performance of simultaneous analyses.

    PubMed

    Sota, Teiji; Vogler, Alfried P

    2003-01-01

    We attempted a phylogenetic reconstruction for the carabid subgenus Ohomopterus (genus Carabus), a notable case of radiation with mitochondrial introgression across species. Sequence data from five nuclear single copy loci were used, including wingless (Wg), phosphoenolpyruvate carboxykinase (PepCK), cytochrome c (Cytc), elongation factor-1alpha (EF-1alpha), and an anonymous single copy locus (Carab1). Sequences of Cytc, EF-1alpha, and Carab1 included intron or intron-like parts with length variation. The analysis of individual loci resulted in low resolution of the phylogenetic relationships, and the monophyly of several morphologically recognized species for which multiple specimens were analyzed was not revealed. Several specimens were heterozygous, with non-monophyletic alleles observed in three of the five loci at which alleles in heterozygotes were separated. In a simultaneous analysis of the five loci with ambiguously aligned parts eliminated and heterozygotic sites treated as missing, the resulting tree was well resolved, but the branch support was generally weak because of conflicting phylogenetic signals from different loci. We also attempted to incorporate allelic sequence data plus the ambiguously aligned parts in the analysis, by using all possible combinations of alleles from different loci in heterozygotic individuals, but the resultant tree was not supported more strongly. Nonetheless, these simultaneous analyses provided support for the monophyly of several species and species groups, and revealed the basic evolutionary trend of OHOMOPTERUS: initial widespread groups with simpler genitalia and the origination of exaggerated genitalia in a derived clade. This study exemplifies problems inherent in the phylogenetic reconstruction of closely related organisms where low levels of variation limit the information content from each locus, while heterozygosity, different phylogenetic history of multiple loci, and alignment ambiguity further hamper

  10. Growth and magnetic properties of epitaxial Fe4N films on insulators possessing lattice spacing close to Si(001) plane

    NASA Astrophysics Data System (ADS)

    Ito, Keita; Higashikozono, Soma; Takata, Fumiya; Gushi, Toshiki; Toko, Kaoru; Suemasu, Takashi

    2016-12-01

    We grew ferromagnetic Fe4N films by molecular beam epitaxy on MgO(001), MgAl2O4(MAO)(001), SrTiO3(STO)(001), and CaF2(001) substrates, possessing the lattice spacing close to Si(001) plane. Highly oriented epitaxial growth was confirmed for the Fe4N films on the MgO, MAO, and STO by reflection high-energy electron diffraction and x-ray diffractions. The degree of orientation of the Fe4N film on the STO was the best among these samples. This was attributed to the smallest lattice mismatch of -2.8% between Fe4N(001) and STO(001). On the other hand, crystallinity of the Fe4N film on the CaF2(001) substrate was poor due to a very large lattice mismatch of -30% between Fe4N(001) and CaF2(001) arising from the unexpected epitaxial relationship as Fe4N(001)[100] || CaF2(001)[100]. The saturation magnetization of the Fe4N films was approximately 1200 emu/cm3 at room temperature for all the samples, and the magnetization easy axis was in-plane Fe4N[100]. We consider that STO is the suitable buffer layer for the growth of Fe4N on Si(001), hence to realize the Si-based spintronics devices using highly spin-polarized Fe4N.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  12. Transition from half metal to semiconductor in Li doped g-C4N3

    NASA Astrophysics Data System (ADS)

    Hashmi, Arqum; Hu, Tao; Hong, Jisang

    2014-03-01

    We have investigated the structural and magnetic properties of Li doped graphitic carbon nitride (g-C4N3) using the van der Waals density functional theory. A free standing g-C4N3 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-C4N3 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-C4N3 are substantially modified by Li doping.

  13. 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).

  14. 17 CFR 4.11 - Exemption from section 4n(3)(B).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 17 Commodity and Securities Exchanges 1 2011-04-01 2011-04-01 false Exemption from section 4n(3)(B). 4.11 Section 4.11 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION COMMODITY POOL OPERATORS AND COMMODITY TRADING ADVISORS General Provisions, Definitions and Exemptions §...

  15. 17 CFR 4.11 - Exemption from section 4n(3)(B).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 17 Commodity and Securities Exchanges 1 2010-04-01 2010-04-01 false Exemption from section 4n(3)(B). 4.11 Section 4.11 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION COMMODITY POOL OPERATORS AND COMMODITY TRADING ADVISORS General Provisions, Definitions and Exemptions §...

  16. 17 CFR 4.11 - Exemption from section 4n(3)(B).

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 17 Commodity and Securities Exchanges 1 2013-04-01 2013-04-01 false Exemption from section 4n(3)(B). 4.11 Section 4.11 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION COMMODITY POOL OPERATORS AND COMMODITY TRADING ADVISORS General Provisions, Definitions and Exemptions §...

  17. 17 CFR 4.11 - Exemption from section 4n(3)(B).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 17 Commodity and Securities Exchanges 1 2012-04-01 2012-04-01 false Exemption from section 4n(3)(B). 4.11 Section 4.11 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION COMMODITY POOL OPERATORS AND COMMODITY TRADING ADVISORS General Provisions, Definitions and Exemptions §...

  18. 17 CFR 4.11 - Exemption from section 4n(3)(B).

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 17 Commodity and Securities Exchanges 1 2014-04-01 2014-04-01 false Exemption from section 4n(3)(B). 4.11 Section 4.11 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION COMMODITY POOL OPERATORS AND COMMODITY TRADING ADVISORS General Provisions, Definitions and Exemptions §...

  19. Effect of Na+ impregnated activated carbon on the adsorption of NH4(+)-N from aqueous solution.

    PubMed

    Shi, Mo; Wang, Zhengfang; Zheng, Zheng

    2013-08-01

    Two kinds of activated carbons modified by Na+ impregnation after pre-treatments involving oxidation by nitric acid or acidification by hydrochloric acid (denoted as AC/N-Na and AC/HCl-Na, respectively), were used as adsorbents to remove NH4(+)-N. The surface features of samples were investigated by BET, SEM, XRD and FT-IR. The adsorption experiments were conducted in equilibrium and kinetic conditions. Influencing factors such as initial solution pH and initial concentration were investigated. A possible mechanism was proposed. Results showed that optimal NH4(+)-N removal efficiency was achieved at a neutral pH condition for the modified ACs. The Langmuir isotherm adsorption equation provided a better fit than other models for the equilibrium study. The adsorption kinetics followed both the pseudo second-order kinetics model and intra-particle kinetic model. Chemical surface analysis indicated that Na+ ions form ionic bonds with available surface functional groups created by pre-treatment, especially oxidation by nitric acid, thus increasing the removal efficiency of the modified ACs for NH4(+)-N. Na(+)-impregnated ACs had a higher removal capability in removing NH4(+)-N than unmodified AC, possibly resulting from higher numbers of surface functional groups and better intra-particle diffusion. The good fit of Langmuir isotherm adsorption to the data indicated the presence of monolayer NH4(+)-N adsorption on the active homogenous sites within the adsorbents. The applicability of pseudo second-order and intra-particle kinetic models revealed the complex nature of the adsorption mechanism. The intra-particle diffusion model revealed that the adsorption process consisted not only of surface adsorption but also intra-particle diffusion.

  20. 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.

  1. Phytoplasma plasmid DNA extraction.

    PubMed

    Andersen, Mark T; Liefting, Lia W

    2013-01-01

    Phytoplasma plasmids have generally been detected from DNA extracted from plants and insects using methods designed for the purification of total phytoplasma DNA. Methods include extraction from tissues that are high in phytoplasma titre, such as the phloem of plants, with the use of CsCl-bisbenzimide gradients that exploit the low G+C content of phytoplasma DNA. Many of the methods employed for phytoplasma purification have been described elsewhere in this book. Here we describe in detail two methods that are specifically aimed at isolating plasmid DNA.

  2. 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

  3. 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.

  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. 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.

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

    PubMed

    Das, Manas; O'Shea, Donal F

    2014-06-20

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

  7. Nqrs Data for C8H24CdI4N2 (Subst. No. 1142)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C8H24CdI4N2 (Subst. No. 1142)

  8. Nqrs Data for C10H10Cl4N2Ti (Subst. No. 1237)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C10H10Cl4N2Ti (Subst. No. 1237)

  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. [Acceptor activity of 4-N-acetylcytidine in the synthesis of (3'-5')-internucleotide bond catalyzed by pancreatic nuclease].

    PubMed

    Kavunenko, A P; Piaĭvinen, E A; Tikhomirova-Sidorova, N S

    1976-04-01

    Cytidine and 4-N-acetylcytidine were compared as phosphate acceptors in dinucleoside monophosphate synthesis catalyzed by pancreatic ribonuclease with uridine-2',3'-cyclophosphate and cytidine-2',3'-cyclo phosphate as phosphate donors. Because of low solubility of 4-N-acetylcytidine in water, the synthesis was carried out in aqueus-organic media. The results obtained indicate that acetylation of the exoaminogroup of cytidine decreases its acceptor activity. For the first time uridilyl-(3'-5')-4-N-acetylcytidine and cytidilyl-(3'-5')-4-N-acetylcytidine are prepared enzymatically by pancreatic ribonuclease.

  11. Content Wizard.

    ERIC Educational Resources Information Center

    Ehlers-Zavala, Fabiola P.

    2001-01-01

    This classroom tip focuses on sustained-content language teaching. The game described--content wizard-- illustrates a practical technique for incorporating a range of language and academic skills into subject matter lessons for English-as-a-Second-Language learners. (Author/VWL)

  12. 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.

  13. Laser pyrolysis fabrication of ferromagnetic γ'-Fe4N and FeC nanoparticles

    NASA Astrophysics Data System (ADS)

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

    2000-05-01

    Using the laser pyrolysis method, single phase γ'-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.

  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. Photochemical study on the reactivity of tetrasulfur tetranitride, S4N4.

    PubMed

    Pritchina, Elena A; Gritsan, Nina P; Zibarev, Andrey V; Bally, Thomas

    2009-05-04

    To elucidate the multifaceted but poorly understood chemistry of the pivotal polysulfur-nitrogen heterocycle, tetrasulfur tetranitride (S(4)N(4), 1), its photochemistry was studied in Ar matrices. Thereby two primary intermediates and a secondary one (2-4) were detected, and their UV-vis and IR spectra were identified through specific interconversions of 1-4 that can be induced by selective irradiations. The structures associated with these spectra were assigned with the help of DFT calculations. From these assignments it follows that, under the conditions of the present experiments, the cage structure of 1 transforms into isomeric structures 2-4, one of which is a boat-shaped 8-membered cycle (2), and the two other are novel 6-membered S(3)N(3) cycles carrying exocyclic (N)S[triple bond]N (3) or (S)N=S (4) groups, respectively, which have not been previously described. These three intermediates probably play a pivotal role in the formation of the diverse products that are observed in the reactions of S(4)N(4) even under mild reaction conditions.

  16. Second hyperpolarizabilities of the lithium salt of pyridazine Li-H3C4N2 and lithium salt electride Li-H3C4N2⋯Na2

    NASA Astrophysics Data System (ADS)

    Silveira, Orlando; Castro, Marcos A.; Leão, Salviano A.; Fonseca, Tertius L.

    2015-07-01

    This Letter reports static and dynamic second hyperpolarizabilities of the lithium salt of pyridazine Li-H3C4N2 and lithium salt electride Li-H3C4N2⋯Na2. The results show strong dependence of the computed values with respect to the electron correlation treatment. The static value obtained at the CCSD level with the aug-cc-pVDZ basis set for the Li-H3C4N2⋯Na2 is 1.1 × 109 au. This extremely large value of the second hyperpolarizability reinforces the potential of this system for application in nonlinear optics.

  17. Human marrow megakaryocyte differentiation: multiparameter correlative analysis identifies von Willebrand factor as a sensitive and distinctive marker for early (2N and 4N) megakaryocytes.

    PubMed

    Tomer, Aaron

    2004-11-01

    Human megakaryocyte differentiation and maturation were studied in fresh marrow aspirates by using multiparameter flow cytometric correlative analysis. The expression of glycoprotein (GP)IIb/IIIa, GPIIIa, GPIb, and CD36 correlated directly with cell size and ploidy (r > 0.97); however, GPIb acquisition was relatively slow. von Willebrand factor (VWF) is robustly expressed by early (2N and 4N) megakaryocytes, enabling their complete resolution from the other marrow cells at a level superior to that achieved with GPIIb/IIIa. Expression of myeloid CD45 and immunoglobulin G (IgG)-FcgammaRII receptor (CDw32) increased with megakaryocyte maturation and contrasted with the declining expression of HLA-DR (negative in platelets). Interleukin-6 receptor expression in megakaryocytes was higher than in other marrow cells. By using the time-of-flight technique, the diameter of the megakaryocyte population was 37 +/- 4 microm (mean +/- 1 SD) compared with 14 +/- 2 microm for the total marrow cells, ranging from 21 +/- 4 microm for 2N cells to 56 +/- 8 microm for 64N cells. Cell size directly correlated with cell DNA (r = 0.98). Receptor density of GPIIb/IIIa and GPIb decreased with the transition from 2N to 4N cells, then reached maximum at 32N cells. In conclusion, the present methods are useful for studying in vivo human megakaryocytopoiesis in normal and altered states. The expression of VWF is a sensitive and distinctive marker for the identification of young marrow megakaryocytes.

  18. Solvent-dependent absorption and electronic relaxation dynamics of iron (III) tetra-4-N-methylpyridylporphine

    NASA Astrophysics Data System (ADS)

    Williams, Lenzi J.; Knappenberger, Kenneth L.

    2017-03-01

    Solvent-dependent excited-state relaxation dynamics of iron (III) tetra-4-N-methylpyridylporphine (FeTMPyP) were investigated using steady-state and femtosecond spectroscopies. Soret absorption for water-dispersed FeTMPyP consisted of two spectrally broad components centered at 3.12 eV and 2.92 eV, corresponding to π → π∗ and charge-transfer (C-T) transitions. The C-T transition exhibited inverse-dielectric-dependent energy shifts. Following 400-nm excitation, dynamics proceeded by femtosecond internal conversion from the initially prepared π∗ state to the C-T state, followed by solvent-dependent C-T relaxation. The C-T energy shifts and relaxation rates exhibited correlated dielectric dependences. C-T absorption energy and relaxation dynamics of FeTMPyP are sensitive indicators of surrounding dielectric environments.

  19. Photophysics of 4-( N, N-dimethylamino)cinnamaldehyde/α-cyclodextrin inclusion complex

    NASA Astrophysics Data System (ADS)

    Panja, Subhasis; Chakravorti, Sankar

    2002-01-01

    This paper reports the probing of α-cyclodextrin (α-CD) cavities with the help of dual emission properties of 4- N, N dimethylamino cinnamaldehyde (DMACA) in aqueous solution. An interesting feature could be observed that due to 1:1 complexation DMACA is encapsulated within α-CD in two distinctly different types of orientation as revealed from the relative positions and the intensity of locally excited state localized within donor and acceptor subunits (LE) and twisted intramolecular charge transfer (TICT) bands. In one situation the dimethylamino group is directed towards the larger rim of the cavity and in other the orientation is just the opposite. The different types of complexes were found to be excited selectively in different wavelength regions.

  20. Megagametophyte organization in diploid alfalfa meiotic mutants producing 4n pollen and 2n eggs.

    PubMed

    Calderini, O; Mariani, A

    1995-01-01

    Megagametogenesis was studied in five diploid alfalfa mutants producing 4n pollen and 2n eggs, using a stain-clearing technique. All mutants produced embryo sacs with a variable number of supernumerary nuclei both at the early (bi- and tetra-nucleate) and at the late (eight-nucleate) stages of development. The presence of supernumerary nuclei is considered to be a consequence of the production of coenocytic megaspores. The production of 2n eggs was confirmed through cytological investigation by means of the diameter of the egg-cell nucleolus. The frequency of 2n eggs was lower than the frequency of binucleated macrospores as previously determined. This discrepancy may be due to environmental effects but also to the fact that binucleated macrospores may degenerate or may, after two mitotic divisions, give rise to eight-nucleated embryo sacs counted as normals.

  1. 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

  2. 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.

  3. 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

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Brihaye, Yves; Hartmann, Betti

    2005-01-01

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

  6. Theoretical Study of the Dual Fluorescence of 4-(N,N-Dimethylamino)benzonitrile in Solution.

    PubMed

    Galván, Ignacio Fdez; Martín, M Elena; Aguilar, Manuel A

    2010-08-10

    We have performed high-level quantum calculations of absorption and emission properties of 4-(N,N-dimethylamino)benzonitrile (DMABN) in gas phase and in polar solvents, including the solvent effects with an explicit mean field model. Two excited states of DMABN have been found and optimized, corresponding to the two excited states assumed by the generally accepted hypotheses for the dual fluorescence of this molecule: a locally excited (LE) state and a charge transfer (CT) state. The results show that, in the gas phase, the charge transfer state is severely distorted and higher in energy than the locally excited state, while in polar solvents, it becomes almost an ideal twisted intramolecular charge transfer state (TICT) and is stabilized with respect to the locally excited state and the Franck-Condon point. The relative free energies calculated for the two excited states in solution suggest that both states are accessible from initial Franck-Condon excitation, the charge transfer state being highly favored in aqueous solution and less so in tetrahydrofuran. The results support the validity of the TICT model in this system.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Doping Polypyrrole Films with 4-N-Pentylphenylboronic Acid to Enhance Affinity towards Bacteria and Dopamine

    PubMed Central

    Padiolleau, Laurence; Chen, Xi; Jafari, Mohammad Javad; Sheikhzadeh, Elham; Turner, Anthony P. F.; Jager, Edwin W. H.; Beni, Valerio

    2016-01-01

    Here we demonstrate the use of a functional dopant as a fast and simple way to tune the chemical affinity and selectivity of polypyrrole films. More specifically, a boronic-functionalised dopant, 4-N-Pentylphenylboronic Acid (PBA), was used to provide to polypyrrole films with enhanced affinity towards diols. In order to prove the proposed concept, two model systems were explored: (i) the capture and the electrochemical detection of dopamine and (ii) the adhesion of bacteria onto surfaces. The chemisensor, based on overoxidised polypyrrole boronic doped film, was shown to have the ability to capture and retain dopamine, thus improving its detection; furthermore the chemisensor showed better sensitivity in comparison with overoxidised perchlorate doped films. The adhesion of bacteria, Deinococcus proteolyticus, Escherichia coli, Streptococcus pneumoniae and Klebsiella pneumoniae, onto the boric doped polypyrrole film was also tested. The presence of the boronic group in the polypyrrole film was shown to favour the adhesion of sugar-rich bacterial cells when compared with a control film (Dodecyl benzenesulfonate (DBS) doped film) with similar morphological and physical properties. The presented single step synthesis approach is simple and fast, does not require the development and synthesis of functional monomers, and can be easily expanded to the electrochemical, and possibly chemical, fabrication of novel functional surfaces and interfaces with inherent pre-defined sensing and chemical properties. PMID:27875555

  12. [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.

  13. Doping Polypyrrole Films with 4-N-Pentylphenylboronic Acid to Enhance Affinity towards Bacteria and Dopamine.

    PubMed

    Golabi, Mohsen; Padiolleau, Laurence; Chen, Xi; Jafari, Mohammad Javad; Sheikhzadeh, Elham; Turner, Anthony P F; Jager, Edwin W H; Beni, Valerio

    2016-01-01

    Here we demonstrate the use of a functional dopant as a fast and simple way to tune the chemical affinity and selectivity of polypyrrole films. More specifically, a boronic-functionalised dopant, 4-N-Pentylphenylboronic Acid (PBA), was used to provide to polypyrrole films with enhanced affinity towards diols. In order to prove the proposed concept, two model systems were explored: (i) the capture and the electrochemical detection of dopamine and (ii) the adhesion of bacteria onto surfaces. The chemisensor, based on overoxidised polypyrrole boronic doped film, was shown to have the ability to capture and retain dopamine, thus improving its detection; furthermore the chemisensor showed better sensitivity in comparison with overoxidised perchlorate doped films. The adhesion of bacteria, Deinococcus proteolyticus, Escherichia coli, Streptococcus pneumoniae and Klebsiella pneumoniae, onto the boric doped polypyrrole film was also tested. The presence of the boronic group in the polypyrrole film was shown to favour the adhesion of sugar-rich bacterial cells when compared with a control film (Dodecyl benzenesulfonate (DBS) doped film) with similar morphological and physical properties. The presented single step synthesis approach is simple and fast, does not require the development and synthesis of functional monomers, and can be easily expanded to the electrochemical, and possibly chemical, fabrication of novel functional surfaces and interfaces with inherent pre-defined sensing and chemical properties.

  14. 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…

  15. DNA Nanotechnology

    NASA Astrophysics Data System (ADS)

    Taniguchi, Masateru; Kawai, Tomoji

    2002-11-01

    DNA is one candidate of promising molecules for molecular electronic devices, since it has the double helix structure with pi-electron bases for electron transport, the address at 0.4 nm intervals, and the self-assembly. Electrical conductivity and nanostructure of DNA and modified DNA molecules are investigated in order to research the application of DNA in nanoelectronic devices. It has been revealed that DNA is a wide-gap semiconductor in the absence of doping. The conductivity of DNA has been controlled by chemical doping, electric field doping, and photo-doping. It has found that Poly(dG)[middle dot]Poly(dC) has the best conductivity and can function as a conducting nanowire. The pattern of DNA network is controlled by changing the concentration of the DNA solution.

  16. 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)

  17. 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.

  18. Perpendicular Magnetic Anisotropy and High Spin Polarization in Tetragonal Fe4N /BiFeO3 Heterostructures

    NASA Astrophysics Data System (ADS)

    Yin, Li; Mi, Wenbo; Wang, Xiaocha

    2016-12-01

    The tetragonal Fe4N /BiFeO3(001 ) heterostructures aimed at simultaneously gaining the perpendicular magnetic anisotropy (PMA) and high spin polarization have been investigated by the first-principles method. It is found that Fe4N with FeAFeB termination is better for achieving interfacial and inner PMA simultaneously than (FeB)2N termination. When the positions of interfacial FeA and FeB relative to Fe in BiFeO3 are changed, the PMA in Fe4N transforms into the in-plane magnetic anisotropy. Especially, PMA in Fe4N near the heterointerfaces depends on the direction of ferroelectric polarization in BiFeO3 . Finally, the interfacial and inner PMA of Fe4N along with high spin polarization appear in the stable FeAFeB/Fe -O2 case owing to the 3 d -3 d orbital hybridization. These results provide the opportunities for developing multifunctional spintronic devices.

  19. 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.

  20. 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.

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

    PubMed Central

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

    2013-01-01

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

  2. Effects of picoxystrobin and 4-n-nonylphenol on soil microbial community structure and respiration activity.

    PubMed

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

    2013-01-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Production cross sections of {sub 105}{sup 261}Ha from the {sup 250}Cf({sup 15}N,4n) and {sup 243}Am({sup 22}Ne,4n) reactions

    SciTech Connect

    Lane, M.R.; Gregorich, K.E.; Lee, D.M.; Wierczinski, B.; McGrath, C.A.; Hendricks, M.B.; Shaughnessy, D.A.; Strellis, D.A.; Sylwester, E.R.; Wilk, P.A.; Hoffman, D.C. |

    1998-12-01

    We have measured the production cross section of 1.8-s {sup 261}Ha from two different reactions. It was produced in the {sup 250}Cf({sup 15}N,4n) reaction at 84 MeV and in the {sup 243}Am({sup 22}Ne,4n) reaction at 116 MeV. Our rotating wheel system with a special parent-daughter stepping mode was used to detect {alpha}-{alpha} correlations between {sup 261}Ha and {sup 257}Lr. We measured 13 and 9 correlations in the two reactions, respectively. Assuming a 100{percent} {alpha} branch, we have determined the production cross section of {sup 261}Ha to be 0.51{plus_minus}0.20thinspnb in the {sup 250}Cf({sup 15}N,4n) reaction at 84 MeV, and 0.25{plus_minus}0.11thinspnb in the {sup 243}Am({sup 22}Ne,4n) reaction at 116 MeV. Based on the number of fission events observed in the latter reaction, we have been able to set an upper limit of 18{percent} for the spontaneous fission branch of {sup 261}Ha. {copyright} {ital 1998} {ital The American Physical Society}

  9. Influenza A virus surveillance in live-bird markets: first report of influenza A virus subtype H4N6, H4N9, and H10N3 in Thailand.

    PubMed

    Wisedchanwet, Trong; Wongpatcharachai, Manoosak; Boonyapisitsopa, Supanat; Bunpapong, Napawan; Jairak, Waleemas; Kitikoon, Pravina; Sasipreeyajun, Jiroj; Amonsin, Alongkorn

    2011-12-01

    A one-year influenza A survey was conducted in 10 live bird markets (LBMs) in H5N1 high-risk areas in Thailand from January to December 2009. The result from the survey showed that the occurrence of influenza A virus (IAV) in LBMs was 0.36% (19/5304). Three influenza A subtypes recovered from LBMs were H4N6 (n = 2), H4N9 (n = 1), and H10N3 (n = 16) from Muscovy ducks housed in one LBM in Bangkok. These influenza subtypes had never been reported in Thailand, and therefore such genetic diversity raises concern about potential genetic reassortment of the viruses in avian species in a particular setting. Two influenza A subtypes (H4N6 and H4N9) were isolated from oropharyngeal and cloacal swabs of the same duck, suggesting coinfection with two influenza subtypes and possible genetic reassortment in the bird. In addition, H10N3 infection in ducks housed in the same LBM was observed. These findings further support that LBMs are a potential source of IAV transmission and genetic reassortment.

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

    SciTech Connect

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

    2013-01-15

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

  11. 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.

  12. 75 FR 47503 - Schedules of Controlled Substances; Placement of 2,5-Dimethoxy-4-(n)-propylthiophenethylamine and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-06

    ...- (n)-propylthiophenethylamine and N-Benzylpiperazine Into Schedule I of the Controlled Substances Act... scheduling of N- Benzylpiperazine (BZP), and contained an error regarding the potency of BZP relative to... address the scheduling of 2,5-dimethoxy-4-(n)- propylthiophenethylamine (2C-T-7) which was also...

  13. 75 FR 47451 - Schedules of Controlled Substances; Placement of 2,5-Dimethoxy-4-(n)-propylthiophenethylamine and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-06

    ...- (n)-propylthiophenethylamine and N-Benzylpiperazine Into Schedule I of the Controlled Substances Act... the Federal Register of March 18, 2004. The final rule pertained to the scheduling of N... scheduling of 2,5-dimethoxy-4-(n)- propylthiophenethylamine (2C-T-7) which was also placed into schedule I...

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

    ERIC Educational Resources Information Center

    Lucas, Amand A.

    2008-01-01

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

  16. DNA 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

  17. Quality control study by the French Cytometry Association on flow cytometric DNA content and S-phase fraction (S%). The Association Française de Cytométrie.

    PubMed

    D'hautcourt, J L; Spyratos, F; Chassevent, A

    1996-03-15

    Clinical use of flow cytometric (FCM) DNA analysis requires effective quality controls. Thirty-two laboratories with various degrees of FCM experience participated in the first phase of a quality control program organized by the Association Française de Cytométrie. All received diskettes containing ten list-mode files and ten histogram files that were derived from FCM analysis of various unfixed tumor specimens. A total of 610 responses on DNA ploidy and cell cycle were obtained with three different DNA analysis softwares: CellFit used by (44% of responses), MultiCycle (44%), and ModFit (12%). After statistical analysis, 31% of the responses were excluded from the final analysis for precise reasons. The groups were too small to carry out a valid analysis of the slight differences in the percentage of cells in the DNA synthesis phase (S%) between CellFit and MultiCycle. To estimate the influence of gating on the final cell-cycle results, five of the histogram files were derived from corresponding list-mode files, but the participating laboratories were unaware of this. A good correlation (r = 0.98) was obtained for S% values in the five paired files. The fact that 31% of the responses had to be excluded clearly reflects inadequate training in the use of these analysis softwares and, in some cases, a failure to grasp the biological meaning of the results. In contrast, the laboratories fulfilling consensus recommendations obtained remarkably homogeneous results, showing that standardization is feasible.

  18. A first principles study of the thermal stability of Am(MH4)n light complex hydrides

    NASA Astrophysics Data System (ADS)

    Wang, Yong-li; Liu, Shi; Rong, Li-jian; Wang, Yuan-ming

    2010-05-01

    From the physical point of view, the cohesive energy of a reactant is preferable to its formation energy for characterizing its influence on the reaction processes from the reactants to the products. In fact it has been found that there is a certain correlation between the experimental hydrogen desorption temperature and the cohesive energy calculated by a first principles method for a series of Am(MH4)n (A = Li, Na, Mg; M = Be, B, Al) light complex hydrides (including Na2BeH4, Li2BeH4, NaAlH4, LiAlH4, Mg(AlH4)2, LiBH4 and NaBH4), which suggests that cohesive energy may be a useful physical quantity for evaluating the hydrogen desorption ability of complex hydrides, especially in cases when dehydrogenation products have unknown crystal structures, or may even be unknown. To understand this correlation more deeply, the ionic interaction between A and the MH4 complex and the covalent interaction between M and H were calculated and their contributions to the cohesive energy evaluated quantitatively. The calculated results show that the covalent M-H interaction in the MH4 complex is the dominant part of the cohesive energy Ecoh (up to more than 75%) and hardly changes during high-pressure structural transitions of Am(MH4)n. It was also found that low electronegativity of M or high electronegativity of A is responsible for the weak covalent M-H interaction and finally leads to the low thermodynamic stability of Am(MH4)n, suggesting that complex hydrides Am(MH4)n can be destabilized by partial substitution of M (A) with an element with electronegativity lower (higher) than Ms (As). This conclusion has been confirmed by lots of experimental results and may be a useful guideline for the future design of new complex hydrides of the type Am(MH4)n.

  19. Perinatal transmission of human papilomavirus DNA.

    PubMed

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

    2009-06-21

    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

  20. Identification using DNA from skin contact: case reports.

    PubMed

    Tokutomi, Tomoharu; Takada, Yuzo; Kanetake, Jun; Mukaida, Masahiro

    2009-04-01

    The DNA content of different types of forensic materials can vary substantially. "Trace DNA" is the minute quantity of DNA transferred through skin contact. Here, we report three cases of identification of trace DNA using conventional short tandem repeat (STR) or mitochondrial DNA (mtDNA). DNA was successfully obtained from fabrics by swabbing or by direct extraction and subjected to STR genotyping or mtDNA typing. In two cases, there was no amplification of PCR products containing the STR loci. This indicates that the areas chosen for DNA extraction contained trace DNA and DNA from more than one source. Therefore, it is important for forensic investigators performing DNA typing to know where an item has been frequently touched by victims and/or offenders as this will influence the choice of sites on the item to be used for DNA extraction.

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

    PubMed

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

    1992-11-30

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

  2. DNA ligases.

    PubMed

    Tabor, S

    2001-05-01

    DNA ligases catalyze the formation of phosphodiester bonds between juxtaposed 5' phosphate and a 3'-hydroxyl terminus in duplex DNA. This activity can repair single-stranded nicks in duplex DNA and join duplex DNA restriction fragments having either blunt ends or homologous cohesive ends. Two ligases are used for nucleic acid research and their reaction conditions and applications are described in this unit: E. coli ligase and T4 ligase. These enzymes differ in two important properties. One is the source of energy: T4 ligase uses ATP, while E. coli ligase uses NAD. Another important difference is their ability to ligate blunt ends; under normal reaction conditions, only T4 DNA ligase will ligate blunt ends.

  3. 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.

  4. Solid-State Photochemistry as a Formation Mechanism for Titan's Stratospheric C4N2 Ice Clouds

    NASA Technical Reports Server (NTRS)

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

    2016-01-01

    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 per centimeter 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.

  5. 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.

  6. Metallic transport and large anomalous Hall effect at room temperature in ferrimagnetic Mn4N epitaxial thin film

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    We report the electrical transport properties of ferrimagnetic Mn4N (001) epitaxial thin films grown by pulsed laser deposition on MgO (001) substrates. The Mn4N 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/m3, 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.

  7. Patenting DNA.

    PubMed

    Bobrow, Martin; Thomas, Sandy

    2002-12-01

    The protection of inventions based on human DNA sequences has been achieved mainly through application of the patent system. Over the past decade, there has been continuing debate about whether this use of intellectual property rights is acceptable. Companies and universities have been active during this period in filing thousands of patent applications. Although many have argued that to claim a DNA sequence in a patent is to claim a discovery, patent law allows discoveries that are useful to be claimed as part of an invention. As the technology to isolate DNA sequences has advanced, the criterion for inventiveness, necessary for any invention to be eligible for filing, has become more difficult to justify in the case of claims to DNA sequences. Moreover, the discovery that a gene is associated with a particular disease is, it is argued, to discover a fact about the world and undeserving of the status of an invention. Careful examination of the grounds for allowing the patenting of DNA sequences as research tools suggests such rewards will rarely be justified. The patenting of DNA sequences as chemical intermediates necessary for the manufacture of therapeutic proteins is, however, reasonable given that the information within the sequence is applied to produce a tangible substance which has application as a medicine. Despite the legal, technical and political complexities of applying the flexibilities with the current law, it is argued that much could be achieved in the area of patenting DNA by raising the thresholds for patentability.

  8. 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.

  9. 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.

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

    PubMed Central

    Mück, Fabian; Bracharz, Silvia; Marschalek, Rolf

    2016-01-01

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

  11. Nqrs Data for C10H11AuCl4N2O2 (Subst. No. 1239)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C10H11AuCl4N2O2 (Subst. No. 1239)

  12. Characterization of an H4N2 influenza virus from Quails with a multibasic motif in the hemagglutinin cleavage site.

    PubMed

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

    2014-11-01

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

  13. 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.

  14. A first principles study of the thermal stability of A(m)(MH(4))(n) light complex hydrides.

    PubMed

    Wang, Yong-li; Liu, Shi; Rong, Li-jian; Wang, Yuan-ming

    2010-05-05

    From the physical point of view, the cohesive energy of a reactant is preferable to its formation energy for characterizing its influence on the reaction processes from the reactants to the products. In fact it has been found that there is a certain correlation between the experimental hydrogen desorption temperature and the cohesive energy calculated by a first principles method for a series of A(m)(MH(4))(n) (A = Li, Na, Mg; M = Be, B, Al) light complex hydrides (including Na(2)BeH(4), Li(2)BeH(4), NaAlH(4), LiAlH(4), Mg(AlH(4))(2), LiBH(4) and NaBH(4)), which suggests that cohesive energy may be a useful physical quantity for evaluating the hydrogen desorption ability of complex hydrides, especially in cases when dehydrogenation products have unknown crystal structures, or may even be unknown. To understand this correlation more deeply, the ionic interaction between A and the MH(4) complex and the covalent interaction between M and H were calculated and their contributions to the cohesive energy evaluated quantitatively. The calculated results show that the covalent M-H interaction in the MH(4) complex is the dominant part of the cohesive energy E(coh) (up to more than 75%) and hardly changes during high-pressure structural transitions of A(m)(MH(4))(n). It was also found that low electronegativity of M or high electronegativity of A is responsible for the weak covalent M-H interaction and finally leads to the low thermodynamic stability of A(m)(MH(4))(n), suggesting that complex hydrides A(m)(MH(4))(n) can be destabilized by partial substitution of M (A) with an element with electronegativity lower (higher) than Ms (As). This conclusion has been confirmed by lots of experimental results and may be a useful guideline for the future design of new complex hydrides of the type A(m)(MH(4))(n).

  15. 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)

  16. 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.

  17. DNA adductomics.

    PubMed

    Balbo, Silvia; Turesky, Robert J; Villalta, Peter W

    2014-03-17

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

  18. 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 ...

  19. 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.

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    2005-09-01

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

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

    PubMed

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

    2005-09-15

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

  3. Efficient silencing of EGFP reporter gene with siRNA delivered by asymmetrical N4,N9-diacyl spermines.

    PubMed

    Metwally, Abdelkader A; Reelfs, Olivier; Pourzand, Charareh; Blagbrough, Ian S

    2012-07-02

    It is important to obtain structure-activity relationship (SAR) data across cationic lipids for the self-assembly and nonviral intracellular delivery of siRNA. The aims of this work are to carry out a SAR study on the efficiency of asymmetrical N(4),N(9)-diacyl spermines in siRNA delivery and EGFP reporter gene silencing, with comparisons to selected mixtures composed of symmetrical N(4),N(9)-diacyl spermines. Another important aim of these studies is to quantify the changes in cell viability, assayed with alamarBlue, as a function of lipid structure. Therefore, we have designed, synthesized, purified, and assayed novel cationic lipids that are asymmetrical lipopolyamines based on spermine. Flow cytometry and fluorescence microscopy in an EGFP stably transfected HeLa cell line, measuring both delivery of fluorescently tagged siRNAs and silencing the EGFP signal, allowed quantitation of the differences between asymmetrical cationic lipids, mixtures of their symmetrical counterparts, and comparison with commercial nonviral delivery agents. Intracellular delivery of siRNA and gene silencing by siRNA differ with different hydrophobic domains. In these asymmetrical N(4),N(9)-diacyl spermines, lipids that enhance siRNA uptake do not necessarily enhance siRNA-induced inhibition of gene expression: C18 and longer saturated chains promote uptake, while more unsaturated C18 chains promote gene silencing. These properties are efficiently demonstrated in a new nontoxic cationic lipid siRNA vector, N(4)-linoleoyl-N(9)-oleoyl-1,12-diamino-4,9-diazadodecane (LinOS), which is also shown to be comparable with or superior to TransIT-TKO and Lipofectamine 2000.

  4. Postoperative irradiation in patients with pT3-4N0 laryngeal cancer: results and prognostic factors.

    PubMed

    Skóra, Tomasz; Nowak-Sadzikowska, Jadwiga; Mucha-Małecka, Anna; Szyszka-Charewicz, Bogumiła; Jakubowicz, Jerzy; Gliński, Bogdan

    2015-03-01

    Approximately 60 % of patients with locally advanced laryngeal cancer (LALC) treated primarily with surgery require adjuvant radiotherapy. In the available literature predominate series of patients were with pathologically confirmed node-positive status. Subgroups of pN0 patients with LALC are scarce. The aim of the study is to evaluate the efficacy of postoperative radiotherapy in patients with pathological stage T3-4N0M0 and identification of prognostic factors in this group. Between 1975 and 2005, 138 patients with squamous pT3-4N0 laryngeal cancer were irradiated postoperatively. Primary surgical treatment consisted of total laryngectomy and cervical lymphadenectomy. The median time between surgery and the implementation of radiotherapy was 56 days. The median total dose was 60 Gy (range 40-70 Gy). Five-year disease-free survival (DFS5) was achieved in 76 % of patients. Cancer recurrence was observed in 34 patients. In 28 (82 %) cases it was locoregional failure. DFS5 rates for pT3 and pT4 were 92 and 69 %, for margin status R0, R1 and R2 were 82, 72 and 67 %, respectively. The pharyngeal invasion was related to a decrease in DFS5 from 80 to 59 %. Postoperative irradiation in patients with pT3-4N0 LALC is an effective treatment method. The main reason of the failure is local recurrence. The following independent prognostic factors were identified in this group of patients: pT stage, surgical margin status and pharyngeal invasion.

  5. 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.

  6. Exploring the location and orientation of 4-( N, N-dimethylamino) cinnamaldehyde in anionic, cationic and non-ionic micelles

    NASA Astrophysics Data System (ADS)

    Panja, Subhasis; Chowdhury, Papia; Chakravorti, Sankar

    2003-01-01

    This Letter reports probing of non-ionic, anionic and cationic micelles utilizing different dual emission properties of 4-( N, N-dimethylamino) cinnamaldehyde. Twisted intramolecular charge transfer (TICT) band is more enhanced and blue shifted in non-ionic micelle than those are in ionic micelles. In non-ionic micelle, the molecule enters in the core region whereas, in ionic micelles, it is anchored in the interfacial region with different orientations. Micellar-water interface electric field in ionic micelles was found to have profound effect on TICT decay time. Interestingly, inorganic salt-counterion binding helps the acceptor moiety to enter into the core region in anionic micelle.

  7. Temperature Profile of a Stoichiometric CH4/N2O Flame from Laser Excited Fluorescence Measurements on OH,

    DTIC Science & Technology

    1982-07-01

    monitor used to confirm that lasing occurred on only one internal etalon mode. The uv light was transmitted through a Corning 7-54 filter which...Complex ChemicaZ Systems," NASA TN-D- 7056 , 1973. 17 4 1 LL. .20 U .’- 0 in a . IWO2 UA "- W.c Laei (m) unvadwa 4) K H-W- V! 4J 0. a .9- o o . dU 00...Properties of Complex Chemical Systems,", NASA TN D- 7056 , 1973. 13. Anderson, W.R., "Measurement of the Line Reversal Temperature of OH in CH4/N20 Flames

  8. 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.

  9. Creation and electrical properties of p-Cu2ZnSnS4/ n-Si heterojunctions

    NASA Astrophysics Data System (ADS)

    Yusupov, A.; Adambaev, K.; Turaev, Z. Z.; Aliev, S. R.; Kutlimratov, A.

    2017-01-01

    Anisotype p-Cu2ZnSnS4/ n-Si heterojunctions have been manufactured for the first type by sulfidation of base-metal layers predeposited onto polycrystalline silicon substrates. Current-voltage characteristics of the heterojunctions are analyzed, and the mechanisms of current transfer are discussed. It is established that forward-biased structures are characterized by both tunneling-recombination processes and space-charge limited mobility of carriers. In reversely biased heterojunctions, space-charge limited currents predominate.

  10. Mobility of Ions in the Nematic Phase of 4-n-Octyl-4‧-cyanobiphenyl (8CB)

    NASA Astrophysics Data System (ADS)

    Sawada, Atsushi; Naemura, Shohei

    2002-02-01

    The relationship between the mobility of ions and viscosity is discussed for the nematic phase of 4-n-octyl-4‧-cyanobiphenyl (8CB). The Miesowicz viscosity coefficient η2 exhibits a divergence at the nematic-smectic phase transition; nevertheless, normal behavior of the temperature dependence is observed for the mobility of ions. Although the Walden rule is not valid for the entire temperature range in the nematic phase, it is presumed that there is no significant difference in the ionic radius between the nematic and isotropic phases.

  11. Hydrogen CARS (Coherent Antistokes Raman Spectroscopy) Spectra from CH(4)/N(2)O and Nitramine Composite Flames.

    DTIC Science & Technology

    1987-05-01

    that determine the burning rate and (2) an outer flame area where NO is converted to N2 to generate the luminous flame. CARS provides the spectral...ACCESSION NO. 3. RECIPIENT’S CATALOG NUMBER Technical Report ARAED-TR-87014 ADA IfII 4. TITLE (and Subtitle) S. TYPE OF REPORT & PERIOD COVERED Hydrogen CARS ...numbar) The hydrogen spectra from the CH(4)/N(2)0 and nitramine composite flames allow use of each of the concurrent capabilities of CARS : (1

  12. Electron Attachment and Detachment, and the Electron Affinities of C(5)F(5)N and C(5)HF(4)N

    DTIC Science & Technology

    2005-09-19

    detachment rate at 303 K was 520 ± 180 s-1. The attachment/detachment equilibrium yielded experimental electron affinities EA(CsF 5N) = 0.70-0.05 eV and EA...are in good agreement with the present experimental results. 15. SUBJECT TERMS Electron attachment Electron affinity Electron detachment Rate constant...attachment/detachment equilibrium yielded experimental electron affinities EA(C5F5 N)=0.70±0.05 eV and EA(2,3,5,6-C5HF 4N)=0.40±0.08 eV. Electronic

  13. High NH(4)(+)-N concentration wastewater treatment by shortcut nitrification-denitrification using a system of A/O inner loop fluidized bed biofilm reactors.

    PubMed

    Hu, X M; Chen, Y W; Liao, Y G; Yan, W F; Zhu, S M; Shen, S B

    2013-01-01

    In this experiment, a rapid mass-transfer inner loop fluidized bed biofilm reactor (ILFBBR) was employed to treat synthetic high ammonia nitrogen-containing (NH(4)(+)-N) wastewater by shortcut nitrification-denitrification. The reactor operation was stable after a short start-up period. Ammonia oxidizing bacteria (AOB) were predominant and 65% nitrite (NO(2)(-)-N/NO(x)(-)-N) levels were achieved. During the nitrification-denitrification period, the removal rates of NH(4)(+)-N and total nitrogen (TN) reached 94 and 82%, respectively. From the material balance, it was indicated that 87% of NH(4)(+)-N was removed by shortcut nitrification. The features of ILFBBR and the benefits of shortcut nitrification were combined in this experiment, and showed an excellent removal of NH(4)(+)-N from high-concentration NH(4)(+)-N wastewater.

  14. 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.

  15. Transparent half metallic g-C4N3 nanotubes: potential multifunctional applications for spintronics and optical devices

    PubMed Central

    Hu, Tao; Hashmi, Arqum; Hong, Jisang

    2014-01-01

    Multifunctional material brings many interesting issues because of various potential device applications. Using first principles calculations, we predict that the graphitic carbon nitride (g-C4N3) nanotubes can display multifunctional properties for both spintronics and optical device applications. Very interestingly, armchair tubes (n, n) with n = 2, 3, 4, 5, 6 and (5, 0) zigzag tubes are found to be half metallic, while zigzag tubes (n, 0) with n = 4, 6 show an antiferromagnetic ground state with band gaps. However, larger zigzag tubes of (7, 0), (8, 0), and (10, 0) are turned out to be half metallic. Along with the half metallic behavior of the tubes, those tubes seem to be optically transparent in the visible range. Due to these magnetic and optical properties, we suggest that the g-C4N3 nanotubes (CNNTs) can be used for both ideal spintronics and transparent electrode materials. We also explored the stability of magnetic state and nanotube structure using ab initio molecular dynamics. The CNNTs were found to be thermally stable and the magnetic moment was robust against the structural deformation at 300 K. Overall, our theoretical prediction in one dimensional CNNTs may provide a new physics in spintronics and also in other device applications because of potential multifunctional properties. PMID:25317598

  16. Transparent half metallic g-C4N3 nanotubes: potential multifunctional applications for spintronics and optical devices

    NASA Astrophysics Data System (ADS)

    Hu, Tao; Hashmi, Arqum; Hong, Jisang

    2014-08-01

    Multifunctional material brings many interesting issues because of various potential device applications. Using first principles calculations, we predict that the graphitic carbon nitride (g-C4N3) nanotubes can display multifunctional properties for both spintronics and optical device applications. Very interestingly, armchair tubes (n, n) with n = 2, 3, 4, 5, 6 and (5, 0) zigzag tubes are found to be half metallic, while zigzag tubes (n, 0) with n = 4, 6 show an antiferromagnetic ground state with band gaps. However, larger zigzag tubes of (7, 0), (8, 0), and (10, 0) are turned out to be half metallic. Along with the half metallic behavior of the tubes, those tubes seem to be optically transparent in the visible range. Due to these magnetic and optical properties, we suggest that the g-C4N3 nanotubes (CNNTs) can be used for both ideal spintronics and transparent electrode materials. We also explored the stability of magnetic state and nanotube structure using ab initio molecular dynamics. The CNNTs were found to be thermally stable and the magnetic moment was robust against the structural deformation at 300 K. Overall, our theoretical prediction in one dimensional CNNTs may provide a new physics in spintronics and also in other device applications because of potential multifunctional properties.

  17. Transparent half metallic g-C4N3 nanotubes: potential multifunctional applications for spintronics and optical devices.

    PubMed

    Hu, Tao; Hashmi, Arqum; Hong, Jisang

    2014-08-14

    Multifunctional material brings many interesting issues because of various potential device applications. Using first principles calculations, we predict that the graphitic carbon nitride (g-C4N3) nanotubes can display multifunctional properties for both spintronics and optical device applications. Very interestingly, armchair tubes (n, n) with n = 2, 3, 4, 5, 6 and (5, 0) zigzag tubes are found to be half metallic, while zigzag tubes (n, 0) with n = 4, 6 show an antiferromagnetic ground state with band gaps. However, larger zigzag tubes of (7, 0), (8, 0), and (10, 0) are turned out to be half metallic. Along with the half metallic behavior of the tubes, those tubes seem to be optically transparent in the visible range. Due to these magnetic and optical properties, we suggest that the g-C4N3 nanotubes (CNNTs) can be used for both ideal spintronics and transparent electrode materials. We also explored the stability of magnetic state and nanotube structure using ab initio molecular dynamics. The CNNTs were found to be thermally stable and the magnetic moment was robust against the structural deformation at 300 K. Overall, our theoretical prediction in one dimensional CNNTs may provide a new physics in spintronics and also in other device applications because of potential multifunctional properties.

  18. Tiny crystalline grain nanocrystal NiCo2O4/N-doped graphene composite for efficient oxygen reduction reaction

    NASA Astrophysics Data System (ADS)

    Wan, Li-li; Zang, Guo-long; Wang, Xin; Zhou, Le-an; Li, Tian; Zhou, Qi-xing

    2017-03-01

    Oxygen reduction reaction (ORR) plays an important role in green energy conversion, although catalysts are necessary for overcoming its sluggish kinetic. Herein, a nanocrystal NiCo2O4/N-doped graphene composite material showing high ORR electrocatalytic activity is prepared. The resulting NiCo2O4/N-doped graphene composite (NiCo2O4-NG/C) combines the advantages of both component materials and shows enhanced ORR electrocatalytic activity (i.e., more positive peak potential and half-wave potential compared with NiCo2O4) while having higher diffusion-limited current density values (-5.7 mA cm-2, 1600 rpm), better tolerance to methanol, and improved stability than 20 wt% Pt/C. NiCo2O4 anchored on N-doped graphene are demonstrated to be nanocrystal with tiny crystalline grain (diameter < 5 nm) and result in large surface area, thereby allowing more active sites to be exposed. Moreover, the potential exposure of high-index planes may be also responsible for the observed high activity of these materials.

  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.

  20. DNA recovery from soils of diverse composition.

    PubMed

    Zhou, J; Bruns, M A; Tiedje, J M

    1996-02-01

    A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal shearing was developed to address the risk of chimera formation from small template DNA during subsequent PCR. The method was based on lysis with a high-salt extraction buffer (1.5 M NaCl) and extended heating (2 to 3 h) of the soil suspension in the presence of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide, and proteinase K. The extraction method required 6 h and was tested on eight soils differing in organic carbon, clay content, and pH, including ones from which DNA extraction is difficult. The DNA fragment size in crude extracts from all soils was > 23 kb. Preliminary trials indicated that DNA recovery from two soils seeded with gram-negative bacteria was 92 to 99%. When the method was tested on all eight unseeded soils, microscopic examination of indigenous bacteria in soil pellets before and after extraction showed variable cell lysis efficiency (26 to 92%). Crude DNA yields from the eight soils ranged from 2.5 to 26.9 micrograms of DNA g-1, and these were positively correlated with the organic carbon content in the soil (r = 0.73). DNA yields from gram-positive bacteria from pure cultures were two to six times higher when the high-salt-SDS-heat method was combined with mortar-and-pestle grinding and freeze-thawing, and most DNA recovered was of high molecular weight. Four methods for purifying crude DNA were also evaluated for percent recovery, fragment size, speed, enzyme restriction, PCR amplification, and DNA-DNA hybridization. In general, all methods produced DNA pure enough for PCR amplification. Since soil type and microbial community characteristics will influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods on the basis of experimental goals.

  1. 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)

  2. 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)

  3. Synthetic DNA

    PubMed Central

    O’ Driscoll, Aisling; Sleator, Roy D.

    2013-01-01

    With world wide data predicted to exceed 40 trillion gigabytes by 2020, big data storage is a very real and escalating problem. Herein, we discuss the utility of synthetic DNA as a robust and eco-friendly archival data storage solution of the future. PMID:23514938

  4. 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…

  5. 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

  6. Sr(4 + n)Mn(3+)(4)Mn(4+)(n)O(10 + 3n): a new homologous series of oxygen-vacancy-ordered perovskites built from Mn(3+)O(5) pyramids and Mn(4+)O(6) octahedra.

    PubMed

    Suescun, Leopoldo; Dabrowski, Bogdan

    2008-04-01

    A new homologous series of oxygen-vacancy-ordered perovskites with the formula Sr_{4+n}Mn;{3+}_4Mn;{4+}_nO_{10+3n} is proposed based on the structural trends found for the recently described Sr(4)Mn(4)O(10), Sr(5)Mn(5)O(13) and Sr(7)Mn(7)O(19) compounds. These compounds correspond to n = 0 (Sr(4)Mn;{3+}_4O(10)), n = 1 (Sr(5)Mn;{3+}_4Mn(4+)O(13)) and n = 3 (Sr(7)Mn;{3+}_4Mn;{4+}_3O(19)) members of the series. A linear set of four Mn(3+)O(5) pyramids placed on the ab plane and pointing along the +x, -y, +y, -x directions defines the n = 0 building block for the series. The nth members can be constructed from blocks containing four pyramids and n Mn(4+)O(6) octahedra with 2/m symmetry. Compounds in the related systems CaMnO(x) and LaCuO(x), containing Mn(3+) and Cu(2+) pyramids and Mn(4+) and Cu(3+) octahedra have also been found to be members of the series. The size and charge of the A-site cation and the apical distortion of the pyramidally coordinated B-site cation are shown to be important factors in the stabilization of certain members of the series. A qualitative explanation for the absence of some of the possible members of the series is presented based on these factors.

  7. Antidepressant and anxiolytic-like effects of 4n, a novel 5-HT3 receptor antagonist using behaviour based rodent models.

    PubMed

    Kumar, Baldev; Jindal, Ankur; Pandey, Dilip Kumar; Bhatt, Shvetank; Devadoss, Thangaraj; Mahesh, Radhakrishnan

    2012-09-01

    The present study was designed to investigate the putative antidepressant and anxiolytic-like effects of N-n-Butylquinoxalin-2-carboxamide (4n), a novel 5-HT3 receptor antagonist, with an optimal log P (2.01) and pA2 value (7.3) greater than ondansetron (6.9) using rodent behavioural models of depression and anxiety. Acute treatment of 4n (1-4 mg/kg, ip) in mice produced antidepressant-like effect in forced swim test (FST) without affecting the baseline locomotion in actophotometer test in mice. 4n (2-4 mg/kg, ip) treatment also potentiated the 5-hydroxytryptophan (5-HTP) induced head twitch response in mice. Further, 4n (1-4 mg/kg, ip) treatment antagonized reserpine induced hypothermia in rats. Chronic treatment (14 days) with 4n (1-4 mg/kg) and paroxetine (10 mg/kg) significantly attenuated the behavioural anomalies induced by bilateral olfactory bulbectomy in rats in modified open field paradigm. An anxiogenic-like behaviour was induced by light alone as the stimulus using light-dark aversion test. 4n (2-4 mg/kg, ip) treatment significantly increased no. of transitions between dark and lit area and the time spent in the lit area. In conclusion, these preliminary investigations confirm that 4n exhibited antidepressant and anxiolytic-like effects in rodent models of depression and anxiety.

  8. [DNA image-fluorimetry of individual human chromosomes].

    PubMed

    Agafonova, N A; Sakuta, G A; Rozanov, Iu M; Shteĭn, G I; Kudriavtsev, B N

    2013-01-01

    Mucrofluorimetric method for the determination of DNA content in individual human chromosomes has been developed. The method is based on a preliminary identification of chromosomes with Hoechst 33258, followed by staining of the chromosomes with Feulgen reaction using Schiffs reagent type ethidium bromide-SO2, then measuring the fluorescence intensity of the chromosomes using an image analyzer. The method allows to determine the DNA content of individual chromosomes with accuracy up to 4.5 fg. DNA content of individual human chromosomes, their p-and q-arms as well as homologous chromosomes were measured using the developed method. It has been shown that the DNA content in the chromosomes of normal human karyotype is unstable. Fluctuations in the DNA content in some chromosomes can vary 35-40 fg.

  9. T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites

    PubMed Central

    Brunaud, Véronique; Balzergue, Sandrine; Dubreucq, Bertrand; Aubourg, Sébastien; Samson, Franck; Chauvin, Stéphanie; Bechtold, Nicole; Cruaud, Corinne; DeRose, Richard; Pelletier, Georges; Lepiniec, Loïc; Caboche, Michel; Lecharny, Alain

    2002-01-01

    A statistical analysis of 9000 flanking sequence tags characterizing transferred DNA (T-DNA) transformants in Arabidopsis sheds new light on T-DNA insertion by illegitimate recombination. T-DNA integration is favoured in plant DNA regions with an A-T-rich content. The formation of a short DNA duplex between the host DNA and the left end of the T-DNA sets the frame for the recombination. The sequence immediately downstream of the plant A-T-rich region is the master element for setting up the DNA duplex, and deletions into the left end of the integrated T-DNA depend on the location of a complementary sequence on the T-DNA. Recombination at the right end of the T-DNA with the host DNA involves another DNA duplex, 2–3 base pairs long, that preferentially includes a G close to the right end of the T-DNA. PMID:12446565

  10. DNA nanostructure immobilization to lithographic DNA arrays

    NASA Astrophysics Data System (ADS)

    Negrete, Omar D.

    Although DNA is well known for its genetic role in biology, DNA has also been sought-after as a material for the self-assembly of biological and electronic devices. Examples of DNA nanostructure construction include DNA tiled self-assembly and DNA Origami, where by controlling the sequence and concentration of DNA molecules, the rational design of geometric DNA nanostructures is possible. The assembly of DNA nanostructures takes place in solution and thus they are in disorder and require further organization to construct circuitry or devices. Hence, it is essential for future applications of this technology to develop methods to direct the placement of DNA nanostructures on a surface. To address this challenge my research examines the use of DNA microarrays to capture DNA nanostructures via DNA hybridization. Modern DNA arrays offer a high-density of sequence-specific molecular recognition sites where the addressable placement of DNA nanostructures can be achieved. Using Maskless Array Synthesizer (MAS) technology, I have characterized photolithographic DNA arrays for the hybridization of DNA complexes like large DNA molecules (> 1 kb), DNA-gold nanoparticle conjugates, and DNA Origami. Although modern photolithographic DNA arrays can possess a high-density of sequence (106/cm2), the printed DNA areas are on the order of tens of microns. Thus, I have also developed a method to reduce the DNA array spot size to nanoscale dimensions through the combined use of electron beam lithography with photolithographic DNA synthesis. This work addresses the key elements towards developing a surface patterning technology that takes advantage of DNA base-pairing for both molecular sub-assembly and surface patterning.

  11. Cross section limits for the Cm248(Mg25,4n-5n)Hs268,269 reactions

    NASA Astrophysics Data System (ADS)

    Dvorak, J.; Brüchle, W.; Düllmann, Ch. E.; Dvorakova, Z.; Eberhardt, K.; Eichler, R.; Jäger, E.; Nagame, Y.; Qin, Z.; Schädel, M.; Schausten, B.; Schimpf, E.; Schuber, R.; Semchenkov, A.; Thörle, P.; Türler, A.; Wegrzecki, M.; Yakushev, A.

    2009-03-01

    We report on an attempt to produce and detect Hs268 and Hs269 in the nuclear fusion reaction Mg25+Cm248 using the gas phase chemistry apparatus COMPACT. No decay chains attributable to the decay of hassium isotopes were observed during the course of this experiment. From the nonobservation of Hs269 we derive a cross section limit of 0.4 pb (63% confidence limit) for the reaction Cm248(Mg25,4n)Hs269 at a center-of-target beam energy of 140 MeV. The evaluated cross section limit for the Cm248(Mg25,5n)Hs268 reaction depends on the assumed half-life of unknown Hs268. Current systematics of the half-lives for even-even Hs isotopes suggests a value of 0.5 s, resulting in a cross section limit of 1.3 pb.

  12. The unprecedented recurrent diploid/tetraploid mosaicism of trisomy-18 (mixoploidy; 4n+18/2n+18): clinical report.

    PubMed

    Ozler, Sibel; Ersoy, Ali O; Oztas, Efser; Topcu, Vehap; Celen, Sevki; Danisman, Nuri

    2015-07-01

    We report on a 32-year-old woman who presented at gestational age of 14 weeks. During ultrasonographic examination, we discovered that her fetus had several important abnormalities, including a cystic hygroma, craniofacial defects (low-set ears, broad nose), heart defects (single atrium, single ventricle), agenesis of corpus callosum, limb defects (clenched hands, pes equinovarus). Chorionic villus sampling and karyotyping revealed diploid/tetraploid mosaicism with trisomy 18 (mixoploidy; 4n+18/2n+18). Her second pregnancy was terminated because of the same clinical manifestations 1 year prior. Her first pregnancy resulted in the birth of an entirely healthy boy. As far as know, no other similar case has been presented in the literature.

  13. Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

    PubMed

    Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

    2014-05-05

    Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser.

  14. 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.

  15. Dependency of temperature on polarization in CH4/N2 dielectric barrier discharge plasma: A crude assumption

    NASA Astrophysics Data System (ADS)

    Majumdar, Abhijit; Ghosh, Basudev; Hippler, Rainer

    2010-11-01

    We have investigated the variations of polarization (P) and the temperature (ΔT) at the electrode surfaces during the deposition of C-N layer in CH4/N2 (1:2) dielectric barrier discharge plasma. The reactive deposition process influences the surface temperature, polarization, and the value of the in situ dielectric constant. We have developed a crude model that correlates the surface temperature and surface polarization with thin film properties. We assume that during the thin film deposition process, the atomic mean kinetic energy is equal to the electrostatic energy stored in the electrode surface area. Theoretically estimated temperature is found to agree well with the experimental results. However, the linear model thus developed cannot be used to explain the phenomena in the interfacial polarization stage that requires a nonlinear theory.

  16. 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.

  17. Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA templates.

    PubMed

    Kim, Sangjin; Schroeder, Charles M; Xie, X Sunney

    2010-02-05

    HIV-1 RT (human immunodeficiency virus-1 reverse transcriptase) is a multifunctional polymerase responsible for reverse transcription of the HIV genome, including DNA replication on both RNA and DNA templates. During reverse transcription in vivo, HIV-1 RT replicates through various secondary structures on RNA and single-stranded DNA (ssDNA) templates without the need for a nucleic acid unwinding protein, such as a helicase. In order to understand the mechanism of polymerization through secondary structures, we investigated the DNA polymerization activity of HIV-1 RT on long ssDNA templates using a multiplexed single-molecule DNA flow-stretching assay. We observed that HIV-1 RT performs fast primer extension DNA synthesis on single-stranded regions of DNA (18.7 nt/s) and switches its activity to slow strand displacement synthesis at DNA hairpin locations (2.3 nt/s). Furthermore, we found that the rate of strand displacement synthesis is dependent on the GC content in hairpin stems and template stretching force. This indicates that the strand displacement synthesis occurs through a mechanism that is neither completely active nor passive: that is, the opening of the DNA hairpin is driven by a combination of free energy released during dNTP (deoxyribonucleotide triphosphate) hydrolysis and thermal fraying of base pairs. Our experimental observations provide new insight into the interchanging modes of DNA replication by HIV-1 RT on long ssDNA templates.

  18. Ancient plant DNA in lake sediments.

    PubMed

    Parducci, Laura; Bennett, Keith D; Ficetola, Gentile Francesco; Alsos, Inger Greve; Suyama, Yoshihisa; Wood, Jamie R; Pedersen, Mikkel Winther

    2017-04-03

    Contents I. II. III. IV. V. VI. VII. VIII. IX. X. XI. References SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.

  19. Prokaryotic DNA ligases unwind superhelical DNA.

    PubMed

    Ivanchenko, M; van Holde, K; Zlatanova, J

    1996-09-13

    We have studied the effect on DNA topology of binding of prokaryotic DNA ligases (T4 and E. coli) to superhelical or nicked circular DNA. Performing topoisomerase I-mediated relaxation in the presence of increasing amounts of T4 ligase led to a shift in the topoisomer distribution to increasingly more negative values. This result suggested that T4 ligase unwound the DNA and was further substantiated by ligation of nicked circular molecules by E. coli DNA ligase in the presence of increasing amounts of T4 ligase. Such an experiment was possible since the two DNA ligases require different cofactors for enzymatic activity. Performing a similar experiment with reverse partners, using E. coli DNA ligase as ligand, and T4 ligase as sealing agent, we observed that the E. coli enzyme also unwound the DNA. Thus, prokaryotic DNA ligases can be added to an ever-growing list of DNA-binding proteins that unwind the DNA upon binding.

  20. Modulation of photophysics due to orientational selectivity of 4- N, N-dimethylamino cinnamaldehyde β-cyclodextrin inclusion complex in different solvents

    NASA Astrophysics Data System (ADS)

    Panja, Subhasis; Ranjan Bangal, Prakriti; Chakravorti, Sankar

    2000-10-01

    This paper delineates some results on the twisted intramolecular charge transfer (TICT) dynamics of 4- N, N-dimethylamino cinnamaldehyde (DMACA) encapsulated in β-cyclodextrin in aqueous and non-aqueous solvents at room temperature. 4- N, N-Dimethylamino cinnamaldehyde is found to form a 1:1 inclusion complex with β-CD in both aqueous and non-aqueous solvents with a binding constant higher in aqueous solvent. The most important feature of the inclusion complexes of 4- N, N-dimethylamino cinnamaldehyde, as revealed from photophysics of normal and twisted intramolecular charge transfer bands, is that there is a preferential orientation of 4- N, N-dimethylamino cinnamaldehyde inside β-CD cavity in aqueous solvent with dimethyl group sticking outside and in non-aqueous solvents it is just the opposite.

  1. Commentary: Mitochondrial DNA damage and loss in diabetes

    PubMed Central

    Gilkerson, Robert

    2017-01-01

    This commentary discusses damage and loss of mitochondrial DNA (mtDNA) in type 2 diabetes mellitus from both the clinical and experimental perspectives. Increasingly, an array of studies in experimental models and patients suggests that the cellular stresses of insulin resistance in type 2 diabetes damage mtDNA, leading to loss of mitochondrial genetic content. As such, mtDNA is emerging as both a valuable monitoring tool and translational preventive target for metabolic disease. PMID:27253402

  2. 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

    2015-08-04

    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.

  3. A novel yellow-emitting SrAlSi4N7:Ce3+ phosphor for solid state lighting: Synthesis, electronic structure and photoluminescence properties

    NASA Astrophysics Data System (ADS)

    Ruan, Jian; Xie, Rong-Jun; Funahashi, Shiro; Tanaka, Yoshinori; Takeda, Takashi; Suehiro, Takayuki; Hirosaki, Naoto; Li, Yuan-Qiang

    2013-12-01

    Ce3+-doped and Ce3+/Li+-codoped SrAlSi4N7 phosphors were synthesized by gas pressure sintering of powder mixtures of Sr3N2, AlN, α-Si3N4, CeN and Li3N. The phase purity, electronic crystal structure, photoluminescence properties of SrAlSi4N7:Ce3+(Ce3+/Li+) were investigated in this work. The band structure calculated by the DMol3 code shows that SrAlSi4N7 has a direct band gap of 3.87 eV. The single crystal analysis of Ce3+-doped SrAlSi4N7 indicates a disordered Si/Al distribution and nitrogen vacnacy defects. SrAlSi4N7 was identified as a major phase of the fired powders, and Sr5Al5Si21N35O2 and AlN as minor phases. Both Ce3+ and Ce3+/Li+ doped SrAlSi4N7 phosphors can be efficiently excited by near-UV or blue light and show a broadband yellow emission peaking around 565 nm. A highest external quantum efficiency of 38.3% under the 450 nm excitation was observed for the Ce3+/Li+-doped SrAlSi4N7 (5 mol%). A white light LED lamp with color temperature of 6300 K and color rendering index of Ra=78 was achieved by combining Sr0.97Al1.03Si3.997N\\94\\maccounttest14=t0005_18193 7:Ce3+0.03 with a commercial blue InGaN chip. It indicates that SrAlSi4N7:Ce3+ is a promising yellow emitting down-conversion phosphor for white LEDs.

  4. Create and Maintain Content

    EPA Pesticide Factsheets

    Find resources and guidance on writing for the web, keeping your content relevant, using social media, meeting accessibility standards, and how to transform your content into the WebCMS to meet One EPA Web standards.

  5. Metal free half metallicity in 2D system: structural and magnetic properties of g-C4N3 on BN

    PubMed Central

    Hashmi, Arqum; Hong, Jisang

    2014-01-01

    Synthesis of a half metallic material on a substrate is highly desirable for diverse applications. Herein, we have investigated structural, adsorptive, and magnetic properties of metal free graphitic carbon nitride (g-C4N3) layer on hexagonal BN layer (h-BN) using the optB88-vdW van der Waals density functional theory. It is found that g-C4N3 layer can be adsorbed on BN layer due to the change of lattice constant of the hybridized system. The newly found lattice constant of g-C4N3 was 9.89 Å, which is approximately 2% lower and larger than to those of free standing BN and g-C4N3, respectively. Also, 2 × 2 surface reconstruction geometry predicted in free standing g-C4N3 layer disappears on the BN layer. Interestingly, we have found that metal free half metallic behavior in g-C4N3 can be preserved even on BN layer and the characters of spin polarized planar orbitals suggest that our theoretical prediction can be verified using normal incidence of K-edge X-ray magnetic circular dichroism (XMCD) measurement. PMID:24625438

  6. In vivo amelioration of endogenous antitumor autoantibodies via low-dose P4N through the LTA4H/activin A/BAFF pathway

    PubMed Central

    Lin, Yu-Ling; Tsai, Nu-Man; Hsieh, Cheng-Hao; Ho, Shu-Yi; Chang, Jung; Wu, Hsin-Yi; Hsu, Ming-Hua; Chang, Chia-Ching; Liao, Kuang-Wen; Jackson, Tiffany L. B.; Mold, David E.; Huang, Ru Chih C.

    2016-01-01

    Cancer progression is associated with the development of antitumor autoantibodies in patients’ sera. Although passive treatment with antitumor antibodies has exhibited remarkable therapeutic efficacy, inhibitory effects on tumor progression by endogenous antitumor autoantibodies (EAAs) have been limited. In this study, we show that P4N, a derivative of the plant lignan nordihydroguaiaretic acid (NDGA), enhanced the production of EAAs and inhibited tumor growth at low noncytotoxic concentrations via its immunoregulatory activity. Intratumoral injection of P4N improved the quantity and quality of EAAs, and passive transfer of P4N-induced EAAs dramatically suppressed lung metastasis formation and prolonged the survival of mice inoculated with metastatic CT26 tumor cells. P4N-induced EAAs specifically recognized two surface antigens, 78-kDa glucose-regulated protein (GRP78) and F1F0 ATP synthase, on the plasma membrane of cancer cells. Additionally, P4N treatment led to B-cell proliferation, differentiation to plasma cells, and high titers of autoantibody production. By serial induction of autocrine and paracrine signals in monocytes, P4N increased B-cell proliferation and antibody production via the leukotriene A4 hydrolase (LTA4H)/activin A/B-cell activating factor (BAFF) pathway. This mechanism provides a useful platform for studying and seeking a novel immunomodulator that can be applied in targeting therapy by improving the quantity and quality of the EAAs. PMID:27856749

  7. In vivo amelioration of endogenous antitumor autoantibodies via low-dose P4N through the LTA4H/activin A/BAFF pathway.

    PubMed

    Lin, Yu-Ling; Tsai, Nu-Man; Hsieh, Cheng-Hao; Ho, Shu-Yi; Chang, Jung; Wu, Hsin-Yi; Hsu, Ming-Hua; Chang, Chia-Ching; Liao, Kuang-Wen; Jackson, Tiffany L B; Mold, David E; Huang, Ru Chih C

    2016-11-29

    Cancer progression is associated with the development of antitumor autoantibodies in patients' sera. Although passive treatment with antitumor antibodies has exhibited remarkable therapeutic efficacy, inhibitory effects on tumor progression by endogenous antitumor autoantibodies (EAAs) have been limited. In this study, we show that P4N, a derivative of the plant lignan nordihydroguaiaretic acid (NDGA), enhanced the production of EAAs and inhibited tumor growth at low noncytotoxic concentrations via its immunoregulatory activity. Intratumoral injection of P4N improved the quantity and quality of EAAs, and passive transfer of P4N-induced EAAs dramatically suppressed lung metastasis formation and prolonged the survival of mice inoculated with metastatic CT26 tumor cells. P4N-induced EAAs specifically recognized two surface antigens, 78-kDa glucose-regulated protein (GRP78) and F1F0 ATP synthase, on the plasma membrane of cancer cells. Additionally, P4N treatment led to B-cell proliferation, differentiation to plasma cells, and high titers of autoantibody production. By serial induction of autocrine and paracrine signals in monocytes, P4N increased B-cell proliferation and antibody production via the leukotriene A4 hydrolase (LTA4H)/activin A/B-cell activating factor (BAFF) pathway. This mechanism provides a useful platform for studying and seeking a novel immunomodulator that can be applied in targeting therapy by improving the quantity and quality of the EAAs.

  8. Motivation in Content Reading.

    ERIC Educational Resources Information Center

    Tutolo, Daniel

    Motivational devices are useful in content-area reading because the content load of most content textbooks is so extensive that few if any students can be expected to understand all that an author intends to communicate. Many students who are inexperienced with the subject matter are unable to read the assignments independently. The recognition of…

  9. SINGLE-MOLECULE STUDY OF DNA POLYMERIZATION ACTIVITY OF HIV-1 REVERSE TRANSCRIPTASE ON DNA TEMPLATES

    PubMed Central

    Kim, Sangjin; Schroeder, Charles M.; Xie, X. Sunney

    2009-01-01

    Human Immunodeficiency Virus-1 reverse transcriptase (HIV-1 RT) is a multifunctional polymerase responsible for reverse transcription of the HIV genome, including DNA replication on both RNA and DNA templates. During reverse transcription in vivo, HIV-1 RT replicates through various secondary structures on RNA and single-stranded DNA templates without the need for a nucleic acid unwinding protein, such as a helicase. In order to understand the mechanism of polymerization through secondary structures, we investigated the DNA polymerization activity of HIV-1 RT on long single-stranded DNA templates using a multiplexed single-molecule DNA flow-stretching assay. We observed that HIV-1 RT performs fast primer extension DNA synthesis on single-stranded regions of DNA (18.7 nt/s) and switches its activity to slow strand displacement synthesis at DNA hairpin locations (2.3 nt/s). Furthermore, we found that the rate of strand displacement synthesis is dependent on the GC content in hairpin stems and template stretching force. This indicates that the strand displacement synthesis occurs through a mechanism that is neither completely active nor passive, i.e. the opening of the DNA hairpin is driven by a combination of free energy released during dNTP hydrolysis and thermal fraying of base pairs. Our experimental observations provide new insight into the interchanging modes of DNA replication by HIV-1 RT on long single-stranded DNA templates. PMID:19968999

  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. A Transition to a Compact Form of DNA in Polymer Solutions

    PubMed Central

    Lerman, L. S.

    1971-01-01

    In the presence of over-threshold concentrations of simple neutral polymers and salts, DNA undergoes a cooperative change in its solution structure. Sedimentation studies at low DNA concentrations show that phage DNA molecules collapse into particles approaching the compactness of the contents of phage heads. The interaction between DNA and polymers is thought to be nonspecifically replusive. PMID:5288774

  12. DNA nanostructure meets nanofabrication.

    PubMed

    Zhang, Guomei; Surwade, Sumedh P; Zhou, Feng; Liu, Haitao

    2013-04-07

    Recent advances in DNA nanotechnology have made it possible to construct DNA nanostructures of almost arbitrary shapes with 2-3 nm of precision in their dimensions. These DNA nanostructures are ideal templates for bottom-up nanofabrication. This review highlights the challenges and recent advances in three areas that are directly related to DNA-based nanofabrication: (1) fabrication of large scale DNA nanostructures; (2) pattern transfer from DNA nanostructure to an inorganic substrate; and (3) directed assembly of DNA nanostructures.

  13. 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.

  14. All-polymer photovoltaic devices of poly(3-(4-n-octyl)-phenylthiophene) from Grignard Metathesis (GRIM) polymerization.

    PubMed

    Holcombe, Thomas W; Woo, Claire H; Kavulak, David F J; Thompson, Barry C; Fréchet, Jean M J

    2009-10-14

    The synthesis of poly[3-(4-n-octyl)-phenylthiophene] (POPT) from Grignard Metathesis (GRIM) is reported. GRIM POPT is found to have favorable electronic, optical, and processing properties for organic photovoltaics (OPVs). Space-charge limited current and field effect transistor measurements for POPT yielded hole mobilities of 1 x 10(-4) cm(2)/(V s) and 0.05 cm(2)/(V s), respectively. Spincasting GRIM POPT from chlorobenzene yields a thin film with a 1.8 eV band gap, and PC(61)BM:POPT bulk heterojection devices provide a peak performance of 3.1%. Additionally, an efficiency of 2.0% is achieved in an all-polymer, bilayer OPV using poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-(1-cyanovinylene)phenylene] (CNPPV) as an acceptor. This state-of-the-art all-polymer device is analyzed in comparison to the analogous poly(3-hexylthiophene) (P3HT)/CNPPV device. Counter to expectations based on more favorable energy level alignment, greater active layer light absorption, and similar hole mobility, P3HT/CNPPV devices perform less well than POPT/CNPPV devices with a peak efficiency of 0.93%.

  15. 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.

  16. 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.

  17. Analysis of degenerate four-wave mixing spectra of NO in a CH4/N2/O2 flame

    NASA Astrophysics Data System (ADS)

    Farrow, R. L.; Rakestraw, D. J.

    We report comparisons of degenerate four-wave mixing (DFWM) spectra of NO measured in a CH4/N2/O2 flame to spectral simulations based on a two-level theory for stationary, saturable absorbers by Abrams et al. Temperatures determined from least-squares fits of simulations to experimental spectra in the A2Σ+?X2Π+(0,0) band are compared to temperatures obtained from OH absorption spectroscopy and a radiation-corrected thermocouple. We find that DFWM rotational temperatures derived from Q-branch spectra agree with thermocouple and are independent of pump laser intensity for low to moderate saturation (I Isat). However, the temperatures are systematically low and depend on pump intensity if the analysis neglects saturation effects. We demonstrate a method for obtaining an effective pump saturation intensity for use with the two-level model. This approach for analyzing saturated DFWM line intensities differs from previous work in that the use of the theory of Abrams et al. rather than a transition-dipole-moment power law allows treatment of a much wider range of saturation. Based on the observed signal-to-noise ratio an NO detection sensitivity of 25 ppm is projected, limited by a DFWM background interference specific to hydrocarbon flames.

  18. 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

  19. 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.

  20. 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

  1. Multimedia content description framework

    NASA Technical Reports Server (NTRS)

    Bergman, Lawrence David (Inventor); Kim, Michelle Yoonk Yung (Inventor); Li, Chung-Sheng (Inventor); Mohan, Rakesh (Inventor); Smith, John Richard (Inventor)

    2003-01-01

    A framework is provided for describing multimedia content and a system in which a plurality of multimedia storage devices employing the content description methods of the present invention can interoperate. In accordance with one form of the present invention, the content description framework is a description scheme (DS) for describing streams or aggregations of multimedia objects, which may comprise audio, images, video, text, time series, and various other modalities. This description scheme can accommodate an essentially limitless number of descriptors in terms of features, semantics or metadata, and facilitate content-based search, index, and retrieval, among other capabilities, for both streamed or aggregated multimedia objects.

  2. DNA ligase I, the replicative DNA ligase.

    PubMed

    Howes, Timothy R L; Tomkinson, Alan E

    2012-01-01

    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.

  3. 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.

  4. A new architecture for high spin organics based on Baird's rule of 4n electron triplet aromatics.

    PubMed

    Mauksch, Michael; Tsogoeva, Svetlana B

    2017-02-08

    Due to the absence of open subshells (unlike transition metal compounds), stable high spin organic molecules are rare and are mostly limited to states of low multiplicity. As an alternative to high multiplicity polyradicals and polycarbenes, with their small energetic separation of different spin isomers, it is demonstrated that Baird's rule of 4n electron aromaticity in the triplet electronic state allows, in principle, the design of polycyclic high spin organics with high spin multiplicity in the electronic ground state and a large energetic separation for other spin states. Energy spacing between spin isomers is dictated here by the aromaticity or antiaromaticity of individual cycles (taking into account all π electrons), rather than by a spin Hamiltonian alone (accounting only for unpaired spin electrons). As a proof of concept, dyads of the cyclopentadienyl cation (which has been reported to possess a triplet ground state) have been computationally found to possess a quintet electronic ground state with two ferromagnetically coupled Baird aromatic rings (with SCF-GIAO NICS(0) = -4.6 and -4.4, respectively; "NICS" is "nucleus independent chemical shift") at the CASMP2(8,10)/6-311G*//CASSCF(8,10)/6-311G* level, which is 48.3 kcal mol(-1) lower in energy than the C2 open shell singlet with two antiaromatic rings (with NICS = +17.4), and 19.7 kcal mol(-1) below the triplet which has one aromatic and one antiaromatic ring, with NICS = -4.8 and +45.0, respectively. Triads of the cyclopentadienyl cation in linear and branched topologies are also proposed to be ground states of maximum spin multiplicity by computations at the DFT and CCSD(T)/6-31G//UB3LYP/6-311G* levels.

  5. The Richardson constant and barrier inhomogeneity at Au/Si3N4/n-Si (MIS) Schottky diodes

    NASA Astrophysics Data System (ADS)

    Tataroğlu, A.; Pür, F. Z.

    2013-07-01

    Si3N4 films were deposited on n-type silicon substrate by the radio frequency magnetron sputtering technique. The current-voltage (I-V) characteristics of Au/Si3N4/n-Si (metal-insulator-semiconductor) Schottky diodes were investigated in the temperature range of 160-400 K. Experimental results show an abnormal increase in the zero-bias barrier height (BH) (ΦBo) and a decrease in the ideality factor (n) with increasing temperature. This behavior is attributed to barrier inhomogeneities by assuming a Gaussian distribution (GD) of BHs. The conventional Richardson plot (ln(Io/T2) versus 1000/T) exhibits a linearity above about 300 K. The values of activation energy (Ea) and Richardson constant (A*) were found to be 0.350 eV and 1.242 × 10-3 A cm-2 K-2 from the slope and the intercept at the ordinate of the linear region of this plot, respectively. Also, we attempted to draw a ΦBo versus q/2kT plot to determine evidence of the GD of BHs, and the values of \\bar \\Phi _{{\\rm{Bo}}} = 0.999\\,{\\rm{eV}} and σs = 0.137 eV for the mean BH and zero-bias standard deviation, respectively, were obtained from this plot; then, a modified ln(Io/T2) - q2σs2/2k2T2 versus q/kT plot gives \\bar \\Phi _{{\\rm{Bo}}} and A* as 0.992 eV and 108.228 A cm-2 K-2, respectively. This value of A* is very close to the theoretical value of 112 A cm-2 K-2 for n-type Si.

  6. 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.

  7. 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

  8. Superstatistical model of bacterial DNA architecture

    PubMed Central

    Bogachev, Mikhail I.; Markelov, Oleg A.; Kayumov, Airat R.; Bunde, Armin

    2017-01-01

    Understanding the physical principles that govern the complex DNA structural organization as well as its mechanical and thermodynamical properties is essential for the advancement in both life sciences and genetic engineering. Recently we have discovered that the complex DNA organization is explicitly reflected in the arrangement of nucleotides depicted by the universal power law tailed internucleotide interval distribution that is valid for complete genomes of various prokaryotic and eukaryotic organisms. Here we suggest a superstatistical model that represents a long DNA molecule by a series of consecutive ~150 bp DNA segments with the alternation of the local nucleotide composition between segments exhibiting long-range correlations. We show that the superstatistical model and the corresponding DNA generation algorithm explicitly reproduce the laws governing the empirical nucleotide arrangement properties of the DNA sequences for various global GC contents and optimal living temperatures. Finally, we discuss the relevance of our model in terms of the DNA mechanical properties. As an outlook, we focus on finding the DNA sequences that encode a given protein while simultaneously reproducing the nucleotide arrangement laws observed from empirical genomes, that may be of interest in the optimization of genetic engineering of long DNA molecules. PMID:28225058

  9. Superstatistical model of bacterial DNA architecture

    NASA Astrophysics Data System (ADS)

    Bogachev, Mikhail I.; Markelov, Oleg A.; Kayumov, Airat R.; Bunde, Armin

    2017-02-01

    Understanding the physical principles that govern the complex DNA structural organization as well as its mechanical and thermodynamical properties is essential for the advancement in both life sciences and genetic engineering. Recently we have discovered that the complex DNA organization is explicitly reflected in the arrangement of nucleotides depicted by the universal power law tailed internucleotide interval distribution that is valid for complete genomes of various prokaryotic and eukaryotic organisms. Here we suggest a superstatistical model that represents a long DNA molecule by a series of consecutive ~150 bp DNA segments with the alternation of the local nucleotide composition between segments exhibiting long-range correlations. We show that the superstatistical model and the corresponding DNA generation algorithm explicitly reproduce the laws governing the empirical nucleotide arrangement properties of the DNA sequences for various global GC contents and optimal living temperatures. Finally, we discuss the relevance of our model in terms of the DNA mechanical properties. As an outlook, we focus on finding the DNA sequences that encode a given protein while simultaneously reproducing the nucleotide arrangement laws observed from empirical genomes, that may be of interest in the optimization of genetic engineering of long DNA molecules.

  10. Advances in forensic DNA quantification: a review.

    PubMed

    Lee, Steven B; McCord, Bruce; Buel, Eric

    2014-11-01

    This review focuses upon a critical step in forensic biology: detection and quantification of human DNA from biological samples. Determination of the quantity and quality of human DNA extracted from biological evidence is important for several reasons. Firstly, depending on the source and extraction method, the quality (purity and length), and quantity of the resultant DNA extract can vary greatly. This affects the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use-standard short-tandem repeat (STR) typing, mini-STR typing or mitochondrial DNA sequencing. Secondly, because it is important in forensic analysis to preserve as much of the evidence as possible for retesting, it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. Lastly, results from initial quantitative and qualitative evaluations permit a more informed interpretation of downstream analytical results. Newer quantitative techniques involving real-time PCR can reveal the presence of degraded DNA and PCR inhibitors, that provide potential reasons for poor genotyping results and may indicate methods to use for downstream typing success. In general, the more information available, the easier it is to interpret and process the sample resulting in a higher likelihood of successful DNA typing. The history of the development of quantitative methods has involved two main goals-improving precision of the analysis and increasing the information content of the result. This review covers advances in forensic DNA quantification methods and recent developments in RNA quantification.

  11. 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.

  12. Sperm DNA oxidative damage and DNA adducts

    PubMed Central

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-01-01

    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

  13. Quantifying quality in DNA self-assembly

    PubMed Central

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

    2014-01-01

    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. PMID:24751596

  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. 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…

  16. 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…

  17. 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…

  18. Synthesis and cytotoxic activity of 4-N-carboxybutyl-5-fluorocytosyl-Arg-Gln-Trp-Arg-Arg-Trp-Trp-Gln-Arg-NH₂.

    PubMed

    Somlai, Csaba; Correche, Estela; Olivella, Monica; Tolosa, Laia; Lechon, Maria José Gomez; Dombi, György; Tóth, Gábor K; Penke, Botond; Enriz, Ricardo D

    2012-07-01

    The chemical synthesis of 4-N-carboxybutyl-5-fluorocytosine (II) in solution phase starting from 5-fluorocytosine and the solid phase synthesis of Arg-Gln-Trp-Arg-Arg-Trp-Trp-Gln-Arg-NH(2) attached to the 4-N-carboxybutyl-5-fluorocytosine residue at the N-terminus of the peptide (III) via peptide bond formation is reported. The target compound exhibited a significant cytotoxic activity against a culture of HepG2 cells. In addition our results demonstrated that this new compound affect cell viability, produce mitochondrial dysfunction as well as interfere with intracellular calcium homeostasis control; leading to cell malfunction and death.

  19. DNA encoding a DNA repair protein

    DOEpatents

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  20. 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

  1. Base composition at mtDNA boundaries suggests a DNA triple helix model for human mitochondrial DNA large-scale rearrangements.

    PubMed

    Rocher, Christophe; Letellier, Thierry; Copeland, William C; Lestienne, Patrick

    2002-06-01

    Different mechanisms have been proposed to account for mitochondrial DNA (mtDNA) instability based on the presence of short homologous sequences (direct repeats, DR) at the potential boundaries of mtDNA rearrangements. Among them, slippage-mispairing of the replication complex during the asymmetric replication cycle of the mammalian mitochondrial DNA has been proposed to account for the preferential localization of deletions. This mechanism involves a transfer of the replication complex from the first neo-synthesized heavy (H) strand of the DR1, to the DR2, thus bypassing the intervening sequence and producing a deleted molecule. Nevertheless, the nature of the bonds between the DNA strands remains unknown as the forward sequence of DR2, beyond the replication complex, stays double-stranded. Here, we have analyzed the base composition of the DR at the boundaries of mtDNA deletions and duplications and found a skewed pyrimidine content of about 75% in the light-strand DNA template. This suggests the possible building of a DNA triple helix between the G-rich neo-synthesized DR1 and the base-paired homologous G.C-rich DR2. In vitro experiments with the purified human DNA polymerase gamma subunits enabled us to show that the third DNA strand may be used as a primer for DNA replication, using a template with the direct repeat forming a hairpin, with which the primer could initiate DNA replication. These data suggest a novel molecular basis for mitochondrial DNA rearrangements through the distributive nature of the DNA polymerase gamma, at the level of the direct repeats. A general model accounting for large-scale mitochondrial DNA deletion and duplication is proposed. These experiments extend to a DNA polymerase from an eucaryote source the use of a DNA triple helix strand as a primer, like other DNA polymerases from phage and bacterial origins.

  2. Presequence-Independent Mitochondrial Import of DNA Ligase Facilitates Establishment of Cell Lines with Reduced mtDNA Copy Number.

    PubMed

    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.

  3. 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

  4. 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.

  5. 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)

  6. Mitochondrial DNA mutations in ageing and disease: implications for HIV?

    PubMed

    Payne, Brendan A I; Gardner, Kristian; Chinnery, Patrick F

    2015-01-01

    Mitochondrial DNA (mtDNA) mutations cause neurological and multisystem disease. Somatic (acquired) mtDNA mutations are also associated with degenerative diseases and with normal human ageing. It is well established that certain nucleoside reverse transcriptase inhibitor (NRTI) antiretroviral drugs cause inhibition of the mtDNA polymerase, pol γ, leading to a reduction in mtDNA content (depletion). Given this effect of NRTI therapy on mtDNA replication, it is plausible that NRTI treatment may also lead to increased mtDNA mutations. Here we review recent evidence for an effect of HIV infection or NRTI therapy on mtDNA mutations, as well as discussing the methodological challenges in addressing this question. Finally, we discuss the possible implications for HIV-infected persons, with particular reference to ageing.

  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. Molecular DNA switches and DNA chips

    NASA Astrophysics Data System (ADS)

    Sabanayagam, Chandran R.; Berkey, Cristin; Lavi, Uri; Cantor, Charles R.; Smith, Cassandra L.

    1999-06-01

    We present an assay to detect single-nucleotide polymorphisms on a chip using molecular DNA switches and isothermal rolling- circle amplification. The basic principle behind the switch is an allele-specific oligonucleotide circularization, mediated by DNA ligase. A DNA switch is closed when perfect hybridization between the probe oligonucleotide and target DNA allows ligase to covalently circularize the probe. Mismatches around the ligation site prevent probe circularization, resulting in an open switch. DNA polymerase is then used to preferentially amplify the closed switches, via rolling-circle amplification. The stringency of the molecular switches yields 102 - 103 fold discrimination between matched and mismatched sequences.

  9. DNA interaction studies of a platinum (II) complex containing an antiviral drug, ribavirin: the effect of metal on DNA binding.

    PubMed

    Shahabadi, Nahid; Mirzaei kalar, Zeinab; Moghadam, Neda Hosseinpour

    2012-10-01

    The water-soluble Pt (II) complex, [PtCl (DMSO)(N(4)N(7)-ribavirin)]· H(2)O (ribavirin is an antiviral drug) has been synthesized and characterized by physico-chemical and spectroscopic methods. The binding interactions of this complex with calf thymus DNA (CT-DNA) were investigated using fluorimetry, spectrophotometry, circular dichroism and viscosimetry. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant, K(b), was 7.2×10(5) M(-1). In fluorimetric studies, the enthalpy (ΔH<0) and entropy (ΔS>0) changes of the reaction between the Pt (II) complex with CT-DNA showed hydrophobic interaction. In addition, CD study showed stabilization of the right-handed B form of CT-DNA. All these results prove that the complex interacts with CT-DNA via intercalative mode of binding. In comparison with the previous study of the DNA interaction with ribavirin, these results show that platinum complex has greater affinity to CT-DNA.

  10. 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.

  11. DNA vaccines: a simple DNA sensing matter?

    PubMed

    Coban, Cevayir; Kobiyama, Kouji; Jounai, Nao; Tozuka, Miyuki; Ishii, Ken J

    2013-10-01

    Since the introduction of DNA vaccines two decades ago, this attractive strategy has been hampered by its low immunogenicity in humans. Studies conducted to improve the immunogenicity of DNA vaccines have shown that understanding the mechanism of action of DNA vaccines might be the key to successfully improving their immunogenicity. Our current understanding is that DNA vaccines induce innate and adaptive immune responses in two ways: (1) encoded protein (or polypeptide) antigen(s) by the DNA plasmid can be expressed in stromal cells (i.e., muscle cells) as well as DCs, where these antigens are processed and presented to naïve CD4 or CD8 T cells either by direct or cross presentation, respectively; and (2) the transfected DNA plasmid itself may bind to an un-identified cytosolic DNA sensor and activate the TBK1-STING pathway and the production of type I interferons (IFNs) which function as an adjuvant. Recent studies investigating double-stranded cytosolic DNA sensor(s) have highlighted new mechanisms in which cytosolic DNA may release secondary metabolites, which are in turn recognized by a novel DNA sensing machinery. Here, we discuss these new metabolites and the possibilities of translating this knowledge into improved immunogenicity for DNA vaccines.

  12. DNA Repair by Reversal of DNA Damage

    PubMed Central

    Yi, Chengqi; He, Chuan

    2013-01-01

    Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology. PMID:23284047

  13. 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.

  14. 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...

  15. Effects of substitutional atoms on the properties of γ'-(Fe 1- xTM x) 4N (TM = Co, Ni) compounds

    NASA Astrophysics Data System (ADS)

    Xue, Desheng; Li, Fashen; Yang, Jingbo; Kong, Yong; Gao, Meizhen

    1997-02-01

    We report on the influence of substitutional atoms TM (TM = Co, Ni) on the properties of (Fe 1- xTM x) 4N compounds. The structure and magnetic properties were studied by X-ray diffraction, vibrating-sample magnetometer measurement and Mössbauer spectroscopy. All the samples exhibit a γ'-Fe 4N-type structure. The substitution of Co for iron is random, but Ni has a preference for the comer sites. The hyperfine field and the isomer shift of γ'-(Fe 1- xTM x) 4N are closely related to the concentration of the substitutional atom and its site occupation. All these can be readily explained by the increase of 3d electrons and the decrease of unit-cell volume. Combining the saturation magnetization and the hyperfine field, the magnetic moment of transition-metal atom in γ'-(Fe 1- xTM x) 4N has been derived. Using high-pressure Mössbauer spectra, the magnetovolume effect and the chemical bonding effect of the TM atom has been investigated for the first time.

  16. 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.

  17. Cloning and comparative mapping of a human chromosome 4-specific alpha satellite DNA sequence.

    PubMed

    D'Aiuto, L; Antonacci, R; Marzella, R; Archidiacono, N; Rocchi, M

    1993-11-01

    We 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.

  18. 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

  19. 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.

  20. 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.

  1. The Efficacy and Safety of 4-n-butylresorcinol 0.1% Cream for the Treatment of Melasma: A Randomized Controlled Split-face Trial

    PubMed Central

    Huh, Sun Young; Shin, Jung-Won; Na, Jung-Im; Huh, Chang-Hun; Youn, Sang-Woong

    2010-01-01

    Background Melasma is a common acquired symmetrical hypermelanosis that occurs on sun-exposed areas, and it is frequently observed among women. Various treatment modalities have been tried, but none are completely satisfactory. 4-n-butylresorcinol, which is a resorcinol derivative that has an inhibitory effect on both tyrosinase and tyrosinase-related protein-1, was introduced in 1995 and it has received increasing attention as a new hypopigmenting agent. However, the hypopigmenting effect of 4-n-butylresorcinol in human subjects has only been shown in a few studies. Objective The aim of this study was to investigate the hypopigmenting efficacy and safety of 4-n-butylresorcinol 0.1% cream for the treatment of melasma. Methods Twenty patients with melasma were enrolled to this randomized, double-blind, vehicle-controlled, split-face comparative study. The patients were instructed to apply 4-n-butylresorcinol 0.1% cream or vehicle to each side of the face twice daily for 8 weeks. Mexameter measurements were performed along with photography at baseline, 4 weeks and 8 weeks. Adverse events were observed and recorded throughout the study. Results All the patients completed the study. Mexameter measurements demonstrated that the melanin index of the treated side showed a significant decrease when compared with that of the vehicle-treated side after 4 weeks (p=0.006) and after 8 weeks (p<0.0005). All the adverse reactions were mild and transient. Conclusion 4-n-butylresorcinol 0.1% cream showed rapid efficacy and it was well tolerated when used for the treatment of melasma. PMID:20548876

  2. Poxvirus DNA Replication

    PubMed Central

    Moss, Bernard

    2013-01-01

    Poxviruses are large, enveloped viruses that replicate in the cytoplasm and encode proteins for DNA replication and gene expression. Hairpin ends link the two strands of the linear, double-stranded DNA genome. Viral proteins involved in DNA synthesis include a 117-kDa polymerase, a helicase–primase, a uracil DNA glycosylase, a processivity factor, a single-stranded DNA-binding protein, a protein kinase, and a DNA ligase. A viral FEN1 family protein participates in double-strand break repair. The DNA is replicated as long concatemers that are resolved by a viral Holliday junction endonuclease. PMID:23838441

  3. Microwave Plasma-Activated Chemical Vapor Deposition of Nitrogen-Doped Diamond. II: CH4/N2/H2 Plasmas

    PubMed Central

    2016-01-01

    We report a combined experimental and modeling study of microwave-activated dilute CH4/N2/H2 plasmas, as used for chemical vapor deposition (CVD) of diamond, under very similar conditions to previous studies of CH4/H2, CH4/H2/Ar, and N2/H2 gas mixtures. Using cavity ring-down spectroscopy, absolute column densities of CH(X, v = 0), CN(X, v = 0), and NH(X, v = 0) radicals in the hot plasma have been determined as functions of height, z, source gas mixing ratio, total gas pressure, p, and input power, P. Optical emission spectroscopy has been used to investigate, with respect to the same variables, the relative number densities of electronically excited species, namely, H atoms, CH, C2, CN, and NH radicals and triplet N2 molecules. The measurements have been reproduced and rationalized from first-principles by 2-D (r, z) coupled kinetic and transport modeling, and comparison between experiment and simulation has afforded a detailed understanding of C/N/H plasma-chemical reactivity and variations with process conditions and with location within the reactor. The experimentally validated simulations have been extended to much lower N2 input fractions and higher microwave powers than were probed experimentally, providing predictions for the gas-phase chemistry adjacent to the diamond surface and its variation across a wide range of conditions employed in practical diamond-growing CVD processes. The strongly bound N2 molecule is very resistant to dissociation at the input MW powers and pressures prevailing in typical diamond CVD reactors, but its chemical reactivity is boosted through energy pooling in its lowest-lying (metastable) triplet state and subsequent reactions with H atoms. For a CH4 input mole fraction of 4%, with N2 present at 1–6000 ppm, at pressure p = 150 Torr, and with applied microwave power P = 1.5 kW, the near-substrate gas-phase N atom concentration, [N]ns, scales linearly with the N2 input mole fraction and exceeds the concentrations [NH]ns, [NH2]ns

  4. Mechanism of extraordinary DNA digestion by pepsin.

    PubMed

    Zhang, Yanfang; Li, Chunchuan; Liu, Yu; Wang, Xiaoqian; Dong, Ping; Liang, Xingguo

    2016-03-25

    Recently, the protein-specific enzyme pepsin was found be capable of digesting nucleic acids unexpectedly. In this study, the effects of DNA sequence specificity, purine content (AG content), depurination and length on the nucleic acid (NA) digestion by pepsin were investigated. The results showed that pepsin functioned similar as endonuclease, and presented a moderate sequence preference compared with restriction enzymes and non-specific nuclease. The digestion was specific (sequence dependent to some extent), and pepsin preferred to cleave purine-rich sequences. The digestion of favorable sequence was dramatically accelerated when the purine base at the cleavage site was removed (created an apurinic (AP) site). However, the AP site did not help to cleave the sequence that pepsin could not cleave originally. Moreover, the results indicated that pepsin preferred to digest longer DNA (e.g. > 59 bases) than shorter one, and sequence shorter than 30 bases was barely digested. The mechanism of DNA digestion by pepsin was also discussed.

  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. DNA Damage, DNA Repair, Aging, and Neurodegeneration.

    PubMed

    Maynard, Scott; Fang, Evandro Fei; Scheibye-Knudsen, Morten; Croteau, Deborah L; Bohr, Vilhelm A

    2015-09-18

    Aging in mammals is accompanied by a progressive atrophy of tissues and organs, and stochastic damage accumulation to the macromolecules DNA, RNA, proteins, and lipids. The sequence of the human genome represents our genetic blueprint, and accumulating evidence suggests that loss of genomic maintenance may causally contribute to aging. Distinct evidence for a role of imperfect DNA repair in aging is that several premature aging syndromes have underlying genetic DNA repair defects. Accumulation of DNA damage may be particularly prevalent in the central nervous system owing to the low DNA repair capacity in postmitotic brain tissue. It is generally believed that the cumulative effects of the deleterious changes that occur in aging, mostly after the reproductive phase, contribute to species-specific rates of aging. In addition to nuclear DNA damage contributions to aging, there is also abundant evidence for a causative link between mitochondrial DNA damage and the major phenotypes associated with aging. Understanding the mechanistic basis for the association of DNA damage and DNA repair with aging and age-related diseases, such as neurodegeneration, would give insight into contravening age-related diseases and promoting a healthy life span.

  7. 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.

  8. Microbial Biofertilizer Decreases Nicotine Content by Improving Soil Nitrogen Supply.

    PubMed

    Shang, Cui; Chen, Anwei; Chen, Guiqiu; Li, Huanke; Guan, Song; He, Jianmin

    2017-01-01

    Biofertilizers have been widely used in many countries for their benefit to soil biological and physicochemical properties. A new microbial biofertilizer containing Phanerochaete chrysosporium and Bacillus thuringiensis was prepared to decrease nicotine content in tobacco leaves by regulating soil nitrogen supply. Soil NO3(-)-N, NH4(+)-N, nitrogen supply-related enzyme activities, and nitrogen accumulation in plant leaves throughout the growing period were investigated to explore the mechanism of nicotine reduction. The experimental results indicated that biofertilizer can reduce the nicotine content in tobacco leaves, with a maximum decrement of 16-18 % in mature upper leaves. In the meantime, the total nitrogen in mature lower and middle leaves increased with the application of biofertilizer, while an opposite result was observed in upper leaves. Protein concentration in leaves had similar fluctuation to that of total nitrogen in response to biofertilizer. NO3(-)-N content and nitrate reductase activity in biofertilizer-amended soil increased by 92.3 and 42.2 %, respectively, compared to those in the control, whereas the NH4(+)-N and urease activity decreased by 37.8 and 29.3 %, respectively. Nitrogen uptake was improved in the early growing stage, but this phenomenon was not observed during the late growth period. Nicotine decrease is attributing to the adjustment of biofertilizer in soil nitrogen supply and its uptake in tobacco, which result in changes of nitrogen content as well as its distribution in tobacco leaves. The application of biofertilizer containing P. chrysosporium and B. thuringiensis can reduce the nicotine content and improve tobacco quality, which may provide some useful information for tobacco cultivation.

  9. 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

  10. Lead Content of Foodstuffs

    PubMed Central

    Mitchell, Douglas G.; Aldous, Kenneth M.

    1974-01-01

    The lead content of a number of foodstuffs, particularly baby fruit juices and milk, is reported. Samples were analyzed in quadruplicate by using an automated Delves cup atomic absorption procedure. A large proportion of the products examined contained significant amounts of lead. Of 256 metal can examined, the contents of 62% contained a lead level of 100 μg/l. or more, 37% contained 200 μg/l. or more and 12% contained 400 μg/l. lead or more. Of products in glass and aluminum containers, only 1% had lead levels in excess of 200 μg/l. Lead levels of contents also correlate with the seam length/volume ratio of the leaded seam can. A survey of bulk milk showed a mean lead level of 40 μg/l. for 270 samples; for canned evaporated milk the mean level was 202 μg/l. These data indicate a potential health hazard. PMID:4406645

  11. 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.

  12. Mammalian DNA helicase.

    PubMed Central

    Hübscher, U; Stalder, H P

    1985-01-01

    A forked DNA was constructed to serve as a substrate for DNA helicases. It contains features closely resembling a natural replication fork. The DNA was prepared in large amounts and was used to assay displacement activity during isolation from calf thymus DNA polymerases alpha holoenzyme. One form of DNA polymerase alpha holoenzyme is possibly involved leading strand replication at the replication fork and possesses DNA dependent ATPase activity (Ottiger, H.-P. and Hübscher, U. (1984) Proc. Natl. Acad. Sci. USA 81, 3993-3997). The enzyme can be separated from DNA polymerase alpha by velocity sedimentation in conditions of very low ionic strength and then be purified by chromatography on Sephacryl S-200 and ATP-agarose. At all stages of purification, DNA dependent ATPase and displacement activity profiles were virtually superimposable. The DNA dependent ATPase can displace a hybridized DNA fragment with a short single-stranded tail at its 3'hydroxyl end only in the presence of ATP, and this displacement relies on ATP hydrolysis. Furthermore, homogeneous single-stranded binding proteins from calf thymus as well as from other tissues cannot perform this displacement reaction. By all this token the DNA dependent ATPase appears to be a DNA helicase. It is suggested that this DNA helicase might act in concert with DNA polymerase alpha at the leading strand, possibly pushing the replication fork ahead of the polymerase. Images PMID:3162158

  13. 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.

  14. Regulating contents and furnishings.

    PubMed

    Koffel, W E

    1991-01-01

    The criteria in the 1991 edition of the Life Safety Code are a first attempt to address the fire hazards associated with upholstered furniture and mattresses. Recognizing that the criteria do not represent a complete hazard analysis, it is anticipated that the subcommittee will continue its efforts and will evaluate the appropriateness of additional criteria. The NFPA Standards Council also has appointed a Technical Committee on Contents and Furnishings, which will meet in August 1991. This committee will have primary responsibility for developing fire hazard calculation procedures and documents that other committees can use to control the fire hazards of contents and furnishings.

  15. '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

  16. DNA microarray technology. Introduction.

    PubMed

    Pollack, Jonathan R

    2009-01-01

    DNA microarray technology has revolutionized biological research by enabling genome-scale explorations. This chapter provides an overview of DNA microarray technology and its application to characterizing the physical genome, with a focus on cancer genomes. Specific areas discussed include investigations of DNA copy number alteration (and loss of heterozygosity), DNA methylation, DNA-protein (i.e., chromatin and transcription factor) interactions, DNA replication, and the integration of diverse genome-scale data types. Also provided is a perspective on recent advances and future directions in characterizing the physical genome.

  17. 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.

  18. Spectrophotometric studies of 4-[N'-(4-imino-2-oxo-thiazolidin-5-ylidene)-hydrazino]-benzenesulfonic acid as a reagent for the determination of palladium.

    PubMed

    Lozynska, Lesya; Tymoshuk, Oleksandr; Chaban, Taras

    2015-01-01

    The spectrophotometric behavior of a new, first-time synthesized reagent - 4-[N'-(4-imino-2-oxo-thiazolidin-5-ylidene)hydrazino]-benzenesulfonic acid (ITHBA), has been investigated. A simple, rapid, accurate, selective and sensitive method for the spectrophotometric determination of Pd(II) ions using this reagent was developed. The optimal conditions for the formation of the complexes were found. The molar absorptivity at λ = 438 nm is 7.5 × 10(3) L mol(-1) cm(-1), and Beer's law is observed for the concentrations ranging from 0.2-2.2 µg mL-1Pd(II). The effects of extraneous ions were investigated. The method proved to be successful in determination of palladium in the intermetallides and resistor. The accuracy of spectrophotometric palladium assay in real objects with 4-[N'-(4-imino-2-oxo-thiazolidin-5-ylidene)-hydrazino]-benzenesulfonic acid has been confirmed by voltammetric or atomic absorption spectroscopy method.

  19. Discovery of 1-[4-(N-benzylamino)phenyl]-3-phenylurea derivatives as non-peptidic selective SUMO-sentrin specific protease (SENP)1 inhibitors.

    PubMed

    Uno, Masaharu; Koma, Yosuke; Ban, Hyun Seung; Nakamura, Hiroyuki

    2012-08-15

    We developed 1-[4-(N-benzylamino)phenyl]-3-phenylurea derivative 4 (GN6958) as a non-peptidic selective SUMO-sentrin specific protease (SENP)1 protease inhibitor based on the hypoxia inducible factor (HIF)-1α inhibitor 1 (GN6767). The direct interaction of compound 1 with SENP1 protein in cells was observed by the pull-down experiments using the biotin-tagged compound 2 coated on the streptavidin affinity column. Among the various 1-[4-(N-benzylamino)phenyl]-3-phenylurea derivatives tested, compounds 3 and 4 suppressed HIF-1α accumulation in a concentration-dependent manner without affecting the expression level of tubulin protein in HeLa cells. Both compounds inhibited SENP1 protease activity in a concentration-dependent manner, and compound 4 exhibited more potent inhibition than compound 3. Compound 4 exhibited selective inhibition against SENP1 protease activity without inhibiting other protease enzyme activities in vitro.

  20. Large-scale purification of pharmaceutical-grade plasmid DNA using tangential flow filtration and multi-step chromatography.

    PubMed

    Sun, Bo; Yu, XiangHui; Yin, Yuhe; Liu, Xintao; Wu, Yongge; Chen, Yan; Zhang, Xizhen; Jiang, Chunlai; Kong, Wei

    2013-09-01

    The demand for pharmaceutical-grade plasmid DNA in vaccine applications and gene therapy has been increasing in recent years. In the present study, a process consisting of alkaline lysis, tangential flow filtration, purification by anion exchange chromatography, hydrophobic interaction chromatography and size exclusion chromatography was developed. The final product met the requirements for pharmaceutical-grade plasmid DNA. The chromosomal DNA content was <1 μg/mg plasmid DNA, and RNA was not detectable by agarose gel electrophoresis. Moreover, the protein content was <2 μg/mg plasmid DNA, and the endotoxin content was <10 EU/mg plasmid DNA. The process was scaled up to yield 800 mg of pharmaceutical-grade plasmid DNA from approximately 2 kg of bacterial cell paste. The overall yield of the final plasmid DNA reached 48%. Therefore, we have established a rapid and efficient production process for pharmaceutical-grade plasmid DNA.

  1. 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.

  2. 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.

  3. Nqrs Data for C10H12Br4N2Zn [Br4Zn·2(C5H6N)] (Subst. No. 1253)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C10H12Br4N2Zn [Br4Zn·2(C5H6N)] (Subst. No. 1253)

  4. Nqrs Data for C10H12Cl4N2Pd [Cl4H2Pd·2(C5H5N)] (Subst. No. 1261)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C10H12Cl4N2Pd [Cl4H2Pd·2(C5H5N)] (Subst. No. 1261)

  5. Nqrs Data for C10H8Br4N2Sn [Br4Sn·C10H8N2] (Subst. No. 1214)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C10H8Br4N2Sn [Br4Sn·C10H8N2] (Subst. No. 1214)

  6. Nqrs Data for C10H12Cl4N2Pt [Cl4H2Pt·2(C5H5N)] (Subst. No. 1262)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C10H12Cl4N2Pt [Cl4H2Pt·2(C5H5N)] (Subst. No. 1262)

  7. Semantische Content Management Systeme

    NASA Astrophysics Data System (ADS)

    Gams, Erich; Mitterdorfer, Daniel

    Content Management Systeme (CMS) sind in vielen Organisationen bereits seit längerer Zeit fester Bestandteil zur Verwaltung und kollaborativen Bearbeitung von Text- und Multimedia-Inhalten. Im Zuge der rasch ansteigenden Fülle an Informationen und somit auch Wissen wird die Überschaubarkeit der Datenbestände jedoch massiv eingeschränkt. Diese und zusätzliche Anforderungen, wie automatisch Datenquellen aus dem World Wide Web (WWW) zu extrahieren, lassen traditionelle CMS immer mehr an ihre Grenzen stoßen. Dieser Beitrag diskutiert die neuen Herausforderungen an traditionelle CMS und bietet Lösungsvorschläge, wie CMS kombiniert mit semantischen Technologien diesen Herausforderungen begegnen können. Die Autoren stellen eine generische Systemarchitektur für Content Management Systeme vor, die einerseits Inhalte für das Semantic Web generieren, andererseits Content aus dem Web 2.0 syndizieren können und bei der Aufbereitung des Content den User mittels semantischer Technologien wie Reasoning oder Informationsextraktion unterstützen. Dabei wird auf Erfahrungen bei der prototypischen Implementierung von semantischer Technologie in ein bestehendes CMS System zurückgegriffen.

  8. 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.…

  9. 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…

  10. 21-Day Content Screen

    EPA Pesticide Factsheets

    Under PRIA, EPA has 21 days after it receives the pesticide application and the fee to conduct an initial screen of the application’s contents for completeness and for the applicant to make necessary corrections. This page provides the checklists we use.

  11. 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.

  12. 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…

  13. Content Area Instructional Strategies

    ERIC Educational Resources Information Center

    Montgomery, Joel R.

    2008-01-01

    The aim of this working paper is to identify research-supported strategies for content that can be integrated effectively to promote the development of biliterate academic literacy by English language learners (ELLs) in middle-school bilingual classrooms. The paper provides a research-based summary of relevant learning needs of adolescent…

  14. Basic Structure Content Scaling.

    ERIC Educational Resources Information Center

    Jackson, Douglas N.; Helmes, Edward

    1979-01-01

    A basic structure approach is proposed for obtaining multidimensional scale values for attitude, achievement, or personality items from response data. The technique permits the unconfounding of scale values due to response bias and content and partitions item indices of popularity or difficulty among a number of relevant dimensions. (Author/BH)

  15. 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…

  16. Content in Health Education.

    ERIC Educational Resources Information Center

    Health Education (Washington D.C.), 1985

    1985-01-01

    Six articles from health journals since 1898 discuss content in health education: (1) "Mental Health and the Schools" (Cromwell); (2) "You Must Relax--But How?" (Nash); (3) "School Hygiene and the Teaching of Hygiene in the Public Schools" (Egbert); (4) "A Sex Education Program" (Leibee); (5) "Sexual Education" (McCurdy); and (6) "Sex Education"…

  17. Local electronic states of Fe4N films revealed by x-ray absorption spectroscopy and x-ray magnetic circular dichroism

    NASA Astrophysics Data System (ADS)

    Ito, Keita; Toko, Kaoru; Takeda, Yukiharu; Saitoh, Yuji; Oguchi, Tamio; Suemasu, Takashi; Kimura, Akio

    2015-05-01

    We performed x-ray absorption spectroscopy (XAS) and x-ray magnetic circular dichroism (XMCD) measurements at Fe L2,3 and N K-edges for Fe4N epitaxial films grown by molecular beam epitaxy. In order to clarify the element specific local electronic structure of Fe4N, 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 L2,3-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 Fe4N.

  18. 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.

  19. 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

    2012-04-03

    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.

  20. 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.

  1. 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

    2016-04-07

    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.

  2. Synthesis of p-Co3O4/n-TiO2 Nanoparticles for Overall Water Splitting under Visible Light Irradiation

    PubMed Central

    Zhang, Qiang; Hai, Zhenyin; Jian, Aoqun; Xu, Hongyan; Xue, Chenyang; Sang, Shengbo

    2016-01-01

    p-Co3O4/n-TiO2 nanoparticles (~400 nm) for photocatalysis were prepared via carbon assisted method and sol-gel method in this work. The paper also studied the application of visible light illuminated p-Co3O4/n-TiO2 nanocomposites cocatalyst to the overall pure water splitting into H2 and O2. In addition, the H2 evolution rate of the p-Co3O4/n-TiO2 nanocomposites is 25% higher than that of the pure Co3O4 nanoparticles. Besides, according to the results of the characterizations, the scheme of visible light photocatalytic water splitting is proposed, the Co3O4 of the nanocomposites is excited by visible light, and the photo-generated electrons and holes existing on the conduction band of Co3O4 and valence band of TiO2 have endowed the photocatalytic evolution of H2 and O2 with higher efficiency. The optimal evolution rate of H2 and O2 is 8.16 μmol/h·g and 4.0 μmol/h·g, respectively. PMID:28335266

  3. 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.

  4. 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.

  5. 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.

  6. 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)

  7. 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.

  8. 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)

  9. Loss of mitochondrial DNA with aging in Drosophila melanogaster.

    PubMed

    Massie, H R; Baird, M B; McMahon, M M

    1975-01-01

    The buoyant densities of nuclear and mitochondrial DNA from Drosophila melanogaster lysates has been found to show no change with increasing age in both CsCl and Cs2SO4 equilibrium density gradients. Whole fly homogenates were used to demonstrate no change in nuclear DNA content during adult life. Mitochondrial DNA increased from 1.2 to 4.3% of the total DNA during the first week of adult life and then decreased during senescence to a minimum of 1.5% at 10 weeks of age which represented a 65% loss in mitochondrial DNA content with age. These data are interpreted to support the proposal that mitochondria destruction occurs during senescence.

  10. DNA quantification of basidiomycetous fungi during storage of logging residues

    PubMed Central

    Alfredsen, Gry; Filbakk, Tore; Fossdal, Carl Gunnar

    2015-01-01

    The demand for bioenergy caused an increased use of logging residues, branches and treetops that were previously left on the ground after harvesting. Residues are stored outdoors in piles and it is unclear to what extent fungi transform this material. Our objective was to quantify the amount of wood degrading fungi during storage using quantitative real-time PCR (qPCR) to detect basidiomycetous DNA in logging residues, a novel approach in this field. We found that the qPCR method was accurate in quantifying the fungal DNA during storage. As the moisture content of the piled logging residues decreased during the storage period, the fungal DNA content also decreased. Scots pine residues contained more fungal DNA than residues from Norway spruce. Loose piles had generally more fungal DNA than bundled ones. PMID:25870777

  11. DNA quantification of basidiomycetous fungi during storage of logging residues.

    PubMed

    Børja, Isabella; Alfredsen, Gry; Filbakk, Tore; Fossdal, Carl Gunnar

    2015-01-01

    The demand for bioenergy caused an increased use of logging residues, branches and treetops that were previously left on the ground after harvesting. Residues are stored outdoors in piles and it is unclear to what extent fungi transform this material. Our objective was to quantify the amount of wood degrading fungi during storage using quantitative real-time PCR (qPCR) to detect basidiomycetous DNA in logging residues, a novel approach in this field. We found that the qPCR method was accurate in quantifying the fungal DNA during storage. As the moisture content of the piled logging residues decreased during the storage period, the fungal DNA content also decreased. Scots pine residues contained more fungal DNA than residues from Norway spruce. Loose piles had generally more fungal DNA than bundled ones.

  12. Cellular content and biosynthesis of polyamines during rooster spermatogenesis.

    PubMed Central

    Oliva, R; Vidal, S; Mezquita, C

    1982-01-01

    The natural polyamines spermine and spermidine, and the diamine putrescine, were extracted from rooster testis cells separated by sedimentation at unit gravity, and from vas-deferens spermatozoa. The ratios spermine/DNA and spermidine/DNA were kept relatively constant throughout spermatogenesis, whereas the ratio putrescine/DNA rose in elongated spermatids. The cellular content of spermine, spermidine and putrescine decreased markedly in mature spermatozoa. Two rate-limiting enzymes in the biosynthetic pathway of polyamines, ornithine decarboxylase and S-adenosyl-L-methionine decarboxylase, showed their highest activities at the end of spermiogenesis and were not detectable in vas-deferens spermatozoa. A marked reduction in cell volume during spermiogenesis without a parallel decrease in the cellular content of polyamines suggests the possibility that the marked changes in chromatin composition and structure occurring in rooster late spermatids could take place in an ambience of high polyamine concentration. Images PLATE 1 PMID:7159401

  13. Commentary: Mitochondrial DNA damage and loss in diabetes.

    PubMed

    Gilkerson, Robert

    2016-10-01

    This commentary discusses damage and loss of mitochondrial DNA (mtDNA) in type 2 diabetes mellitus from both the clinical and experimental perspectives. Increasingly, an array of studies in experimental models and patients suggests that the cellular stresses of insulin resistance in type 2 diabetes damage mtDNA, leading to loss of mitochondrial genetic content. As such, mtDNA is emerging as both a valuable monitoring tool and translational preventive target for metabolic disease. Copyright © 2016 John Wiley & Sons, Ltd.

  14. Genetic analysis of an aphid endosymbiont DNA fragment homologous to the rnpA-rpmH-dnaA-dnaN-gyrB region of eubacteria.

    PubMed

    Lai, C Y; Baumann, P

    1992-04-15

    Buchnera aphidicola is a Gram- eubacterium with a DNA G+C content of 28-30 mol%. This organism is an obligate intracellular symbiont of aphids. To determine its similarity to or difference from other eubacteria, a 4.9-kb DNA fragment from B. aphidicola containing the gene homologous to Escherichia coli dnaA (a gene involved in the initiation of chromosome replication) was cloned into E. coli and sequenced. The order of genes on this fragment, 60K-10K-rnpA-rpmH-dnaA-dnaN-gyrB, was similar to that found in other eubacteria. The sole difference was the absence of recF between dnaN and gyrB. The deduced amino acid sequence of these proteins resembled those of E. coli by a 41 to 83% identity. Except for E. coli, in all the eubacteria so far examined, dnaA is preceded by multiple 9-nucleotide repeats known as a DnaA boxes. No DnaA boxes were detected in the endosymbiont DNA. The possibility that this observation is a consequence of the low G+C content of this DNA fragment (14 mol% G+C) is unlikely since in Mycoplasma capricolum this fragment (19 mol% G+C) has eight DnaA boxes (Fujita et al., 1992). The presence of the sequence, GATC, recognized by the Dam methyl-transferase system, only within six regions coding for proteins suggests that methylation is not a factor in the regulation of the initiation of endosymbiont chromosome replication.

  15. 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…

  16. Nanopores: Flossing with DNA

    NASA Astrophysics Data System (ADS)

    Kasianowicz, John J.

    2004-06-01

    Passing a DNA strand many times back-and-forth through a protein nanopore would enable the interaction between them to be studied more closely. This may now be possible, using a dumbbell-shaped DNA-polymer complex, which may lead to a more reliable analysis of DNA sequences using nanopores.

  17. Development of a Vero cell DNA reference standard for residual DNA measurement in China.

    PubMed

    Cao, Shouchun; Dong, Guanmu; Tang, Jianrong; Li, Jia; Liu, Jinghua; Shi, Leitai; Li, Changgui; Wang, Junzhi

    2013-02-01

    This collaborative study developed a Vero cell DNA reference for standardizing dot blot hybridization, an assay widely employed to measure residual DNA contents of viral vaccines prepared with Vero cells. High purity of Vero cell DNA was extracted and characterized by Hind III enzyme digestion and DNA sequencing. Then, with a cooperative calibration, the concentration of Vero cell DNA reference bulk solution was determined (64.0 ± 1.9 μg/mL, OD 260/OD 280 = 1.87) and diluted (40 ng/mL) with Tris-EDTA buffer containing bovine serum albumin as freeze-dried excipients. With industrial filling apparatus, the diluted bulk was loaded into ampoules (0.5 mL each) which were heat sealed after nitrogen filling. Finally, a collaborative study showed that the Vero cell DNA reference could reach a sensitivity of 1 to 5 pg/dot and maintained good stability after accelerated destruction test. The successful establishment of the Vero cell DNA quantitative reference will facilitate the standardization of dot blot hybridization for testing residual host cell DNA.

  18. Three-Dimensional DNA Nanostructures Assembled from DNA Star Motifs.

    PubMed

    Tian, Cheng; Zhang, Chuan

    2017-01-01

    Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.

  19. Sugarcane genes associated with sucrose content

    PubMed Central

    Papini-Terzi, Flávia S; Rocha, Flávia R; Vêncio, Ricardo ZN; Felix, Juliana M; Branco, Diana S; Waclawovsky, Alessandro J; Del Bem, Luiz EV; Lembke, Carolina G; Costa, Maximiller DL; Nishiyama, Milton Y; Vicentini, Renato; Vincentz, Michel GA; Ulian, Eugênio C; Menossi, Marcelo; Souza, Glaucia M

    2009-01-01

    Background - Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcane's sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants. Results - We have evaluated thirty genotypes that have different Brix (sugar) levels and identified genes differentially expressed in internodes using cDNA microarrays. These genes were compared to existing gene expression data for sugarcane plants subjected to diverse stress and hormone treatments. The comparisons revealed a strong overlap between the drought and sucrose-content datasets and a limited overlap with ABA signaling. Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation. The data also indicate that aquaporins, as well as lignin biosynthesis and cell wall metabolism genes, are strongly related to sucrose accumulation. Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways. Conclusion - Gene expression analysis of sugarcane populations contrasting for sucrose content indicated a possible overlap with drought and cell wall metabolism processes and suggested signaling and transcriptional regulators to be

  20. Content Addressable Memory Project

    DTIC Science & Technology

    1990-11-01

    The Content Addressable M1-emory Project consists of the development of several experimental software systems on an AMT Distributed Array Processor...searching (database) compiler algorithms memory management other systems software) Linear C is an unlovely hybrid language which imports the CAM...memory from AMT’s operating system for the DAP; how- ever, other than this limitation, the memory management routines work exactly as their C counterparts

  1. 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).

  2. 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!

  3. 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.

  4. DNA profiling from heroin street dose packages.

    PubMed

    Zamir, Ashira; Cohen, Yaron; Azoury, Myriam

    2007-03-01

    A large amount of heroin street doses are seized and examined for drug content by the Israel police. These are generally wrapped in heat-sealed plastic. Occasionally it is possible to visualize latent fingerprints on the plastic wrap itself, but the small size of the plastic item and the sealing process makes the success rate very low. In this study, the possibility of extracting and profiling DNA from the burnt edge of the plastic wrap was investigated. The idea was based on the assumption that epithelial cells might be trapped during the sealing process. The results show that there are sufficient quantities of DNA deposited at the "amorphic" burnt edges of sealed street doses for DNA profiling to be carried out. A controlled experiment using a known donor was performed. This subject carried out sealing of "street drug" packages and consequent DNA extractions were performed to show that known DNA profiles could be recovered from such packages, as a result of handling by the "packer." "Square-like" burnt edges did not yield DNA profiles, probably because of differences in the sealing process. It was also shown that DNA could be recovered from the plastic wrap itself and not only from the amorphic burnt edges. As heroin dealers and drug users are often involved in other crimes and run-ins with the law, the effective extraction and addition of their DNA profiles from such items of evidence to the newly established DNA database in Israel provides new avenues in the continued fight against crime and drug traffickers.

  5. 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.

  6. Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice.

    PubMed

    Ferrand, Janina; Patron, Kevin; Legrand-Frossi, Christine; Frippiat, Jean-Pol; Merlin, Christophe; Alauzet, Corentine; Lozniewski, Alain

    2014-10-01

    Analysis of bacterial DNA from fecal samples of mice is commonly performed in experimental studies. Although DNA extraction is a critical step in various molecular approaches, the efficiency of methods that may be used for DNA extraction from mice fecal samples has never been evaluated. We compared the efficiencies of six widely used commercial kits (MasterPure™ Gram Positive DNA Purification Kit, QIAamp® DNA Stool Mini Kit; NucliSENS® easyMAG®, ZR Fecal DNA MiniPrep™, FastDNA® SPIN Kit for Feces and FastDNA® SPIN Kit for Soil) and a non-commercial method for DNA isolation from mice feces and cecal contents. DNA quantity and quality were assessed by fluorometry, spectrophotometry, gel electrophoresis and qPCR. Cell lysis efficiencies were evaluated by qPCR targeting three relevant bacteria in spiked specimens. For both feces and intestinal contents, the most efficient extraction method was the FastDNA® SPIN Kit for Soil.

  7. Properties of extracellular DNA from the cerebrospinal fluid and blood plasma during Parkinson's disease.

    PubMed

    Glebova, K V; Konorova, I L; Poleshchuk, V V; Baidakova, G V; Veiko, N N

    2014-04-01

    The cerebrospinal fluid of patients with Parkinson's disease was shown to contain extracellular DNA. Extracellular DNA concentration in the cerebrospinal fluid was 3.3-fold lower than in blood plasma from these patients. HPLC-mass spectrometry analysis showed that the pool of extracellular DNA from the liquor is characterized by a lower content of deoxythymidine, but greater amounts of deoxycytidine and deoxyguanosine than the pool of extracellular DNA from the plasma. The level of deoxyguanosine was 2 times lower than that of deoxycytidine (as differentiated from plasma extracellular DNA with similar content of these substances). Our findings indicate that extracellular DNA from the cerebrospinal fluid contains considerable amounts of modified deoxyguanosine. These data attest to significant differences in the quantitative and qualitative characteristics of extracellular DNA from the blood and cerebrospinal fluid of patients. Specific features of extracellular DNA from the cerebrospinal fluid of patients suggest its involvement in the pathogenesis of Parkinson's disease.

  8. Identifying stabilizers of plasmid DNA for pharmaceutical use.

    PubMed

    Zeng, Yuhong; Ramsey, Joshua D; King, Robert; Leviten, Michael; Mcguire, Ruth; Volkin, David B; Joshi, Sangeeta B; Middaugh, C Russell

    2011-03-01

    To better address the need for developing stable formulations of plasmid DNA-based biopharmaceuticals, 37 compounds from a generally regarded as safe library were examined for their potential use as stabilizers. A plasmid DNA-based therapeutic vaccine, BHT-DNA, was used as a model system. Initial studies were performed to compare the biophysical properties of BHT-DNA plasmid from bulk drug substance and finished drug product. An agarose gel electrophoresis-based assay was then employed in excipient compatibility studies for the drug product by monitoring supercoiled plasmid DNA content in various formulations. After incubation at 40 °C for 30 days, eight out of the 37 excipients tested were able to better retain the supercoil content compared to the control. Sodium citrate appeared to be the most effective stabilizer and its protective capability plateaued at an ionic strength of about 0.4. Several other excipients including malic acid, ethanol, and Pluronic F-68 were also identified as promising stabilizers for BHT-DNA plasmid DNA. Additionally, compounds, including ferrous chloride, ascorbic acid, human serum albumin, and PEG 1000, which significantly destabilized the supercoiled plasmid DNA were identified. These data may also be applicable to other plasmid DNA-based pharmaceuticals for storage stability improvement, due to chemical and structural similarities of these macromolecules.

  9. 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.

  10. 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)

  11. DNA-Mediated Electrochemistry

    PubMed Central

    Gorodetsky, Alon A.; Buzzeo, Marisa C.

    2009-01-01

    The base pair stack of DNA has been demonstrated as a medium for long range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry. PMID:18980370

  12. 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.

  13. 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.

  14. DNA Functionalization of Nanoparticles.

    PubMed

    Lu, Fang; Gang, Oleg

    2017-01-01

    DNA-nanoparticle conjugates are hybrid nanoscale objects that integrate different types of DNA molecules and inorganic nanoparticles with a typical architecture of a DNA shell around an inorganic core. Such incorporation provides particles with unique properties of DNA, addressability and recognition, but, at the same time, allows exploiting the properties of the particle's inorganic core. Thus, these hybrid nano-objects are advantageous for rational fabrication of functional materials and for biomedical applications. Here, we describe several established DNA functionalization procedures for different types of surface ligands and nanoparticle core materials.

  15. 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.

  16. 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.

  17. THE DESOXYRIBONUCLEIC ACID CONTENT OF ANIMAL CELLS AND ITS EVOLUTIONARY SIGNIFICANCE

    PubMed Central

    Mirsky, A. E.; Ris, Hans

    1951-01-01

    1. Evidence is summarized for the constancy of DNA content for each set of chromosomes in the various cells of an organism. 2. The DNA contents of the egg and sperm nuclei are the same. 3. A brief survey is given of DNA contents per cell in invertebrates and vertebrates. (a) In invertebrates there is some slight evidence that when primitive and higher forms are compared the amount of DNA per cell is increased in the latter. (b) In fishes there is a tendency for the amount of DNA per cell to remain constant within the different species of a family. (c) The values of DNA per cell in lung fishes, amphibians, reptiles, and birds suggest that in the evolution of these vertebrates there has been a decline in DNA content per cell. 4. Concerning the significance of quantity of DNA per cell in vertebrates: (a) It appears not to be in proportion to the number of different genes in a cell. (b) It may be related to the number of strands in the chromosomes. (c) In homologous cells of different animals it is directly related to the mass of the cell. PMID:14824511

  18. 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…

  19. 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.

  20. Supramolecular DNA assembly.

    PubMed

    McLaughlin, Christopher K; Hamblin, Graham D; Sleiman, Hanadi F

    2011-12-01

    The powerful self-assembly features of DNA make it a unique template to finely organize and control matter on the nanometre scale. While DNA alone offers a high degree of fidelity in its self-assembly, a new area of research termed 'supramolecular DNA assembly' has recently emerged. This field combines DNA building blocks with synthetic organic, inorganic and polymeric structures. It thus brings together the toolbox of supramolecular chemistry with the predictable and programmable nature of DNA. The result of this molecular partnership is a variety of hybrid architectures, that expand DNA assembly beyond the boundaries of Watson-Crick base pairing into new structural and functional properties. In this tutorial review we outline this emerging field of study, and describe recent research aiming to synergistically combine the properties inherent to DNA with those of a number of supramolecular scaffolds. This ultimately creates structures with numerous potential applications in materials science, catalysis and medicine.

  1. Isolation of DNA from plants with large amounts of secondary metabolites.

    PubMed

    Friar, Elizabeth A

    2005-01-01

    Many plant species have high contents of polysaccharides, polyphenols, or other secondary metabolites that can interfere with DNA extraction and purification. These contaminating compounds can lead to poor DNA yield and prevent access by modifying enzymes, such as restriction endonucleases and Taq polymerase. A number of factors, including choice of plant tissue, tissue preparation, and modifications of the extraction buffer, can help in DNA extraction for difficult plant species. This chapter presents some of the DNA extraction protocols developed for various plants.

  2. 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.

  3. [DNA methylation and epigenetics].

    PubMed

    Vaniushin, B F

    2006-09-01

    In eukaryotic cells, nuclear DNA is subject to enzymatic methylation with the formation of 5-methylcytosine residues, mostly within the CG and CNG sequences. In plants and animals this DNA methylation is species-, tissue-, and organelle-specific. It changes (decreases) with age and is regulated by hormones. On the other hand, genome methylation can control hormonal signal. Replicative and post-replicative DNA methylation types are distinguished. They are mediated by multiple DNA methyltransferases with different site-specificity. Replication is accompanied by the appearance of hemimethylated DNA sites. Pronounced asymmetry of the DNA strand methylation disappears to the end of the cell cycle. A model of methylation-regulated DNA replication is proposed. DNA methylation controls all genetic processes in the cell (replication, transcription, DNA repair, recombination, and gene transposition). It is the mechanism of cell differentiation, gene discrimination and silencing. In animals, suppression of DNA methylation stops development (embryogenesis), switches on apoptosis, and is usually lethal. Disruption of DNA methylation pattern results in the malignant cell transformation and serves as one of the early diagnostic features of carcinogenesis. In malignant cell the pattern of DNA methylation, as well as the set of DNA methyltransferase activities, differs from that in normal cell. In plants inhibition of DNA methylation is accompanied by the induction of seed storage and florescence genes. In eukaryotes one and the same gene can be simultaneously methylated both at cytosine and adenine residues. It can be thus suggested, that the plant cell contains at least two different, and probably, interdependent systems of DNA methylation. The first eukaryotic adenine DNA methyltransferase was isolated from plants. This enzyme methylates DNA with the formation of N6-methyladenine residues in the sequence TGATCA (TGATCA-->TGm6ATCA). Plants possess AdoMet-dependent endonucleases

  4. 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.

  5. Associated chromosomal DNA changes in polyploids.

    PubMed

    Raina, S N; Parida, A; Koul, K K; Salimath, S S; Bisht, M S; Raja, V; Khoshoo, T N

    1994-08-01

    The 2C and 4C nuclear DNA amounts were estimated in eight diploid species, belonging to three diverse genera (Vicia, Tephrosia, and Phlox) and their corresponding colchitetraploids. In P. drummondii, T. purpurea, and T. oxygona tetraploids the deviation from the expectation was highly significant. The DNA in P. drummondii was further discarded in subsequent (C1, C2) generations, thus attaining an overall reduction of about 25%. The DNA content in the subsequent generations was the same as that of C2. It is concluded that rapid DNA loss in the first and subsequent generations was not only associated with the substantial increase (30-66%) in the seed set, but it also helped in the establishment and stabilization of the tetraploid. The possible relationship between such a nucleotypic change and success of polyploids is discussed. The DNA change from the expected value in the P. drummondii tetraploid was achieved by equal decrement to each chromosome independent of size, i.e., small chromosomes loose the same amount of DNA as the large chromosomes.

  6. ELOVL4 protein preferentially elongates 20:5n3 to very long chain PUFAs over 20:4n6 and 22:6n3[S

    PubMed Central

    Yu, Man; Benham, Aaron; Logan, Sreemathi; Brush, R. Steven; Mandal, Md Nawajes A.; Anderson, Robert E.; Agbaga, Martin-Paul

    2012-01-01

    We hypothesized that reduction/loss of very long chain PUFAs (VLC-PUFAs) due to mutations in the ELOngase of very long chain fatty acid-4 (ELOVL4) protein contributes to retinal degeneration in autosomal dominant Stargardt-like macular dystrophy (STGD3) and age-related macular degeneration; hence, increasing VLC-PUFA in the retina of these patients could provide some therapeutic benefits. Thus, we tested the efficiency of elongation of C20-C22 PUFA by the ELOVL4 protein to determine which substrates are the best precursors for biosynthesis of VLC-PUFA. The ELOVL4 protein was expressed in pheochromocytoma cells, while green fluorescent protein-expressing and nontransduced cells served as controls. The cells were treated with 20:5n3, 22:6n3, and 20:4n6, either individually or in equal combinations. Both transduced and control cells internalized and elongated the supplemented FAs to C22-C26 precursors. Only ELOVL4-expressing cells synthesized C28-C38 VLC-PUFA from these precursors. In general, 20:5n3 was more efficiently elongated to VLC-PUFA in the ELOVL4-expressing cells, regardless of whether it was in combination with 22:6n3 or with 20:4n6. In each FA treatment group, C34 and C36 VLC-PUFAs were the predominant VLC-PUFAs in the ELOVL4-expressing cells. In summary, 20:5n3, followed by 20:4n6, seems to be the best precursor for boosting the synthesis of VLC-PUFA by ELOVL4 protein. PMID:22158834

  7. AT–1001: a high-affinity α3β4 nAChR ligand with novel nicotine-suppressive pharmacology

    PubMed Central

    Cippitelli, Andrea; Wu, Jinhua; Gaiolini, Kelly A; Mercatelli, Daniela; Schoch, Jennifer; Gorman, Michelle; Ramirez, Alejandra; Ciccocioppo, Roberto; Khroyan, Taline V; Yasuda, Dennis; Zaveri, Nurulain T; Pascual, Conrado; Xie, Xinmin (Simon); Toll, Lawrence

    2015-01-01

    Background and Purpose The α3β4 subtype of nicotinic acetylcholine receptors (nAChRs) has been implicated in mediating nicotine reinforcement processes. AT-1001 has been recently described as a high-affinity and selective α3β4 nAChR antagonist that blocks nicotine self-administration in rats. The aim of this study was to investigate the mechanism of action underlying the nicotine-suppressive effects of AT-1001. Experimental Approach Effects of AT-1001 were determined using in vitro assays and rat models of nicotine addiction, and compared with varenicline. Key Results AT-1001 and its analogue AT-1012 were functionally selective as antagonists for α3β4 over α4β2 nAChRs, but not to the same extent as the binding selectivity, and had partial agonist activity at α3β4 nAChRs. In contrast, varenicline was a partial agonist at α4β2, a weak agonist at α3β4 and inhibited α4β2 at a much lower concentration than it inhibited α3β4 nAChRs. AT-1001 and varenicline also had very different in vivo properties. Firstly, AT-1001 did not exhibit reinforcing properties per se while varenicline was self-administered. Secondly, systemic treatment with AT-1001 did not induce reinstatement of nicotine seeking but rather attenuated reinstatement induced by varenicline, as well as nicotine. Finally, unlike varenicline, AT-1001 selectively blocked nicotine self-administration without altering alcohol lever pressing as assessed in an operant co-administration paradigm. Conclusions and Implications These findings describe a more complex AT-1001 in vitro profile than previously appreciated and provide further support for the potential of AT-1001 and congeners as clinically useful compounds for smoking cessation, with a mechanism of action distinct from currently available medications. PMID:25440006

  8. 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.

  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. 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.

  11. Improved PCR Amplification of Broad Spectrum GC DNA Templates.

    PubMed

    Guido, Nicholas; Starostina, Elena; Leake, Devin; Saaem, Ishtiaq

    2016-01-01

    Many applications in molecular biology can benefit from improved PCR amplification of DNA segments containing a wide range of GC content. Conventional PCR amplification of DNA sequences with regions of GC less than 30%, or higher than 70%, is complex due to secondary structures that block the DNA polymerase as well as mispriming and mis-annealing of the DNA. This complexity will often generate incomplete or nonspecific products that hamper downstream applications. In this study, we address multiplexed PCR amplification of DNA segments containing a wide range of GC content. In order to mitigate amplification complications due to high or low GC regions, we tested a combination of different PCR cycling conditions and chemical additives. To assess the fate of specific oligonucleotide (oligo) species with varying GC content in a multiplexed PCR, we developed a novel method of sequence analysis. Here we show that subcycling during the amplification process significantly improved amplification of short template pools (~200 bp), particularly when the template contained a low percent of GC. Furthermore, the combination of subcycling and 7-deaza-dGTP achieved efficient amplification of short templates ranging from 10-90% GC composition. Moreover, we found that 7-deaza-dGTP improved the amplification of longer products (~1000 bp). These methods provide an updated approach for PCR amplification of DNA segments containing a broad range of GC content.

  12. 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

  13. 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

  14. Influence of incommensurate modulation on the optical properties of the solid solution ((CH3)4N)2ZnCl2.8Br1.2

    NASA Astrophysics Data System (ADS)

    Kremers, M.; Meekes, H.

    1996-08-01

    This paper reports on measurements with a high-accuracy universal polarimeter of the birefringence, optical activity, and indicatrix rotation in incommensurately modulated ((CH3)4N)2ZnCl2.8Br1.2 crystals. It is shown that in this solid solution the inversion symmetry is broken already in the paraelastic phase, due to the inhomogeneous distribution of Cl and Br over the zinc-halide tetrahedra. This, however, allows one to study the influence of the incommensurate modulation on a nonzero optical activity. This influence is clearly shown for a sample in which, moreover, the modulation wave vector is believed to lock at several commensurate values.

  15. Predicting the Conditions for Homeotropic Anchoring of Liquid Crystals at a Soft Surface. 4-n-Pentyl-4'-cyanobiphenyl on Alkylsilane Self-Assembled Monolayers.

    PubMed

    Roscioni, Otello Maria; Muccioli, Luca; Zannoni, Claudio

    2017-04-05

    We have studied, using atomistic molecular dynamics simulations, the alignment of the nematic liquid-crystal 4-n-pentyl-4'-cyanobiphenyl (5CB) on self-assembled monolayers (SAMs) formed from octadecyl- and/or hexyltrichlorosilane (OTS and HTS) attached to glassy silica. We find a planar alignment on OTS at full coverage and an intermediate situation at partial OTS coverage because of the penetration of 5CB molecules into the monolayer, which also removes the tilt of the OTS SAM. Binary mixtures of HTS and OTS SAMs instead induce homeotropic (i.e., perpendicular) alignment. A comparison with the existing experimental literature is provided.

  16. The transformation of α-Fe into γ'-Fe4N in nanocrystalline Fe-N system: Influence of Gibbs-Thomson effect

    NASA Astrophysics Data System (ADS)

    Moszyński, Dariusz; Moszyńska, Izabela; Arabczyk, Walerian

    2013-12-01

    A nanocrystalline iron sample of non-uniform grain size distribution was nitrided at 500 °C under gas atmosphere with gradually increased nitriding potential. Mixtures of α-Fe and γ'-Fe4N phases were observed at a broad range of the nitriding potential. Unexpectedly, the mean size of the product's crystallites at small conversion degrees was much higher than the one observed initially for the substrate and gradually decreased with the advancement of the reaction. The observed behavior was explained by the reaction mechanism regarding the influence of the Gibbs-Thomson effect.

  17. 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.

  18. Enzymatic initiation of DNA synthesis by yeast DNA polymerases.

    PubMed Central

    Plevani, P; Chang, L M

    1977-01-01

    Partially purified yeast RNA polymerases (RNA nucleotidyltransferases) initiate DNA synthesis by yeast DNA polymerase (DNA nucleotidyltransferase) I and to a lesser extent yeast DNA polymerase II in the replication of single-stranded DNA. The enzymatic initiation of DNA synthesis on phage fd DNA template occurs with dNTPs alone and is further stimulated by the presence of rNTPs in DNA polymerase I reactions. The presence of rNTPs has no effect on the RNA polymerase initiation of the DNA polymerase II reaction. RNA polymerases I and III are more efficient in initiation of DNA synthesis than RNA polymerase II. Analyses of the products of fd DNA replication show noncovalent linkage between the newly synthesized DNA and the template DNA, and covalent linkage between the newly synthesized RNA and DNA. PMID:325562

  19. Functional DNA Nanomaterials

    NASA Astrophysics Data System (ADS)

    Zhao, Zhao

    The discovery of DNA helical structure opened the door of modern molecular biology. Ned Seeman utilized DNA as building block to construct different nanoscale materials, and introduced a new field, know as DNA nanotechnology. After several decades of development, different DNA structures had been created, with different dimension, different morphology and even with complex curvatures. In addition, after construction of enough amounts DNA structure candidates, DNA structure template, with excellent spatial addressability, had been used to direct the assembly of different nanomaterials, including nanoparticles and proteins, to produce different functional nanomaterials. However there are still many challenges to fabricate functional DNA nanostructures. The first difficulty is that the present finite sized template dimension is still very small, usually smaller than 100nm, which will limit the application for large amount of nanomaterials assembly or large sized nanomaterials assembly. H