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Sample records for mixed dna chromatograms

  1. DNA sequence chromatogram browsing using JAVA and CORBA.

    PubMed

    Parsons, J D; Buehler, E; Hillier, L

    1999-03-01

    DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.

  2. Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms

    PubMed Central

    Fantin, Yuri S.; Neverov, Alexey D.; Favorov, Alexander V.; Alvarez-Figueroa, Maria V.; Braslavskaya, Svetlana I.; Gordukova, Maria A.; Karandashova, Inga V.; Kuleshov, Konstantin V.; Myznikova, Anna I.; Polishchuk, Maya S.; Reshetov, Denis A.; Voiciehovskaya, Yana A.; Mironov, Andrei A.; Chulanov, Vladimir P.

    2013-01-01

    Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3–14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing. PMID:23382983

  3. Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling.

    PubMed

    Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

    2012-01-01

    The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3.

  4. Current developments in forensic interpretation of mixed DNA samples (Review)

    PubMed Central

    HU, NA; CONG, BIN; LI, SHUJIN; MA, CHUNLING; FU, LIHONG; ZHANG, XIAOJING

    2014-01-01

    A number of recent improvements have provided contemporary forensic investigations with a variety of tools to improve the analysis of mixed DNA samples in criminal investigations, producing notable improvements in the analysis of complex trace samples in cases of sexual assult and homicide. Mixed DNA contains DNA from two or more contributors, compounding DNA analysis by combining DNA from one or more major contributors with small amounts of DNA from potentially numerous minor contributors. These samples are characterized by a high probability of drop-out or drop-in combined with elevated stutter, significantly increasing analysis complexity. At some loci, minor contributor alleles may be completely obscured due to amplification bias or over-amplification, creating the illusion of additional contributors. Thus, estimating the number of contributors and separating contributor genotypes at a given locus is significantly more difficult in mixed DNA samples, requiring the application of specialized protocols that have only recently been widely commercialized and standardized. Over the last decade, the accuracy and repeatability of mixed DNA analyses available to conventional forensic laboratories has greatly advanced in terms of laboratory technology, mathematical models and biostatistical software, generating more accurate, rapid and readily available data for legal proceedings and criminal cases. PMID:24748965

  5. Polyphenols and DNA Damage: A Mixed Blessing

    PubMed Central

    Azqueta, Amaya; Collins, Andrew

    2016-01-01

    Polyphenols are a very broad group of chemicals, widely distributed in plant foods, and endowed with antioxidant activity by virtue of their numerous phenol groups. They are widely studied as putative cancer-protective agents, potentially contributing to the cancer preventive properties of fruits and vegetables. We review recent publications relating to human trials, animal experiments and cell culture, grouping them according to whether polyphenols are investigated in whole foods and drinks, in plant extracts, or as individual compounds. A variety of assays are in use to study genetic damage endpoints. Human trials, of which there are rather few, tend to show decreases in endogenous DNA damage and protection against DNA damage induced ex vivo in blood cells. Most animal experiments have investigated the effects of polyphenols (often at high doses) in combination with known DNA-damaging agents, and generally they show protection. High concentrations can themselves induce DNA damage, as demonstrated in numerous cell culture experiments; low concentrations, on the other hand, tend to decrease DNA damage. PMID:27918471

  6. Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media

    SciTech Connect

    Lee,C.; Gamble, L.; Grainger, D.; Castner, D.

    2006-01-01

    Reliable, direct 'sample-to-answer' capture of nucleic acid targets from complex media would greatly improve existing capabilities of DNA microarrays and biosensors. This goal has proven elusive for many current nucleic acid detection technologies attempting to produce assay results directly from complex real-world samples, including food, tissue, and environmental materials. In this study, we have investigated mixed self-assembled thiolated single-strand DNA (ssDNA) monolayers containing a short thiolated oligo(ethylene glycol) (OEG) surface diluent on gold surfaces to improve the specific capture of DNA targets from complex media. Both surface composition and orientation of these mixed DNA monolayers were characterized with x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS). XPS results from sequentially adsorbed ssDNA/OEG monolayers on gold indicate that thiolated OEG diluent molecules first incorporate into the thiolated ssDNA monolayer and, upon longer OEG exposures, competitively displace adsorbed ssDNA molecules from the gold surface. NEXAFS polarization dependence results (followed by monitoring the N 1s{yields}{pi}* transition) indicate that adsorbed thiolated ssDNA nucleotide base-ring structures in the mixed ssDNA monolayers are oriented more parallel to the gold surface compared to DNA bases in pure ssDNA monolayers. This supports ssDNA oligomer reorientation towards a more upright position upon OEG mixed adlayer incorporation. DNA target hybridization on mixed ssDNA probe/OEG monolayers was monitored by surface plasmon resonance (SPR). Improvements in specific target capture for these ssDNA probe surfaces due to incorporation of the OEG diluent were demonstrated using two model biosensing assays, DNA target capture from complete bovine serum and from salmon genomic DNA mixtures. SPR results demonstrate that OEG incorporation into the ssDNA adlayer improves surface resistance to both nonspecific DNA and protein

  7. [Study on HPLC fingerprint chromatograms of Arisaematis Rhizoma].

    PubMed

    Luo, Fen; Lu, Dan; Chi, Yumei; Wu, Hao; Yu, Hongli

    2011-12-01

    The fingerprint chromatograms of Arisaematis Rhizoma were established by HPLC. The analysis was performed on a Lichrospher C18 (4.6 mm x 200 mm, 5 microm) column with acetonitrile-water (containing 0.1% acetic acid) as mobile phase at a flow rate of 1.0 mL x min(-1). The detection wavelength was set at 270 nm, and the column temperature was 30 degrees C. The similarities of the fingerprint chromatograms were calculated over 0.9 between 11 batches of Arisaematis Rhizoma samples by analyzing 14 common peaks with adenosine as reference substance. However, their fingerprint chromatograms were significantly different from those of Pinellia pedatisecta and P. ternate. Adenine, hypoxanthine, xanthine, uridine, guanosine, adenosine, schaftoside, and isoschaftoside were identified by comparing the retention times and their ultraviolet spectra. The method is repeatable, exclusive and can be used for identification and evaluation of Arisaematis Rhizoma.

  8. A new mathematical procedure to evaluate peaks in complex chromatograms.

    PubMed

    Steffen, B; Müller, K P; Komenda, M; Koppmann, R; Schaub, A

    2005-04-15

    Automatic peak evaluation in chromatograms and subsequent quantification of compound concentrations is still a challenge in the analysis of complex samples containing hundreds or thousands of compounds. Although a number of software packages for peak evaluation exist, baseline definition and overlapping peaks of different shapes are the main reasons which prevent reliable automatic analysis of complex chromatograms. A new mathematical procedure is presented which uses peak shapes extracted from the chromatogram itself and modified by nonlinear (in fact, hyperbolic) stretching of the peak head and tail. With this approach, the peak parameters are position, height, scale of front, scale of tail, and smoothness of transition from front to tail scaling. This approach is found to give a substantially better fit than traditional analytically defined peak shapes. Together with a good peak finding heuristic and nonlinear optimization of parameters this allows a reliable automatic analysis of chromatograms with a large number of peaks, even with large groups of overlapping peaks. The analysis matches the quality of standard interactive methods, but still permits interactive refinement. This approach has been implemented and tested on a large set of data from chromatography of hydrocarbons in ambient air samples.

  9. Two-dimensional semi-parametric alignment of chromatograms.

    PubMed

    de Boer, Wim P H; Lankelma, Jan

    2014-06-06

    We present a comprehensive alignment algorithm that extends the semi-parametric approach to two dimensions. The algorithm is based on modeling shifts with a two-dimensional "warp function" such that the sample chromatogram - its shifts corrected with the warp function - is adjusted to the reference chromatogram by minimizing the squared intensity difference. A warp function approach has the advantage that overlapping peaks are easily dealt with compared to other proposed two-dimensional algorithms. Another advantage is that missing peaks are allowed if the absence of these peaks has little numerical effect on the warp function computation and if these peaks occur between existing peaks. Performance of the algorithm is demonstrated using GC×GC data from three batches of three diesel oil samples and LC-MS data from a mouse breast cancer data set.

  10. Enthused research on DNA-binding and DNA-cleavage aptitude of mixed ligand metal complexes

    NASA Astrophysics Data System (ADS)

    Mahalakshmi, Rajkumar; Raman, Natarajan

    2013-08-01

    Five new Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) mixed ligand complexes have been synthesized using a Schiff base precursor (obtained by the condensation of N-(4-aminophenyl)acetamide and 4-chlorobenzaldehyde) as main ligand and 1,10-phenanthroline as co-ligand. They have been characterized by microanalytical data, IR, UV-Vis, magnetic moment values, conductivity and electrochemical measurements. The spectral data reveal that all the complexes exhibit octahedral geometry. The high electrical conductance of the complexes supports their electrolytic nature. The monomeric nature of the complexes has been assessed from their magnetic susceptibility values. These complexes are better antimicrobial active agents than the free ligands. DNA (CT) binding properties of these complexes have been explored by UV-Vis., viscosity measurements, cyclic voltammetry, and differential pulse voltammetry measurements. The oxidative cleavage activity of the complexes has been studied using supercoiled pUC19 DNA by gel electrophoresis. The experimental results show that the complexes are good intercalators.

  11. Enthused research on DNA-binding and DNA-cleavage aptitude of mixed ligand metal complexes.

    PubMed

    Mahalakshmi, Rajkumar; Raman, Natarajan

    2013-08-01

    Five new Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) mixed ligand complexes have been synthesized using a Schiff base precursor (obtained by the condensation of N-(4-aminophenyl)acetamide and 4-chlorobenzaldehyde) as main ligand and 1,10-phenanthroline as co-ligand. They have been characterized by microanalytical data, IR, UV-Vis, magnetic moment values, conductivity and electrochemical measurements. The spectral data reveal that all the complexes exhibit octahedral geometry. The high electrical conductance of the complexes supports their electrolytic nature. The monomeric nature of the complexes has been assessed from their magnetic susceptibility values. These complexes are better antimicrobial active agents than the free ligands. DNA (CT) binding properties of these complexes have been explored by UV-Vis., viscosity measurements, cyclic voltammetry, and differential pulse voltammetry measurements. The oxidative cleavage activity of the complexes has been studied using supercoiled pUC19 DNA by gel electrophoresis. The experimental results show that the complexes are good intercalators.

  12. Controlling the surface‐mediated release of DNA using ‘mixed multilayers’

    PubMed Central

    Appadoo, Visham; Carter, Matthew C. D.

    2016-01-01

    Abstract We report the design of erodible ‘mixed multilayer’ coatings fabricated using plasmid DNA and combinations of both hydrolytically degradable and charge‐shifting cationic polymer building blocks. Films fabricated layer‐by‐layer using combinations of a model poly(β‐amino ester) (polymer 1) and a model charge‐shifting polymer (polymer 2) exhibited DNA release profiles that were substantially different than those assembled using DNA and either polymer 1 or polymer 2 alone. In addition, the order in which layers of these two cationic polymers were deposited during assembly had a profound impact on DNA release profiles when these materials were incubated in physiological buffer. Mixed multilayers ∼225 nm thick fabricated by depositing layers of polymer 1/DNA onto films composed of polymer 2/DNA released DNA into solution over ∼60 days, with multi‐phase release profiles intermediate to and exhibiting some general features of polymer 1/DNA or polymer 2/DNA films (e.g., a period of rapid release, followed by a more extended phase). In sharp contrast, ‘inverted’ mixed multilayers fabricated by depositing layers of polymer 2/DNA onto films composed of polymer 1/DNA exhibited release profiles that were almost completely linear over ∼60‐80 days. These and other results are consistent with substantial interdiffusion and commingling (or mixing) among the individual components of these compound materials. Our results reveal this mixing to lead to new, unanticipated, and useful release profiles and provide guidance for the design of polymer‐based coatings for the local, surface‐mediated delivery of DNA from the surfaces of topologically complex interventional devices, such as intravascular stents, with predictable long‐term release profiles. PMID:27981243

  13. Reciprocal symmetry plots as a representation of countercurrent chromatograms.

    PubMed

    Friesen, J Brent; Pauli, Guido F

    2007-03-15

    Traditionally, chromatograms in countercurrent chromatography (CCC) have been plotted with retention volume or time on the x-axis. However, the distribution constant (K) is a more appropriate, reproducible value for the x-axis, because it is a physicochemical property of a particular analyte in a particular solvent system. Therefore, K is independent of both the total column volume and the stationary-phase volume ratio (SF) of the column. Going one step beyond simple K plots, the reciprocal symmetry (ReS) plot, with K and 1/K positioned on either side of a line of symmetry on the x-axis, represents all K values, zero to infinity. Based on experimental evidence, using a mixture of CCC reference standards, the ReS plot demonstrates both the invertible and "symmetric" nature of CCC, a consequence of the exchange of the mobile and stationary phases by reversing the direction of the flow and the symmetry of the liquid-liquid partitioning process between two immiscible phases, respectively. Moreover, the interval of optimal resolution can be centered on the ReS plot to focus on K values of interest, establishing the reciprocal shifted symmetry (ReSS) plots in CCC. Improved representation of peak shape across the whole CCC polarity range is an added advantage of ReSS plots over both K and classical retention volume plots.

  14. Evaluation of parameters in mixed male DNA profiles for the Identifiler® multiplex system

    PubMed Central

    HU, NA; CONG, BIN; GAO, TAO; HU, RONG; CHEN, YI; TANG, HUI; XUE, LUYAN; LI, SHUJIN; MA, CHUNLING

    2014-01-01

    The analysis of complex DNA mixtures is challenging for forensic DNA testing. Accurate and sensitive methods for profiling these samples are urgently required. In this study, we developed 11 groups of mixed male DNA samples (n=297) with scientific validation of D-value [>95% of D-values ≤0.1 with average peak height (APH) of the active alleles ≤2,500 rfu]. A strong linear correlation was detected between the peak height (PH) and peak area (PA) in the curve fit using the least squares method (P<2e-16). The Kruskal-Wallis rank-sum test revealed significant differences in the heterozygote balance ratio (Hb) at 16 short tandem repeat (STR) loci (P=0.0063) and 9 mixed gradients (P=0.02257). Locally weighted regression fitting of APH and Hb (inflection point at APH = 1,250 rfu) showed 92.74% of Hb >0.6 with the APH ≥1,250. The variation of Hb distribution in the different STR loci suggested the different forensic efficiencies of these loci. Allelic drop-out (ADO) correlated with the APH and mixed gradient. All ADOs had an APH of <1,000 rfu, and the number of ADO increased when the APH of mixed DNA profiles gradually decreased. These results strongly suggest that calibration parameters should be introduced to correct the deviation in the APH at each STR locus during the analysis of mixed DNA samples. PMID:24821391

  15. Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms.

    PubMed

    Dominiak, Dominik Marek; Nielsen, Jeppe Lund; Nielsen, Per Halkjaer

    2011-03-01

    A new approach for quantification of extracellular DNA (eDNA) in mixed biofilms at microscale resolution was developed and combined with other staining techniques to assess the origin, abundance and role of eDNA in activated sludge biofilms. Most eDNA was found in close proximity to living cells in microcolonies, suggesting that most of it originated from an active secretion or alternatively, by lysis of a sub-population of cells. When the staining was combined with fluorescence in situ hybridization for identification of the microorganisms, it was found that the eDNA content varied among the different probe-defined species. The highest amount of eDNA was found in and around the microcolonies of denitrifiers belonging to the genera Curvibacter and Thauera, the ammonium-oxidizing Nitrosomonas and the nitrite-oxidizing Nitrospira. Other floc-formers also produced eDNA, although in lower amounts. The total eDNA content in activated sludge varied from 4 to 52 mg per gram volatile suspended solids in different wastewater treatment plants. Very high local concentrations within some microcolonies were found with up to approximately 300 mg of eDNA per g of organic matter. DNase digestion of activated sludge led to general floc disintegration and disruption of the microcolonies with high eDNA content, implying that eDNA was an important structural component in activated sludge biofilms.

  16. Differentiation of mixed biological traces in sexual assaults using DNA fragment analysis

    PubMed Central

    Apostolov, Аleksandar

    2014-01-01

    During the investigation of sexual abuse, it is not rare that mixed genetic material from two or more persons is detected. In such cases, successful profiling can be achieved using DNA fragment analysis, resulting in individual genetic profiles of offenders and their victims. This has led to an increase in the percentage of identified perpetrators of sexual offenses. The classic and modified genetic models used, allowed us to refine and implement appropriate extraction, polymerase chain reaction and electrophoretic procedures with individual assessment and approach to conducting research. Testing mixed biological traces using DNA fragment analysis appears to be the only opportunity for identifying perpetrators in gang rapes. PMID:26019514

  17. Application of mixsep software package: Performance verification of male-mixed DNA analysis.

    PubMed

    Hu, Na; Cong, Bin; Gao, Tao; Chen, Yu; Shen, Junyi; Li, Shujin; Ma, Chunling

    2015-08-01

    An experimental model of male-mixed DNA (n=297) was constructed according to the mixed DNA construction principle. This comprised the use of the Applied Biosystems (ABI) 7500 quantitative polymerase chain reaction system, with scientific validation of mixture proportion (Mx; root-mean-square error ≤ 0.02). Statistical analysis was performed on locus separation accuracy using mixsep, a DNA mixture separation R-package, and the analytical performance of mixsep was assessed by examining the data distribution pattern of different mixed gradients, short tandem repeat (STR) loci and mixed DNA types. The results showed that locus separation accuracy had a negative linear correlation with the mixed gradient (R(2)=-0.7121). With increasing mixed gradient imbalance, locus separation accuracy first increased and then decreased, with the highest value detected at a gradient of 1:3 (≥ 90%). The mixed gradient, which is the theoretical Mx, was one of the primary factors that influenced the success of mixed DNA analysis. Among the 16 STR loci detected by Identifiler®, the separation accuracy was relatively high (>88%) for loci D5S818, D8S1179 and FGA, whereas the median separation accuracy value was lowest for the D7S820 locus. STR loci with relatively large numbers of allelic drop-out (ADO; >15) were all located in the yellow and red channels, including loci D18S51, D19S433, FGA, TPOX and vWA. These five loci featured low allele peak heights, which was consistent with the low sensitivity of the ABI 3130xl Genetic Analyzer to yellow and red fluorescence. The locus separation accuracy of the mixsep package was substantially different with and without the inclusion of ADO loci; inclusion of ADO significantly reduced the analytical performance of the mixsep package, which was consistent with the lack of an ADO functional module in this software. The present study demonstrated that the mixsep software had a number of advantages and was recommended for analysis of mixed DNA. This

  18. [Influence of combination on the specific chromatogram of Glycyrrhiza in sini decoctions by HPLC].

    PubMed

    Zhao, Huai-Bin; Hong, Yan-Long; Wang, You-Jie; Shen, Lan; Wu, Fei; Feng, Yi; Ruan, Ke-Feng

    2012-04-01

    The paper is to report the establishment of an HPLC specific chromatogram of Glycyrrhiza in Sini decoctions and the influence of combination on the specific chromatogram. The RP-HPLC method was used with a Phenomenex Gemini C18 column (250 mm x 4.6 mm ID, 5 microm), and acetonitrile-0.05% trifluoroacetic acid (gradient elution) as mobile phase. Flow rate was 0.8 mL x min(-1) and the detection wavelength was set at 232 nm. The temperature of column was 30 degrees C. The method is stable and reliable with a good reproducibility, it can be used to determine the specific chromatogram of Glycyrrhiza in Sini Decoctions. Twenty peaks were selected as specific peaks in Sini Decoction with liquiritin peak as the reference peak. Six of them were from Glycyrrhiza and the other 6 peaks were from both Glycyrrhiza and Ganjiangfuzi Decoction. The areas of specific peaks of Sini Decoctions were smaller than those in the chromatogram of Glycyrrhiza. The specific chromatogram of Glycyrrhiza in Sini Decoctions is markedly influenced by Radix Aconiti Carmichaeli and Rhizoma Zingiberis. The areas of the specific peaks in Sini Decoctions were reduced obviously. The method is stable and reliable with a good reproducibility, it can be used to determine the specific chromatogram of Glycyrrhiza in Sini Decoctions.

  19. Nonlinear alignment of chromatograms by means of moving window fast Fourier transfrom cross-correlation.

    PubMed

    Li, Zhong; Wang, Jia-Jun; Huang, Jing; Zhang, Zhi-Min; Lu, Hong-Mei; Zheng, Yi-Bao; Zhan, De-Jian; Liang, Yi-Zeng

    2013-05-01

    The preprocessing of chromatograms is essential to modern chromatography for further qualitative and quantitative analysis, especially when chromatographic instruments are used for herb products analysis involving large number of samples. To accurately compare and analyze the obtained chromatograms, it is necessary to preprocess, especially align retention time shifts. Here moving window fast Fourier transform (FFT) cross-correlation is introduced to perform nonlinear alignment of high-throughput chromatograms. Since elution characteristics of chromatograms will produce local similarity in retention time shifts, moving window procedure seems to be a better substitute of segmentation steps. The retention time shifts can be calculated and accelerated by FFT cross-correlation. The artifacts can be detected and eliminated from the retention time shifts profile since the continuity of moving window procedure. The proposed method is demonstrated in comparison with recursive alignment by FFT on chromatographic datasets from herb products analysis. It is shown that the proposed method can address nonlinear retention time shift problem in chromatograms with the simple moving window procedure, which will not introduce segments size optimization problem. In additional, the parameters are intuitive and easy to adjust, which makes it off-the-shelf toolbox for alignment of chromatograms.

  20. Electrical detection and quantification of single and mixed DNA nucleotides in suspension

    NASA Astrophysics Data System (ADS)

    Ahmad, Mahmoud Al; Panicker, Neena G.; Rizvi, Tahir A.; Mustafa, Farah

    2016-09-01

    High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical properties. In this study, the four different types of nucleotides that constitute a DNA molecule were suspended in a buffer followed by performing several types of electrical measurements. These electrical parameters were then used to quantify the suspended DNA nucleotides. Thus, we present a purely electrical counting scheme based on the semiconductor theory that allows one to determine the number of nucleotides in a solution by measuring their capacitance-voltage dependency. The nucleotide count was observed to be similar to the multiplication of the corresponding dopant concentration and debye volume after de-embedding the buffer contribution. The presented approach allows for a fast and label-free quantification of single and mixed nucleotides in a solution.

  1. Electrical detection and quantification of single and mixed DNA nucleotides in suspension

    PubMed Central

    Ahmad, Mahmoud Al; Panicker, Neena G.; Rizvi, Tahir A.; Mustafa, Farah

    2016-01-01

    High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical properties. In this study, the four different types of nucleotides that constitute a DNA molecule were suspended in a buffer followed by performing several types of electrical measurements. These electrical parameters were then used to quantify the suspended DNA nucleotides. Thus, we present a purely electrical counting scheme based on the semiconductor theory that allows one to determine the number of nucleotides in a solution by measuring their capacitance-voltage dependency. The nucleotide count was observed to be similar to the multiplication of the corresponding dopant concentration and debye volume after de-embedding the buffer contribution. The presented approach allows for a fast and label-free quantification of single and mixed nucleotides in a solution. PMID:27677329

  2. Natural DNA mixed with trehalose persists in B-form double-stranding even in the dry state.

    PubMed

    Zhu, Bo; Furuki, Takao; Okuda, Takashi; Sakurai, Minoru

    2007-05-24

    Desiccated calf-thymus DNA has been found to persist in the B-form double-stranding when mixed with trehalose. The stabilization effect on natural DNA depends on the trehalose content, and should basically arise from its ability to tightly hydrogen bond to phosphate groups of DNA, which leads to screening of the large phosphate-phosphate repulsion.

  3. Surface Coverage and Structure of Mixed DNA/Alkylthiol Monolayers on Gold: Characterization by XPS, NEXAFS, and Fluorescence Intensity Measurements

    PubMed Central

    Lee, Chi-Ying; Gong, Ping; Harbers, Gregory M.; Grainger, David W.; Castner, David G.; Gamble, Lara J.

    2006-01-01

    Self-assembly of thiol-terminated single-stranded DNA (HS-ssDNA) on gold has served as an important model system for DNA immobilization at surfaces. Here, we report a detailed study of the surface composition and structure of mixed self-assembled DNA monolayers containing a short alkylthiol surface diluent [11-mercapto-1-undecanol (MCU)] on gold supports. These mixed DNA monolayers were studied with X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and fluorescence intensity measurements. XPS results on sequentially adsorbed DNA/MCU monolayers on gold indicated that adsorbed MCU molecules first incorporate into the HS-ssDNA monolayer and, upon longer MCU exposures, displace adsorbed HS-ssDNA molecules from the surface. Thus, HS-ssDNA surface coverage steadily decreased with MCU exposure time. Polarization-dependent NEXAFS and fluorescence results both show changes in signals consistent with changes in DNA orientation after only 30 min of MCU exposure. NEXAFS polarization dependence (followed by monitoring the N 1s → π* transition) of the mixed DNA monolayers indicated that the DNA nucleotide base ring structures are oriented more parallel to the gold surface compared to DNA bases in pure HS-ssDNA monolayers. This indicates that HS-ssDNA oligomers reorient toward a more-upright position upon MCU incorporation. Fluorescence intensity results using end-labeled DNA probes on gold show little observable fluorescence on pure HS-ssDNA monolayers, likely due to substrate quenching effects between the fluorophore and the gold. MCU diluent incorporation into HS-ssDNA monolayers initially increases DNA fluorescence signal by densifying the chemisorbed monolayer, prompting an upright orientation of the DNA, and moving the terminal fluorophore away from the substrate. Immobilized DNA probe density and DNA target hybridization in these mixed DNA monolayers, as well as effects of MCU diluent on DNA hybridization in complex

  4. Surface Coverage and Structure of Mixed DNA/Alkylthiol Monolayers on Gold: Characterization by XPS, NEXAFS, and Fluorescence Intensity Measurements

    SciTech Connect

    Lee,C.; Gong, P.; Harbers, G.; Grainger, D.; Castner, D.; Gamble, L.

    2006-01-01

    Self-assembly of thiol-terminated single-stranded DNA (HS-ssDNA) on gold has served as an important model system for DNA immobilization at surfaces. Here, we report a detailed study of the surface composition and structure of mixed self-assembled DNA monolayers containing a short alkylthiol surface diluent [11-mercapto-1-undecanol (MCU)] on gold supports. These mixed DNA monolayers were studied with X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and fluorescence intensity measurements. XPS results on sequentially adsorbed DNA/MCU monolayers on gold indicated that adsorbed MCU molecules first incorporate into the HS-ssDNA monolayer and, upon longer MCU exposures, displace adsorbed HS-ssDNA molecules from the surface. Thus, HS-ssDNA surface coverage steadily decreased with MCU exposure time. Polarization-dependent NEXAFS and fluorescence results both show changes in signals consistent with changes in DNA orientation after only 30 min of MCU exposure. NEXAFS polarization dependence (followed by monitoring the N 1s{yields}{pi}* transition) of the mixed DNA monolayers indicated that the DNA nucleotide base ring structures are oriented more parallel to the gold surface compared to DNA bases in pure HS-ssDNA monolayers. This indicates that HS-ssDNA oligomers reorient toward a more-upright position upon MCU incorporation. Fluorescence intensity results using end-labeled DNA probes on gold show little observable fluorescence on pure HS-ssDNA monolayers, likely due to substrate quenching effects between the fluorophore and the gold. MCU diluent incorporation into HS-ssDNA monolayers initially increases DNA fluorescence signal by densifying the chemisorbed monolayer, prompting an upright orientation of the DNA, and moving the terminal fluorophore away from the substrate. Immobilized DNA probe density and DNA target hybridization in these mixed DNA monolayers, as well as effects of MCU diluent on DNA hybridization in

  5. Neutron and X-ray reflectivity studies on DNA adsorption on mixed DPPC/DC-Cholesterol monolayers

    NASA Astrophysics Data System (ADS)

    Wu, Jui-Ching; Lin, Tsang-Lang; Jeng, U.-Ser; Lee, Hsin-Yi; Gutberlet, Thomas

    2006-11-01

    We have studied DNA adsorption on mixed DPPC/DC-Chol monolayers. Solid supported mixed monolayers on silicon wafers were prepared using Langmuir-Blodgett (LB) dipping technique. Neutron and X-ray reflectivity measurements were used to characterize these LB monofilms. For LB monofilms with DNA adsorption, the reflectivity data of the DPPC/DNA film are very close to that from the DPPC film, which indicates only minor DNA adsorption on the pure DPPC monolayer. Increasing the percentage of DC-Chol, film thickness increases. The DC-Chol/DNA film is thicker than the pure DC-Chol film (film thickness 18 Å) by about 9 Å due to the presence of adsorbed DNA. A model is presented to explain the structure of the lipid/DNA film.

  6. Identification of refined petroleum products in contaminated soils using an identification index for GC chromatograms.

    PubMed

    Kwon, Dongwook; Ko, Myoung-Soo; Yang, Jung-Seok; Kwon, Man Jae; Lee, Seung-Woo; Lee, Seunghak

    2015-08-01

    Hydrocarbons found in the environment are typically characterized by gas chromatography (GC). The shape of the GC chromatogram has been used to identify the source of petroleum contamination. However, the conventional practice of simply comparing the peak patterns of source products to those of environmental samples is dependent on the subjective decisions of individual analysts. We have developed and verified a quantitative analytical method for interpreting GC chromatograms to distinguish refined petroleum products in contaminated soils. We found that chromatograms for gasoline, kerosene, and diesel could be divided into three ranges with boundaries at C6, C8, C16, and C26. In addition, the relative peak area (RPA(GC)) of each range, a dimensionless ratio of the peak area within each range to that of the total range (C6-C26), had a unique value for each petroleum product. An identification index for GC chromatograms (ID(GC)), defined as the ratio of RPA(GC) of C8-C16 to that of C16-C26, was able to identify diesel and kerosene sources in samples extracted from artificially contaminated soils even after weathering. Thus, the ID(GC) can be used to effectively distinguish between refined petroleum products in contaminated soils.

  7. Gas Cromatography In Solar System Exploration:decoding Complex Chromatograms Recovered From Space Missions

    NASA Astrophysics Data System (ADS)

    Pietrogrande, M. C.; Tellini, I.; Dondi, F.; Felinger, A.; Sternberg, R.; Szopa, C.; Vidal-Madjar, C.

    GC plays a predominant role in solar system explorations: it has been applied to space research related to exobiology: i.e., Cassini-Huygens mission devoted to characterize chemical composition of TitanSs atmosphere [2], Rosetta mission to investigate the nucleus of comet p/Wirtamen (COSAC experiments) [1]. GC analysis of planetary atmosphere is a difficult analytical task because of the unknown and low level of an- alytes present in the sample, the high degree of automatization required, the strong constraints due to the flight (short analysis time, low power consumption, high accu- racy and reliability under extreme space conditions). In these circumstances the use of a signal processing procedure is practically mandatory to efficiently extract useful in- formation from the raw chromatogram ­ i.e. to decode the complex chromatogram to determine the number of components, the separation efficiency and the retention pat- tern. In this work a chemometric approach based on the Fourier analysis is applied to complex chromatograms related to space research: from the autocovariance function (ACVF) computed on the digitized chromatogram, the chromatographic parameters ­ number of components, peak shape parameters, retention pattern ­ can be estimated [3-7]. The procedure, originally developed for constant peak width [3], was extended to variable peak width [4], in order to describe chromatograms obtained in isother- mal conditions, i.e., analysis condition compatible with space flight constraints. The chemometric procedure was applied to chromatograms of standard mixtures repre- sentative of planetary atmospheres ­ hydrocarbons and oxygenated compounds with carbon atom number ranging from 2 to 8 ­ obtained in flight simulating conditions ­ isothermal or pseudo-isothermal conditions. Both the simplified graphic procedure, based on the assumption of constant peak width [3], and the complete approach de- veloped for variable peak width [4], were applied and the results

  8. Bulged Invader probes: activated duplexes for mixed-sequence dsDNA recognition with improved thermodynamic and kinetic profiles.

    PubMed

    Guenther, Dale C; Karmakar, Saswata; Hrdlicka, Patrick J

    2015-10-18

    Double-stranded oligonucleotides with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides are energetically activated for recognition of mixed-sequence double-stranded DNA. Incorporation of nonyl (C9) bulges at specific positions of these probes, results in more highly affine (>5-fold), faster (>4-fold) and more persistent dsDNA recognition relative to conventional Invader probes.

  9. Confidence interval of the likelihood ratio associated with mixed stain DNA evidence.

    PubMed

    Beecham, Gary W; Weir, Bruce S

    2011-01-01

    Likelihood ratios are necessary to properly interpret mixed stain DNA evidence. They can flexibly consider alternate hypotheses and can account for population substructure. The likelihood ratio should be seen as an estimate and not a fixed value, because the calculations are functions of allelic frequency estimates that were estimated from a small portion of the population. Current methods do not account for uncertainty in the likelihood ratio estimates and are therefore an incomplete picture of the strength of the evidence. We propose the use of a confidence interval to report the consequent variation of likelihood ratios. The confidence interval is calculated using the standard forensic likelihood ratio formulae and a variance estimate derived using the Taylor expansion. The formula is explained, and a computer program has been made available. Numeric work shows that the evidential strength of DNA profiles decreases as the variation among populations increases.

  10. DNA interaction studies of tridentate bridged Ru(II)-Pt(II) mixed-metal supramolecules.

    PubMed

    Prussin, Aaron J; Zhao, Shengliang; Jain, Avijita; Winkel, Brenda S J; Brewer, Karen J

    2009-03-01

    Reported herein are studies of the concentration and temperature dependent interactions with DNA of the stereochemically defined mixed-metal supramolecular complexes, [(tpy)Ru(tppz)PtCl](PF(6))(3) and [ClPt(tppz)Ru(tppz)PtCl](PF(6))(4) (tpy=2,2':6',2''-terpyridine and tppz=2,3,5,6-tetrakis(2-pyridyl)pyrazine). These metal complexes couple a ruthenium based light absorber (LA) to the bioactive platinum sites (BAS) using a tridentate bridging ligand (BL). The complexes exhibit intense Ru-->tppz(pi*) metal to ligand charge transfer (MLCT) transitions in the visible region and adopt a square planar geometry around the Pt(II) center. The effect of incubating these metal complexes with DNA on the subsequent migration of DNA through an agarose gel was found to be more dramatic than that observed for the well known anticancer drug, cis-[Pt(NH(3))(2)Cl(2)] (cisplatin). This effect was enhanced with increased incubation temperature. Unwinding of supercoiled plasmid DNA was found to be more pronounced for the trimetallic complex, [ClPt(tppz)Ru(tppz)PtCl](PF(6))(4), than for the bimetallic complex, [(tpy)Ru(tppz)PtCl](PF(6))(3).

  11. Genome-Wide DNA Methylation in Mixed Ancestry Individuals with Diabetes and Prediabetes from South Africa

    PubMed Central

    Pheiffer, Carmen; Humphries, Stephen E.; Gamieldien, Junaid; Erasmus, Rajiv T.

    2016-01-01

    Aims. To conduct a genome-wide DNA methylation in individuals with type 2 diabetes, individuals with prediabetes, and control mixed ancestry individuals from South Africa. Methods. We used peripheral blood to perform genome-wide DNA methylation analysis in 3 individuals with screen detected diabetes, 3 individuals with prediabetes, and 3 individuals with normoglycaemia from the Bellville South Community, Cape Town, South Africa, who were age-, gender-, body mass index-, and duration of residency-matched. Methylated DNA immunoprecipitation (MeDIP) was performed by Arraystar Inc. (Rockville, MD, USA). Results. Hypermethylated DMRs were 1160 (81.97%) and 124 (43.20%), respectively, in individuals with diabetes and prediabetes when both were compared to subjects with normoglycaemia. Our data shows that genes related to the immune system, signal transduction, glucose transport, and pancreas development have altered DNA methylation in subjects with prediabetes and diabetes. Pathway analysis based on the functional analysis mapping of genes to KEGG pathways suggested that the linoleic acid metabolism and arachidonic acid metabolism pathways are hypomethylated in prediabetes and diabetes. Conclusions. Our study suggests that epigenetic changes are likely to be an early process that occurs before the onset of overt diabetes. Detailed analysis of DMRs that shows gradual methylation differences from control versus prediabetes to prediabetes versus diabetes in a larger sample size is required to confirm these findings. PMID:27555869

  12. Multifunctional DNA interactions of Ru-Pt mixed metal supramolecular complexes with substituted terpyridine ligands.

    PubMed

    Jain, Avijita; Wang, Jing; Mashack, Emily R; Winkel, Brenda S J; Brewer, Karen J

    2009-10-05

    The coupling of a light absorbing unit to a bioactive site allows for the development of supramolecules with multifunctional interactions with DNA. A series of mixed metal supramolecular complexes that couple a DNA-binding cis-Pt(II)Cl(2) center to a ruthenium chromophore via a polyazine bridging ligand have been prepared, and their DNA interactions have been studied, [(TL)RuCl(dpp)PtCl(2)](PF(6)) (TL = tpy (2,2':6',2''-terpyridine), MePhtpy (4'-(4-methylphenyl)-2,2':6',2''-terpyridine), or (t)Bu(3)tpy (4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine and dpp = 2,3-bis(2-pyridyl)pyrazine). This series provides for unique tridentate coordinated Ru(II) systems to photocleave DNA with preassociation with the DNA target via coordination of the Pt(II) center. Electronic absorption spectroscopy of the complexes displays intense ligand-based pi-->pi* transitions in the UV region and metal to ligand charge transfer (MLCT) transitions in the visible region. The Ru(dpi)-->dpp(pi*) MLCT transitions occur at 545 nm, red-shifted relative to the 520 nm maxima for the monometallic synthons, [(TL)RuCl(dpp)](PF(6)). The title RuPt complexes display reversible Ru(II/III) oxidative couples at 1.10, 1.10, and 1.01 V vs Ag/AgCl for TL = tpy, MePhtpy, and (t)Bu(3)tpy, respectively. The TL(0/-) reduction occurred at -1.43, -1.44, and -1.59 V vs Ag/AgCl for TL = tpy, MePhtpy, and (t)Bu(3)tpy, respectively. These complexes display a dpp(0/-) couple (-0.50 -0.55, and -0.59 V) significantly shifted to positive potential relative to their monometallic synthons (-1.15, -1.16, and -1.22 V), consistent with the bridging coordination of the dpp ligand. Coupling of (TL)Ru(II)Cl(BL) subunit to a cis-Pt(II)Cl(2) site provides for the application of photochemically inactive Ru(II)(tpy)-based chromophores in DNA photocleavage applications. The [(TL)RuCl(dpp)PtCl(2)](+) complexes display covalent binding to DNA and photocleavage upon irradiation with visible light modulated by TL identity. The redox

  13. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples

    NASA Astrophysics Data System (ADS)

    Ali, M. E.; Hashim, U.; Mustafa, S.; Che Man, Y. B.; Yusop, M. H. M.; Bari, M. F.; Islam, Kh N.; Hasan, M. F.

    2011-05-01

    We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 °C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 µg ml - 1 swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

  14. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples.

    PubMed

    Ali, M E; Hashim, U; Mustafa, S; Man, Y B Che; Yusop, M H M; Bari, M F; Islam, Kh N; Hasan, M F

    2011-05-13

    We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 °C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 µg ml(-1) swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

  15. A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data

    PubMed Central

    Lea, Amanda J.

    2015-01-01

    Identifying sources of variation in DNA methylation levels is important for understanding gene regulation. Recently, bisulfite sequencing has become a popular tool for investigating DNA methylation levels. However, modeling bisulfite sequencing data is complicated by dramatic variation in coverage across sites and individual samples, and because of the computational challenges of controlling for genetic covariance in count data. To address these challenges, we present a binomial mixed model and an efficient, sampling-based algorithm (MACAU: Mixed model association for count data via data augmentation) for approximate parameter estimation and p-value computation. This framework allows us to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. Using simulations and two real data sets (whole genome bisulfite sequencing (WGBS) data from Arabidopsis thaliana and reduced representation bisulfite sequencing (RRBS) data from baboons), we show that our method provides well-calibrated test statistics in the presence of population structure. Further, it improves power to detect differentially methylated sites: in the RRBS data set, MACAU detected 1.6-fold more age-associated CpG sites than a beta-binomial model (the next best approach). Changes in these sites are consistent with known age-related shifts in DNA methylation levels, and are enriched near genes that are differentially expressed with age in the same population. Taken together, our results indicate that MACAU is an efficient, effective tool for analyzing bisulfite sequencing data, with particular salience to analyses of structured populations. MACAU is freely available at www.xzlab.org/software.html. PMID:26599596

  16. Decoding of complex isothermal chromatograms recovered from space missions. Identification of molecular structure.

    PubMed

    Pietrogrande, Maria Chiara; Tellini, Ilaria; Pasti, Luisa; Dondi, Francesco; Szopa, Cyril; Sternberg, Robert; Vidal-Madjar, Claire

    2003-06-20

    A chemometric approach, based on the study of the autocovariance function, is described to study isothermal GC chromatograms of multicomponent mixtures: isothermal GC analysis is the method of choice in space missions since it is, to date, the only method compatible with flight constraints. Isothermal GC chromatograms look inhomogeneous and disordered with peak density decreasing at higher retention times: a time axis transformation is proposed to make retention an homogeneous process so that CH2 addition in terms of an homologous series yields a constant retention increment. The time axis is transformed into a new scale based on the retention times of n-alkanes, as they are the basis of the universal Kovats indices procedure. The order introduced into the chromatogram by retention time linearization can be simply singled out by the experimental autocorrelation function (EACF) plot: if constant inter-distances are repeated in different regions of the chromatogram, well-shaped peaks are evident in the EACF plot. By comparison, with a standard mixture it is possible to identify peaks diagnostic of specific molecular structures: study of the EACF plot provides information on sample chemical composition. The procedure was applied to standard mixtures containing compounds representative of the planetary atmospheres that will be investigated in the near future: in particular, those related to Titan's atmosphere (Cassini-Huygens mission) and cometary's nucleus (Rosetta mission). The employed experimental conditions simulated those applied to GC instruments installed on space probes and landers in space missions. The method was applied to two specific investigations related to space research, i.e., a comparison of retention selectivity of different GC columns and identification of the chemical composition of an unknown mixture.

  17. Results of the 2003-2004 GEP-ISFG collaborative study on mitochondrial DNA: focus on the mtDNA profile of a mixed semen-saliva stain.

    PubMed

    Crespillo, Manuel; Paredes, Miguel R; Prieto, Lourdes; Montesino, Marta; Salas, Antonio; Albarran, Cristina; Alvarez-Iglesias, V; Amorin, Antonio; Berniell-Lee, Gemma; Brehm, Antonio; Carril, Juan C; Corach, Daniel; Cuevas, Nerea; Di Lonardo, Ana M; Doutremepuich, Christian; Espinheira, Rosa M; Espinoza, Marta; Gómez, Felix; González, Alberto; Hernández, Alexis; Hidalgo, M; Jimenez, Magda; Leite, Fabio P N; López, Ana M; López-Soto, Manuel; Lorente, Jose A; Pagano, Shintia; Palacio, Ana M; Pestano, José J; Pinheiro, Maria F; Raimondi, Eduardo; Ramón, M M; Tovar, Florangel; Vidal-Rioja, Lidia; Vide, Maria C; Whittle, Martín R; Yunis, Juan J; Garcia-Hirschfel, Julia

    2006-07-13

    We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003-2004. Five reference bloodstains from five donors (M1-M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1-M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1-M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.

  18. An improved independent component analysis model for 3D chromatogram separation and its solution by multi-areas genetic algorithm

    PubMed Central

    2014-01-01

    Background The 3D chromatogram generated by High Performance Liquid Chromatography-Diode Array Detector (HPLC-DAD) has been researched widely in the field of herbal medicine, grape wine, agriculture, petroleum and so on. Currently, most of the methods used for separating a 3D chromatogram need to know the compounds' number in advance, which could be impossible especially when the compounds are complex or white noise exist. New method which extracts compounds from 3D chromatogram directly is needed. Methods In this paper, a new separation model named parallel Independent Component Analysis constrained by Reference Curve (pICARC) was proposed to transform the separation problem to a multi-parameter optimization issue. It was not necessary to know the number of compounds in the optimization. In order to find all the solutions, an algorithm named multi-areas Genetic Algorithm (mGA) was proposed, where multiple areas of candidate solutions were constructed according to the fitness and distances among the chromosomes. Results Simulations and experiments on a real life HPLC-DAD data set were used to demonstrate our method and its effectiveness. Through simulations, it can be seen that our method can separate 3D chromatogram to chromatogram peaks and spectra successfully even when they severely overlapped. It is also shown by the experiments that our method is effective to solve real HPLC-DAD data set. Conclusions Our method can separate 3D chromatogram successfully without knowing the compounds' number in advance, which is fast and effective. PMID:25474487

  19. Signal processing using sparse derivatives with applications to chromatograms and ECG

    NASA Astrophysics Data System (ADS)

    Ning, Xiaoran

    In this thesis, we investigate the sparsity exist in the derivative domain. Particularly, we focus on the type of signals which posses up to Mth (M > 0) order sparse derivatives. Efforts are put on formulating proper penalty functions and optimization problems to capture properties related to sparse derivatives, searching for fast, computationally efficient solvers. Also the effectiveness of these algorithms are applied to two real world applications. In the first application, we provide an algorithm which jointly addresses the problems of chromatogram baseline correction and noise reduction. The series of chromatogram peaks are modeled as sparse with sparse derivatives, and the baseline is modeled as a low-pass signal. A convex optimization problem is formulated so as to encapsulate these non-parametric models. To account for the positivity of chromatogram peaks, an asymmetric penalty function is also utilized with symmetric penalty functions. A robust, computationally efficient, iterative algorithm is developed that is guaranteed to converge to the unique optimal solution. The approach, termed Baseline Estimation And Denoising with Sparsity (BEADS), is evaluated and compared with two state-of-the-art methods using both simulated and real chromatogram data. Promising result is obtained. In the second application, a novel Electrocardiography (ECG) enhancement algorithm is designed also based on sparse derivatives. In the real medical environment, ECG signals are often contaminated by various kinds of noise or artifacts, for example, morphological changes due to motion artifact, non-stationary noise due to muscular contraction (EMG), etc. Some of these contaminations severely affect the usefulness of ECG signals, especially when computer aided algorithms are utilized. By solving the proposed convex l1 optimization problem, artifacts are reduced by modeling the clean ECG signal as a sum of two signals whose second and third-order derivatives (differences) are sparse

  20. Differential reporting of mixed DNA profiles and its impact on jurists' evaluation of evidence. An international analysis.

    PubMed

    de Keijser, Jan W; Malsch, Marijke; Luining, Egge T; Weulen Kranenbarg, Marleen; Lenssen, Dominique J H M

    2016-07-01

    While DNA analysis is considered by many the gold standard in forensic science, there is ample room for variation in interpretation and reporting. This seems especially the case when working with (complex) mixed DNA profiles. Two consecutive studies on differential DNA reporting were conducted. In Study 1, we first examined type and magnitude of differences when forensic DNA experts across institutes and jurisdictions are handed an identical forensic case with mixed profiles. In Study 2, we explore the impact of the observed differential reporting on jurists' evaluation of the DNA evidence. 19 DNA expert reports from forensic institutes across Western jurisdictions were obtained. Differences between the reports were many and include extensiveness of the reports, explanations of technical issues, use of explanatory appendices, level of reporting, use of context information, and, most markedly, type and substantive content of the conclusions. In Study 2, a group of criminal law students judged a selection of these reports in a quasi experimental study design. Findings show that these differing reports have quite different evidentiary value for jurists, depending on which expert authored the report. It is argued that the impact of differential reporting on jurists' evaluation was so fundamental and substantive that it is seems reasonable to claim that in an actual court case it could make the difference between acquittal and conviction.

  1. DNA extraction for short tandem repeat typing from mixed samples using anti-human leukocyte CD45 and ABO blood group antibodies.

    PubMed

    Yano, Shizue; Honda, Katsuya; Kaminiwa, Junko; Nishi, Takeki; Iwabuchi, Yayoi; Sugano, Yukiko; Kurosu, Akira; Suzuki, Yasuhito

    2014-05-01

    DNA testing from mixed cell samples can be difficult to use successfully in criminal investigations. Here, we present a method for the extraction of DNA from mixed bloodstains involving plural contributors, after antibody-microbead captured cell separation. This method, together with the multiplex short tandem repeat typing presented, has proven highly successful in the recovery of DNA profiles corresponding to the ABO blood type. Methodological steps include magnetic separation using leukocyte specific CD45 antibody-coated microbeads and centrifugal separation of leukocyte agglutination by ABO antibody. The detection results of variable mixed ratio showed that the target DNA was detected accurately as low as 1:512 mixed ratio, regardless of the large amount of the background DNA present. The method presented here is applicable to PCR-based identification for various kinds of mixed samples.

  2. Identification and quantification of volatile organic compounds using systematic single-ion chromatograms

    SciTech Connect

    Tsuchiya, Yoshio; Kanabus-Kaminska, J.M.

    1996-12-31

    In order to determine the background level of volatile organic compounds (VOCs) in Canadian indoor air, a method of identification and quantification at a level of 0.3 {micro}g/m{sup 3} using systematic single-ion chromatograms (SICs) has been developed. The compounds selected for measurement included several halogenated compounds, oxygen compounds, terpenes, and C8 to C16 n-alkanes. Air samples were taken in 3-layered sorbent tubes and trapped compounds were thermally desorbed into the helium stream of a gas chromatograph/mass spectrometer (GC/MS) analytical system. Total quantities of volatile organic compounds (TVOCs) were measured using a flame ionization detector (FID). Individual compounds were analyzed by a GC/MS. For the identification of compounds in the main stream GC effluent, both the specific GC retention and mass spectra were used. About 50 selected SICs were routinely extracted from a total ion chromatogram (TIC) to detect and quantify compounds. For each compound, a single representative ion was selected. The specific retention was calculated from the elution time on the SIC. For quantification, ion counts under a peak in the SIC were measured. The single-ion MS response factor for some of the compounds was experimentally determined using a dynamic reference procedure.

  3. Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment

    PubMed Central

    Song, Chen; Liu, Yibin; Fontana, Rachel; Makrigiorgos, Alexander; Mamon, Harvey; Kulke, Matthew H.; Makrigiorgos, G. Mike

    2016-01-01

    Presence of excess unaltered, wild-type (WT) DNA providing no information of biological or clinical value often masks rare alterations containing diagnostic or therapeutic clues in cancer, prenatal diagnosis, infectious diseases or organ transplantation. With the surge of high-throughput technologies there is a growing demand for removing unaltered DNA over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), a single-step approach with broad genome coverage that can remove WT-DNA from numerous sequences simultaneously, prior to genomic analysis. NaME-PrO employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating WT-DNA targets and guiding nuclease digestion to these sites. Mutation-containing DNA creates probe-DNA mismatches that inhibit digestion, thus subsequent DNA-amplification magnifies DNA-alterations at all selected targets. We demonstrate several-hundred-fold mutation enrichment in diverse human samples on multiple clinically relevant targets including tumor samples and circulating DNA in 50-plex reactions. Enrichment enables routine mutation detection at 0.01% abundance while by adjusting conditions it is possible to sequence mutations down to 0.00003% abundance, or to scan tumor-suppressor genes for rare mutations. NaME-PrO introduces a simple and highly parallel process to remove un-informative DNA sequences and unmask clinically and biologically useful alterations. PMID:27431322

  4. Mixture interpretation: defining the relevant features for guidelines for the assessment of mixed DNA profiles in forensic casework.

    PubMed

    Budowle, Bruce; Onorato, Anthony J; Callaghan, Thomas F; Della Manna, Angelo; Gross, Ann M; Guerrieri, Richard A; Luttman, Jennifer C; McClure, David Lee

    2009-07-01

    Currently in the United States there is little direction for what constitutes sufficient guidelines for DNA mixture interpretation. While a standardized approach is not possible or desirable, more definition is necessary to ensure reliable interpretation of results is carried out. In addition, qualified DNA examiners should be able to review reports and understand the assumptions made by the analyst who performed the interpretation. Interpretation of DNA mixture profiles requires consideration of a number of aspects of a mixed profile, many of which need to be established by on-site, internal validation studies conducted by a laboratory's technical staff, prior to performing casework analysis. The relevant features include: criteria for identification of mixed specimens, establishing detection and interpretation threshold values, defining allele peaks, defining nonallele peaks, identifying artifacts, consideration of tri-allelic patterns, estimating the minimum number of contributors, resolving components of a mixture, determining when a portion of the mixed profile can be treated as a single source profile, consideration of potential additive effects of allele sharing, impact of stutter peaks on interpretation in the presence of a minor contributor, comparison with reference specimens, and some issues related to the application of mixture calculation statistics. Equally important is using sensible judgment based on sound and documented principles of DNA analyses. Assumptions should be documented so that reliable descriptive information is conveyed adequately concerning that mixture and what were the bases for the interpretations that were carried out. Examples are provided to guide the community. Interpretation guidelines also should incorporate strategies to minimize potential bias that could occur by making inferences based on a reference sample. The intent of this paper is to promote more thought, provide assistance on many aspects for consideration, and to

  5. Quality evaluation of Yin Chen Hao Tang extract based on fingerprint chromatogram and simultaneous determination of five bioactive constituents.

    PubMed

    Wang, Xijun; Lv, Haitao; Sun, Hui; Jiang, Xingang; Wu, Zeming; Sun, Wenjun; Wang, Ping; Liu, Lian; Bi, Kaishun

    2008-01-01

    A completely validated method based on HPLC coupled with photodiode array detector (HPLC-UV) was described for evaluating and controlling quality of Yin Chen Hao Tang extract (YCHTE). First, HPLC-UV fingerprint chromatogram of YCHTE was established for preliminarily elucidating amount and chromatographic trajectory of chemical constituents in YCHTE. Second, for the first time, five mainly bioactive constituents in YCHTE were simultaneously determined based on fingerprint chromatogram for furthermore controlling the quality of YCHTE quantitatively. The developed method was applied to analyze 12 batches of YCHTE samples which consisted of herbal drugs from different places of production, showed acceptable linearity, intraday (RSD <5%), interday precision (RSD <4.80%), and accuracy (RSD <2.80%). As a result, fingerprint chromatogram determined 15 representative general fingerprint peaks, and the fingerprint chromatogram resemblances are all better than 0.9996. The contents of five analytes in different batches of YCHTE samples do not indicate significant difference. So, it is concluded that the developed HPLC-UV method is a more fully validated and complete method for evaluating and controlling the quality of YCHTE.

  6. Analysis of mixed DNA-bisnaphthalimide interactions involving groove association and intercalation with surface-based and solution methodologies.

    PubMed

    González-Bulnes, Luis; Gallego, José

    2012-12-01

    The bisnaphthalimide cytotoxic agent elinafide exhibits a mixed DNA binding mode including groove-association and intercalation. We have compared the interaction of elinafide and two bisnaphthalimide analogues with various natural and modified DNA sequences using solution NMR and UV-melting methods and surface plasmon resonance (SPR) experiments at different pH conditions. The combined data obtained with these techniques established a high-affinity binding mode comprising intercalation and strong electrostatic contacts with guanine bases in the major groove, and a weaker interaction with A·T pairs likely involving groove association. However, the SPR binding constants and the NMR and UV-melting binding parameters responded differently to variations in DNA bases and ligand intercalating moieties. The rates and equilibrium constants determined by SPR clearly responded to changes in pH and DNA groove composition, but were rather insensitive to alterations in drug rings and DNA bases affecting the intercalation process. Conversely, the intermolecular stacking interactions detected by NMR and the ligand-induced thermal stabilizations measured by UV depended on both sets of factors and were controlled by the sequence-dependent properties of the DNA helices, indicating that these data were modulated by naphthalimide stacking in addition to groove association. A two-step binding process where a groove-bound state is required prior to intercalation is proposed as an explanation for these observations. These findings may be useful for studying other classes of DNA- and RNA-binding drugs, which frequently combine groove-binding and stacking moieties.

  7. Relative stability of transgene DNA fragments from GM rapeseed in mixed ruminal cultures.

    PubMed

    Sharma, Ranjana; Alexander, Trevor W; John, S Jacob; Forster, Robert J; McAllister, Tim A

    2004-05-01

    The use of transgenic crops as feeds for ruminant animals has prompted study of the possible uptake of transgene fragments by ruminal micro-organisms and/or intestinal absorption of fragments surviving passage through the rumen. The persistence in buffered ruminal contents of seven different recombinant DNA fragments from GM rapeseed expressing the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) transgene was tracked using PCR. Parental and transgenic (i.e. glyphosphate-tolerant; Roundup Ready, Monsanto Company, St Louis, MO, USA) rapeseed were incubated for 0, 2, 4, 8, 12, 24 and 48 h as whole seeds, cracked seeds, rapeseed meal, and as pelleted, barley-based diets containing 65 g rapeseed meal/kg. The seven transgene fragments ranged from 179 to 527 bp and spanned the entire 1363 bp EPSPS transgene. A 180 bp ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit fragment and a 466 bp 16S rDNA fragment were used as controls for endogenous rapeseed DNA and bacterial DNA respectively. The limit of detection of the PCR assay, established using negative controls spiked with known quantities of DNA, was 12.5 pg. Production of gas and NH3 was monitored throughout the incubation and confirmed active in vitro fermentation. Bacterial DNA was detected in all sample types at all time points. Persistence patterns of endogenous (Rubisco) and recombinant (EPSPS) rapeseed DNA were inversely related to substrate digestibility (amplifiable for 48, 8 and 4 h in whole or cracked seeds, meal and diets respectively), but did not differ between parental and GM rapeseed, nor among fragments. Detection of fragments was representative of persistence of the whole transgene. No EPSPS fragments were amplifiable in microbial DNA, suggesting that transformation had not occurred during the 48 h incubation. Uptake of transgenic DNA fragments by ruminal bacteria is probably precluded or time-limited by rapid degradation of plant DNA upon plant cell lysis.

  8. Preferential interaction between DNA and small ions in mixed-size counterion systems: Monte Carlo simulation and density functional study

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Yu, Yang-Xin; Gao, Guang-Hua; Luo, Guang-Sheng

    2007-04-01

    Competitive binding between counterions around DNA molecule is characterized using the preferential interaction coefficient of individual ion in single and mixed electrolyte solutions. The canonical Monte Carlo (MC) simulation, nonlinear Poisson-Boltzmann (PB) equation, and density functional theory (DFT) proposed in our previous work [Wang, Yu, Gao, and Luo, J. Chem. Phys. 123, 234904 (2005)] are utilized to calculate the preferential interaction coefficients. The MC simulations and theoretical results show that for single electrolyte around DNA, the preferential interaction coefficient of electrolyte decreases as the cation size is increased, indicating that the larger cation has less accumulation ability in the vicinity of DNA. For the mixed electrolyte solution, it is found that cation diameter has a significant effect on the competitive ability while anion diameter has a negligible effect. It proves that the preferential interaction coefficients of all ions decrease as the total ionic concentration is increased. The DFT generally has better performance than the PB equation does when compared to the MC simulation data. The DFT behaves quite well for the real ionic solutions such as the KCl -NaCl-H2O, NaCl -CaCl2-H2O, and CaCl2-MgCl2-H2O systems.

  9. Synthesis and DNA interaction of a mixed proflavine-phenanthroline Tröger base.

    PubMed

    Baldeyrou, Brigitte; Tardy, Christelle; Bailly, Christian; Colson, Pierre; Houssier, Claude; Charmantray, Franck; Demeunynck, Martine

    2002-04-01

    We report the synthesis of an asymmetric Tröger base containing the two well characterised DNA binding chromophores, proflavine and phenanthroline. The mode of interaction of the hybrid molecule was investigated by circular and linear dichroism experiments and a biochemical assay using DNA topoisomerase I. The data are compatible with a model in which the proflavine moiety intercalates between DNA base pairs and the phenanthroline ring occupies the DNA groove. DNase I cleavage experiments were carried out to investigate the sequence preference of the hybrid ligand and a well resolved footprint was detected at a site encompassing two adjacent 5'-GTC.5-GAC triplets. The sequence preference of the asymmetric molecule is compared to that of the symmetric analogues.

  10. Studies on Photocleavage, DNA Binding, Cytotoxicity, and Docking Studies of Ruthenium(II) Mixed Ligand Complexes.

    PubMed

    Kumar, Yata Praveen; Devi, C Shobha; Srishailam, A; Deepika, N; Kumar, V Ravi; Reddy, P Venkat; Nagasuryaprasad, K; Singh, Surya S; Nagababu, Penumaka; Satyanarayana, S

    2016-11-01

    This article describes the synthesis and characterization of three new Ru(II) polypyridyl complexes including [Ru(phen)2(dpphz)](2+) (1), [Ru(bpy)2(dpphz)](2+) (2) and [Ru(dmb)2(dpphz)](2+) (3) where dpphz = dipyrido[3,2-a:2',3'-c] phenazine-11-hydrazide, phen =1,10-phenanthroline, bpy = 2,2'-bipyridine and dmb = 4,4'-dimethyl2,2'-bipyridine. The binding behaviors of these complexes to calf thymus DNA (CT-DNA) were explored by spectroscopic titrations, viscosity measurements. Results suggest that these complexes can bind to CT-DNA through intercalation. However, their binding strength differs from each other; this may be attributed to difference in the ancillary ligand. The cytotoxicity of 1-3 was evaluated by MTT assay; results indicated that all complexes have significant dose dependent cytotoxicity with HeLa tumor cell line. All complexes exhibited efficient photocleavage of pBR322 DNA upon irradiation. The DNA binding ability of 1-3 was also studied by docking the complexes into B-DNA using docking program.

  11. Synchronized Analysis of FTIR Spectra and GCMS Chromatograms for Evaluation of the Thermally Degraded Vegetable Oils

    PubMed Central

    Mohd Irwan Lu, Nurul Aida Lu; Samling, Benedict

    2014-01-01

    Fourier Transform Infrared (FTIR) and Gas Chromatography Mass Spectrometry (GCMS) are two common instruments used for analysis of edible oils. The output signal is often analysed on the software attached to the workstations. The processing software is usually individualised for a specific source. The output of GCMS cannot be analysed on the FTIR hence analysts often need to juggle between instruments when multiple techniques are employed. This could become exhaustive when a large dataset is involved. This paper reports a synchronised approach for analysis of signal from FTIR and GCMS. The algorithm is demonstrated on a dataset of edible oils to investigate the thermal degradation of seven types of edible oils treated at 100°C and 150°C. The synchronised routines identify peaks present in FTIR and GCMS spectra/chromatograms where the information is subsequently extracted onto peak tables for further analysis. In this study, it is found that palm based products and corn oils were relatively more stable with higher content of antioxidants tocopherols and squalene. As a conclusion, this approach allows simultaneous analysis of signal from multiple sources and samples enhancing the efficiency of the signal processing process. PMID:24563804

  12. [Determination of 13C enrichment in soil amino acid enantiomers by gas chromatogram/mass spectrometry].

    PubMed

    He, Hong-Bo; Zhang, Wei; Ding, Xue-Li; Bai, Zhen; Liu, Ning; Zhang, Xu-Dong

    2008-06-01

    The transformation and renewal of amino acid enantiomers is of significance in indicating the turnover mechanism of soil organic matter. In this paper, a method of gas chromatogram/mass spectrometry combined with U-13 C-glucose incubation was developed to determine the 13C enrichment in soil amino acid enantiomers, which could effectively differentiate the original and the newly synthesized amino acids in soil matrix. The added U-13 C-glucose was utilized rapidly to structure the amino acid carbon skeleton, and the change of relative abundance of isotope ions could be determined by mass spectrometry. The direct incorporation of U-13 C glucose was estimated by the intensity increase of m/z (F + n) to F (F was parent fragment, and n was the carbon number in the fragment), while the total isotope incorporation from the added 13C could be calculated according to the abundance ratio increment summation from m/z (Fa + 1) through (Fa + T) (Fa was the fragment containing all original skeleton carbons, and T was the carbon number in the amino acid molecule). The 13C enrichment in the target compound was expressed as atom percentage excess (APE), and that of D-amino acid needed to be corrected by the coefficient of hydrolysis-induced racemization. The 13C enrichment reflected the carbon turnover velocity of individual amino acid enantiomers, and was powerful to investigate the dynamics of soil amino acids.

  13. RNA cell typing and DNA profiling of mixed samples: can cell types and donors be associated?

    PubMed

    Harteveld, Joyce; Lindenbergh, Alexander; Sijen, Titia

    2013-09-01

    Forensic samples regularly involve mixtures, which are readily recognised in forensic analyses. Combined DNA and mRNA profiling is an upcoming forensic practice to examine donors and cell types from the exact same sample. From DNA profiles individual genotypes may be deconvoluted, but to date no studies have established whether the cell types identified in corresponding RNA profiles can be associated with individual donors. Although RNA expression levels hold many variables from which an association may not be expected, proof of concept is important to forensic experts who may be cross examined about this possible correlation in court settings. Clearly, the gender-specificity of certain body fluids (semen, vaginal mucosa, menstrual secretion) can be instructive. However, when donors of the same gender or gender-neutral cell types are involved, alternatives are needed. Here we analyse basic two-component mixtures (two cell types provided by different donors) composed of six different cell types, and assess whether the heights of DNA and RNA peaks may guide association of donor and cell type. Divergent results were obtained; for some mixtures RNA peak heights followed the DNA results, but for others the major DNA component did not present higher RNA peaks. Also, variation in mixture ratios was observed for RNA profiling replicates and when different donor couples gave the same two body fluids. As sample degradation may affect the two nucleic acids and/or distinct cell types differently (and thus influence donor and cell type association), mixtures were subjected to elevated temperature or UV-light. Variation in DNA and RNA stability was observed both between and within cell types and depended on the method inducing degradation. Taken together, we discourage to associate cell types and donors from peak heights when performing RNA and DNA profiling.

  14. Solvent fluctuations drive the hole transfer in DNA: a mixed quantum-classical study.

    PubMed

    Kubar, Tomás; Kleinekathöfer, Ulrich; Elstner, Marcus

    2009-10-01

    We studied the hole transfer across adenine bridges in double-stranded DNA by means of a multiscale approach, propagating the hole in the framework of time-dependent DFT coupled to classical molecular dynamics simulation using a QM/MM scheme. The hole transfer in DNA is codetermined by the large fluctuations of site energies on the order of 0.4 eV, induced by the solvent degrees of freedom. These fluctuations lead to charge-transfer active conformations with large transfer efficiency, which are characterized by a favorable alignment of site energies along the DNA strand. This reduces the barrier for the hole transfer dramatically. Consequently, we find that a charge hopping mechanism is operative already for short bridges with fewer than four adenines, in contrast to the charge-transfer models assuming static DNA structures, where only tunneling occurs. The solvent fluctuations introduce a significant correlation between neighboring sites, enhancing the charge-transfer rate, while the fluctuation of electronic couplings has only a minor impact on the charge-transfer characteristics. Our results emphasize the importance of an accurate description of solvent effects as well as proper sampling, and it is suggested that charge transfer in DNA is gated by the dynamics of solvent.

  15. Evaluation of mixed-source, low-template DNA profiles in forensic science.

    PubMed

    Balding, David J

    2013-07-23

    Enhancements in sensitivity now allow DNA profiles to be obtained from only tens of picograms of DNA, corresponding to a few cells, even for samples subject to degradation from environmental exposure. However, low-template DNA (LTDNA) profiles are subject to stochastic effects, such as "dropout" and "dropin" of alleles, and highly variable stutter peak heights. Although the sensitivity of the newly developed methods is highly appealing to crime investigators, courts are concerned about the reliability of the underlying science. High-profile cases relying on LTDNA evidence have collapsed amid controversy, including the case of Hoey in the United Kingdom and the case of Knox and Sollecito in Italy. I argue that rather than the reliability of the science, courts and commentators should focus on the validity of the statistical methods of evaluation of the evidence. Even noisy DNA evidence can be more powerful than many traditional types of evidence, and it can be helpful to a court as long as its strength is not overstated. There have been serious shortcomings in statistical methods for the evaluation of LTDNA profile evidence, however. Here, I propose a method that allows for multiple replicates with different rates of dropout, sporadic dropins, different amounts of DNA from different contributors, relatedness of suspected and alternate contributors, "uncertain" allele designations, and degradation. R code implementing the method is open source, facilitating wide scrutiny. I illustrate its good performance using real cases and simulated crime scene profiles.

  16. Evaluation of mixed-source, low-template DNA profiles in forensic science

    PubMed Central

    Balding, David J.

    2013-01-01

    Enhancements in sensitivity now allow DNA profiles to be obtained from only tens of picograms of DNA, corresponding to a few cells, even for samples subject to degradation from environmental exposure. However, low-template DNA (LTDNA) profiles are subject to stochastic effects, such as “dropout” and “dropin” of alleles, and highly variable stutter peak heights. Although the sensitivity of the newly developed methods is highly appealing to crime investigators, courts are concerned about the reliability of the underlying science. High-profile cases relying on LTDNA evidence have collapsed amid controversy, including the case of Hoey in the United Kingdom and the case of Knox and Sollecito in Italy. I argue that rather than the reliability of the science, courts and commentators should focus on the validity of the statistical methods of evaluation of the evidence. Even noisy DNA evidence can be more powerful than many traditional types of evidence, and it can be helpful to a court as long as its strength is not overstated. There have been serious shortcomings in statistical methods for the evaluation of LTDNA profile evidence, however. Here, I propose a method that allows for multiple replicates with different rates of dropout, sporadic dropins, different amounts of DNA from different contributors, relatedness of suspected and alternate contributors, “uncertain” allele designations, and degradation. R code implementing the method is open source, facilitating wide scrutiny. I illustrate its good performance using real cases and simulated crime scene profiles. PMID:23818643

  17. Recovery of genomic DNA from archived PCR product mixes for subsequent multiplex amplification and typing of additional loci: forensic significance for older unsolved criminal cases.

    PubMed

    Patchett, Kylie L; Cox, Ken J; Burns, Dennis M

    2002-07-01

    A method for genomic DNA recovery from different types of PCR product mixes suitable for multiplex amplification and typing using the Profiler Plus STR typing system has been investigated. The application of this method is of significance in cases where the original DNA samples have been exhausted due to repeated typing analyses in an effort to maximize their evidentiary value. Such cases typically involve samples analyzed using the available DNA typing systems of the time which gave a markedly lower power of discrimination, either alone or in combination, compared to that of modern multiplex STR typing systems. It was found that an effective method for recovering genomic DNA from HLA-DQA1 +PM and CTT triplex amplification mixes, suitable for reproducible achievement of the complete Profiler Plus profile, involved the use of Amicon Microcon-100 microconcentrators. Interestingly, this method was not required to achieve the complete nine STR profile using D1S80 amplification mixes.

  18. Toward a DNA Taxonomy of Alpine Rhithrogena (Ephemeroptera: Heptageniidae) Using a Mixed Yule-Coalescent Analysis of Mitochondrial and Nuclear DNA

    PubMed Central

    Vuataz, Laurent; Sartori, Michel; Wagner, André; Monaghan, Michael T.

    2011-01-01

    Aquatic larvae of many Rhithrogena mayflies (Ephemeroptera) inhabit sensitive Alpine environments. A number of species are on the IUCN Red List and many recognized species have restricted distributions and are of conservation interest. Despite their ecological and conservation importance, ambiguous morphological differences among closely related species suggest that the current taxonomy may not accurately reflect the evolutionary diversity of the group. Here we examined the species status of nearly 50% of European Rhithrogena diversity using a widespread sampling scheme of Alpine species that included 22 type localities, general mixed Yule-coalescent (GMYC) model analysis of one standard mtDNA marker and one newly developed nDNA marker, and morphological identification where possible. Using sequences from 533 individuals from 144 sampling localities, we observed significant clustering of the mitochondrial (cox1) marker into 31 GMYC species. Twenty-one of these could be identified based on the presence of topotypes (expertly identified specimens from the species' type locality) or unambiguous morphology. These results strongly suggest the presence of both cryptic diversity and taxonomic oversplitting in Rhithrogena. Significant clustering was not detected with protein-coding nuclear PEPCK, although nine GMYC species were congruent with well supported terminal clusters of nDNA. Lack of greater congruence in the two data sets may be the result of incomplete sorting of ancestral polymorphism. Bayesian phylogenetic analyses of both gene regions recovered four of the six recognized Rhithrogena species groups in our samples as monophyletic. Future development of more nuclear markers would facilitate multi-locus analysis of unresolved, closely related species pairs. The DNA taxonomy developed here lays the groundwork for a future revision of the important but cryptic Rhithrogena genus in Europe. PMID:21611178

  19. Mixed infection of Sida jamaicensis in Jamaica reveals the presence of three recombinant begomovirus DNA A components.

    PubMed

    Stewart, Cheryl; Kon, Tatsuya; Rojas, Maria; Graham, André; Martin, Darren; Gilbertson, Robert; Roye, Marcia

    2014-09-01

    Begomoviruses impose serious constraints on agriculture throughout the temperate, tropical and subtropical regions. Previously, we characterised a sida golden yellow vein virus isolate, SiGYVV-[JM:Lig2:08] (HQ009519-20) from a symptomatic Sida jamaicensis plant. With the aim of establishing whether it was hosting a mixed infection that could facilitate recombination, PCR-RFLP was done on DNA extracted from this plant, and the results suggested the presence of two additional genetically distinct DNA-A molecules. Sequence analysis of these two DNA-A molecules (relying on BLAST searches and the CLUSTAL V algorithm within the DNASTAR MegAlign module) revealed that they belonged to novel species, and we have tentatively named these viruses sida golden mosaic Braco virus-[Jamaica:Liguanea:2008] and sida golden mosaic Liguanea virus-[Jamaica:1:2008]. Using RDP4 (recombination detection program), we determined that all three viruses were recombinant, with bases ~10 to ~440 of both SiGMLigV-[JM:Lig:08] and SiGYVV-[JM:Lig2:08] having been derived from a relative of SiGMBV-[JM:Lig:08] (P<2.070×10(-7) for all seven of the recombination detection methods). SiGMBV-[JM:Lig:08] was itself a product of recombination, deriving bases ~490-1195 from a virus that was ~92% similar to malvastrum yellow mosaic Helshire virus. Phylogenetically, these DNA-A components are most closely related to those of malvaceous weed-infecting begomoviruses from Jamaica, Cuba, Florida and Mexico. The SiGMBV DNA-A was able to elicit symptomatic infection in N. benthamiana.

  20. Forensic science, genetics and wildlife biology: getting the right mix for a wildlife DNA forensics lab.

    PubMed

    Ogden, Rob

    2010-09-01

    Wildlife DNA forensics is receiving increasing coverage in the popular press and has begun to appear in the scientific literature in relation to several different fields. Recognized as an applied subject, it rests on top of very diverse scientific pillars ranging from biochemistry through to evolutionary genetics, all embedded within the context of modern forensic science. This breadth of scope, combined with typically limited resources, has often left wildlife DNA forensics hanging precariously between human DNA forensics and academics keen to seek novel applications for biological research. How best to bridge this gap is a matter for regular debate among the relatively few full-time practitioners in the field. The decisions involved in establishing forensic genetic services to investigate wildlife crime can be complex, particularly where crimes involve a wide range of species and evidential questions. This paper examines some of the issues relevant to setting up a wildlife DNA forensics laboratory based on experiences of working in this area over the past 7 years. It includes a discussion of various models for operating individual laboratories as well as options for organizing forensic testing at higher national and international levels.

  1. Peak alignment and robust principal component analysis of gas chromatograms of fatty acid methyl esters and volatiles.

    PubMed

    Møller, Stina Frosch; Jørgensen, Bo M

    2007-04-01

    Gas chromatograms of fatty acid methyl esters and of volatile lipid oxidation products from fish lipid extracts are analyzed by multivariate data analysis [principal component analysis (PCA)]. Peak alignment is necessary in order to include all sampled points of the chromatograms in the data set. The ability of robust algorithms to deal with outlier problems, including both sample-wise and element-wise outliers, and the advantages and drawbacks of two robust PCA methods, robust PCA (ROBPCA) and robust singular value decomposition when analysing these GC data were investigated. The results show that the usage of ROPCA is advantageous, compared with traditional PCA, when analysing the entire profile of chromatographic data in cases of sub-optimally aligned data. It also demonstrates how choosing the most robust PCA (sample or element-wise) depends on the type of outliers present in the data set.

  2. Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations.

    PubMed

    Trosvik, Pål; Skånseng, Beate; Jakobsen, Kjetill S; Stenseth, Nils C; Naes, Tormod; Rudi, Knut

    2007-08-01

    High-throughput quantification of genetically coherent units (GCUs) is essential for deciphering population dynamics and species interactions within a community of microbes. Current techniques for microbial community analyses are, however, not suitable for this kind of high-throughput application. Here, we demonstrate the use of multivariate statistical analysis of complex DNA sequence electropherograms for the effective and accurate estimation of relative genotype abundance in cell samples from mixed microbial populations. The procedure is no more labor-intensive than standard automated DNA sequencing and provides a very effective means of quantitative data acquisition from experimental microbial communities. We present results with the Campylobacter jejuni strain-specific marker gene gltA, as well as the 16S rRNA gene, which is a universal marker across bacterial assemblages. The statistical models computed for these genes are applied to genetic data from two different experimental settings, namely, a chicken infection model and a multispecies anaerobic fermentation model, demonstrating collection of time series data from model bacterial communities. The method presented here is, however, applicable to any experimental scenario where the interest is quantification of GCUs in genetically heterogeneous DNA samples.

  3. Synthesis, DNA/HSA Interaction Spectroscopic Studies and In Vitro Cytotoxicity of a New Mixed Ligand Cu(II) Complex.

    PubMed

    Gan, Qian; Fu, Xiabing; Chen, Weijiang; Xiong, Yahong; Fu, Yinlian; Chen, Shi; Le, Xueyi

    2016-05-01

    A new mixed ligand copper(II)-dipeptide complex with 2-(2'-pyridyl)benzothiazole (pbt), [Cu(Gly-L-leu)(pbt)(H2O)]·ClO4 (Gly-L-leu = Glycyl-L-leucine anion) was synthesized and characterized by various physico-chemical means. The DNA binding and cleavage properties of the complex investigated by viscosity, agarose gel electrophoresis and multi-spectroscopic techniques (UV, circular dichroism (CD) and fluorescence) showed that the complex was bound to CT-DNA through intercalation mode with moderate binding constant (K b = 3.132 × 10(4) M(-1)), and cleaved pBR322 DNA efficiently (~ 5 μM) in the presence of Vc, probably via an oxidative mechanism induced by •OH. Additionally, the interaction of the complex with human serum albumin (HSA) was explored by UV-visible, CD, fluorescence, synchronous fluorescence and 3D fluorescence spectroscopy. The complex exhibits desired affinity to HSA through hydrophobic interaction. Moreover, the cytotoxicity of the complex against three human carcinoma cell lines (HeLa, HepG2 and A549) was evaluated by MTT assay, which showed that the complex had effective cytotoxicity and higher inhibition toward A549 cell lines with IC50 of 38.0 ± 3.2 μM.

  4. Relative biological effects of neutron mixed-beam irradiation for boron neutron capture therapy on cell survival and DNA double-strand breaks in cultured mammalian cells

    PubMed Central

    Okumura, Kakuji; Kinashi, Yuko; Kubota, Yoshihisa; Kitajima, Erika; Okayasu, Ryuichi; Ono, Koji; Takahashi, Sentaro

    2013-01-01

    Understanding the biological effects of neutron mixed-beam irradiation used for boron neutron capture therapy (BNCT) is important in order to improve the efficacy of the therapy and to reduce side effects. In the present study, cell viability and DNA double-strand breaks (DNA-DSBs) were examined in Chinese hamster ovary cells (CHO-K1) and their radiosensitive mutant cells (xrs5, Ku80-deficient), following neutron mixed-beam irradiation for BNCT. Cell viability was significantly impaired in the neutron irradiation groups compared to the reference gamma-ray irradiation group. The relative biological effectiveness for 10% cell survival was 3.3 and 1.2 for CHO-K1 and xrs5 cells, respectively. There were a similar number of 53BP1 foci, indicators of DNA-DSBs, in the neutron mixed-beam and the gamma-ray groups. In addition, the size of the foci did not differ between groups. However, neutron mixed-beam irradiation resulted in foci with different spatial distributions. The foci were more proximal to each other in the neutron mixed-beam groups than the gamma-ray irradiation groups. These findings suggest that neutron beams may induce another type of DNA damage, such as clustered DNA-DSBs, as has been indicated for other high-LET irradiation. PMID:22966174

  5. Can a mixed damage interfere with DNA-protein cross-links repair?

    PubMed

    Marzano, C; Severin, E; Bordin, F

    2001-01-01

    Some photochemical and photobiological properties of 4,5',8-trimethylpsoralen (TMP) have been studied in comparison with 1,4,6,8-tetramethyl-2H-furo[2,3-h]quinolin-2 one (FQ) and 8-methoxypsoralen (8-MOP). TMP and FQ can photobind to mammalian cell DNA in vivo, by UVA irradiation, forming DNA-protein cross-links (DPC), but only TMP shows a strong capacity of inducing interstrand cross-links (ISC). The mechanism of DPC formation was studied using the double irradiation method in Chinese hamster ovary (CHO) cells, and DPC were detected by alkaline elution. Both TMP and FQ induce covalent diadducts linking together DNA and proteins. Studying the formation of double strand breaks (DSB) in CHO cells we observed that TMP induced a low amount of DSB, similar to 8-MOP. TMP and 8-MOP induced chromosomal aberrations in CHO cells to the same extent, while FQ appeared to be more active. Our data suggest that the ISC induced by TMP could trap enzymes involved in DPC repair.

  6. DNA methylation of cord blood cell types: Applications for mixed cell birth studies.

    PubMed

    Bakulski, Kelly M; Feinberg, Jason I; Andrews, Shan V; Yang, Jack; Brown, Shannon; L McKenney, Stephanie; Witter, Frank; Walston, Jeremy; Feinberg, Andrew P; Fallin, M Daniele

    2016-05-03

    Epigenome-wide association studies of disease widely use DNA methylation measured in blood as a surrogate tissue. Cell proportions can vary between people and confound associations of exposure or outcome. An adequate reference panel for estimating cell proportions from adult whole blood for DNA methylation studies is available, but an analogous cord blood cell reference panel is not yet available. Cord blood has unique cell types and the epigenetic signatures of standard cell types may not be consistent throughout the life course. Using magnetic bead sorting, we isolated cord blood cell types (nucleated red blood cells, granulocytes, monocytes, natural killer cells, B cells, CD4(+)T cells, and CD8(+)T cells) from 17 live births at Johns Hopkins Hospital. We confirmed enrichment of the cell types using fluorescence assisted cell sorting and ran DNA from the separated cell types on the Illumina Infinium HumanMethylation450 BeadChip array. After filtering, the final analysis was on 104 samples at 429,794 probes. We compared cell type specific signatures in cord to each other and methylation at 49.2% of CpG sites on the array differed by cell type (F-test P < 10(-8)). Differences between nucleated red blood cells and the remainder of the cell types were most pronounced (36.9% of CpG sites at P < 10(-8)) and 99.5% of these sites were hypomethylated relative to the other cell types. We also compared the mean-centered sorted cord profiles to the available adult reference panel and observed high correlation between the overlapping cell types for granulocytes and monocytes (both r=0.74), and poor correlation for CD8(+)T cells and NK cells (both r=0.08). We further provide an algorithm for estimating cell proportions in cord blood using the newly developed cord reference panel, which estimates biologically plausible cell proportions in whole cord blood samples.

  7. Considering relatives when assessing the evidential strength of mixed DNA profiles.

    PubMed

    Taylor, Duncan; Bright, Jo-Anne; Buckleton, John

    2014-11-01

    Sophisticated methods of DNA profile interpretation have enabled scientists to calculate weights for genotype sets proposed to explain some observed data. Using standard formulae these weights can be incorporated into an LR calculation that considers two competing propositions. We demonstrate here how consideration of relatedness to the person of interest can be incorporated into a LR calculation and how the same calculation can be used for familial searches of complex mixtures. We provide a general formula that can be used in semi or fully automated methods of calculation and demonstrate their use by working through an example.

  8. Lanthanide mixed ligand chelates for DNA profiling and latent fingerprint detection

    NASA Astrophysics Data System (ADS)

    Menzel, E. R.; Allred, Clay

    1997-02-01

    It is our aim to develop a universally applicable latent fingerprint detection method using lanthanide (rare-earth) complexes as a source of luminescence. Use of these lanthanide complexes offers advantages on several fronts, including benefits from large Stokes shifts, long luminescence lifetimes, narrow emissions, ability of sequential assembly of complexes, and chemical variability of the ligands. Proper exploitation of these advantages would lead to a latent fingerprint detection method superior to any currently available. These same characteristics also lend themselves to many of the problems associated with DNA processing in the forensic science context.

  9. Mixed-stock analysis in green turtles Chelonia mydas: mtDNA decipher current connections among west Atlantic populations.

    PubMed

    Costa Jordao, Juliana; Bondioli, Ana Cristina Vigliar; Almeida-Toledo, Lurdes Foresti de; Bilo, Karin; Berzins, Rachel; Le Maho, Yvon; Chevallier, Damien; de Thoisy, Benoit

    2017-03-01

    The green turtle Chelonia mydas undertakes wide-ranging migrations between feeding and nesting sites, resulting in mixing and isolation of genetic stocks. We used mtDNA control region to characterize the genetic composition, population structure, and natal origins of C. mydas in the West Atlantic Ocean, at one feeding ground (State of Rio de Janeiro, Brazil), and three Caribbean nesting grounds (French Guiana, Guadeloupe, and Suriname). The feeding ground presented considerable frequency of common haplotypes from the South Atlantic, whereas the nesting sites presented a major contribution of the most common haplotype from the Caribbean. MSA revealed multiple origins of individuals at the feeding ground, notably from Ascension Island, Guinea Bissau, and French Guiana. This study enables a better understanding of the dispersion patterns and highlights the importance of connecting both nesting and feeding areas. Effective conservation initiatives need to encompass these ecologically and geographically distinct sites as well as those corridors connecting them.

  10. Structural varieties of selectively mixed G- and C-rich short DNA sequences studied with electrospray ionization mass spectrometry.

    PubMed

    Cao, Yanwei; Gao, Shang; Li, Caijin; Yan, Yuting; Wang, Bing; Guo, Xinhua

    2016-10-01

    Short guanine(G)-repeat and cytosine(C)-repeat DNA strands can self-assemble to form four-stranded G-quadruplexes and i-motifs, respectively. Herein, G-rich and C-rich strands with non-G or non-C terminal bases and different lengths of G- or C-repeats are mixed selectively in pH 4.5 and 6.7 ammonium acetate buffer solutions and studied by electrospray ionization mass spectrometry (ESI-MS). Various strand associations corresponding to bi-, tri- and tetramolecular ions are observed in mass spectra, indicating that the formation of quadruplex structures is a random strand by strand association process. However, with increasing incubation time for the mixtures, initially associated hybrid tetramers will transform into self-assembled conformations, which is mainly driven by the structural stability. The melting temperature values of self-assembled quadruplexes suggest that the length of G-repeats or C-repeats shows more significant effect on the stability of quadruplex structures than that of terminal residues. Accordingly, we can obtain the self-associated tetrameric species generated from the mixtures of various homologous G- or C-strands efficiently by altering the length of G- or C-repeats. Our studies demonstrate that ESI-MS is a very direct, fast and sensitive tool to provide significant information on DNA strand associations and stoichiometric transitions, particularly for complex mixtures. Copyright © 2016 John Wiley & Sons, Ltd.

  11. The Unusual Monomer Recognition of Guanine-Containing Mixed Sequence DNA by a Dithiophene Heterocyclic Diamidine

    PubMed Central

    2015-01-01

    DB1255 is a symmetrical diamidinophenyl-dithiophene that exhibits cellular activity by binding to DNA and inhibiting binding of ERG, an ETS family transcription factor that is commonly overexpressed or translocated in leukemia and prostate cancer [Nhili, R., Peixoto, P., Depauw, S., Flajollet, S., Dezitter, X., Munde, M. M., Ismail, M. A., Kumar, A., Farahat, A. A., Stephens, C. E., Duterque-Coquillaud, M., Wilson, W. D., Boykin, D. W., and David-Cordonnier, M. H. (2013) Nucleic Acids Res. 41, 125–138]. Because transcription factor inhibition is complex but is an attractive area for anticancer and antiparasitic drug development, we have evaluated the DNA interactions of additional derivatives of DB1255 to gain an improved understanding of the biophysical chemistry of complex function and inhibition. DNase I footprinting, biosensor surface plasmon resonance, and circular dichroism experiments show that DB1255 has an unusual and strong monomer binding mode in minor groove sites that contain a single GC base pair flanked by AT base pairs, for example, 5′-ATGAT-3′. Closely related derivatives, such as compounds with the thiophene replaced with furan or selenophane, bind very weakly to GC-containing sequences and do not have biological activity. DB1255 is selective for the ATGAT site; however, a similar sequence, 5′-ATGAC-3′, binds DB1255 more weakly and does not produce a footprint. Molecular docking studies show that the two thiophene sulfur atoms form strong, bifurcated hydrogen bond-type interactions with the G-N-H sequence that extends into the minor groove while the amidines form hydrogen bonds to the flanking AT base pairs. The central dithiophene unit of DB1255 thus forms an excellent, but unexpected, single-GC base pair recognition module in a monomer minor groove complex. PMID:24495039

  12. Mixed-ligand copper(II) phenolate complexes: Synthesis, spectral characterization, phosphate-hydrolysis, antioxidant, DNA interaction and cytotoxic studies

    NASA Astrophysics Data System (ADS)

    Gurumoorthy, Perumal; Mahendiran, Dharmasivam; Prabhu, Durai; Arulvasu, Chinnasamy; Rahiman, Aziz Kalilur

    2015-01-01

    A series of phenol-based mixed-ligand copper(II) complexes of the type [CuL1-4(diimine)] (1-8), where L1-4 = N1,N2-bis(5-substituted-2-hydroxybenzylidene)-1,2-ethylene/phenylenediimine and diimine = 2,2‧-bipyridyl (bpy) or 1,10-phenanthroline (phen), have been isolated and fully characterized by analytical and spectral techniques. Electronic spectra of complexes suggest Cu(II) cation has a d9 electronic configuration, adopting distorted octahedral geometry with axial elongation, due to Jahn-Teller effect. Electrochemical studies of complexes evidenced one-electron irreversible reduction wave in the cathodic region. The observed rate constant (k) values for the hydrolysis of 4-nitrophenylphosphate (4-NPP) are in the range of 0.25-3.82 × 10-2 min-1. The obtained room temperature magnetic moment values (1.79-1.90 BM) lies within the range observed for octahedral copper(II) complexes. Antioxidant studies revealed that these complexes possess considerable radical scavenging potency against DPPH. The binding studies of complexes with calf thymus DNA (CT-DNA) revealed intercalation with minor-groove binding, and the complex 4 exhibits highest binding activity than the other complexes. The cleavage activity on supercoiled pBR322 DNA revealed the involvement of hydroxyl radical and singlet-oxygen as reactive oxygen species, and complexes encourage binding to minor-groove. Further, the cytotoxicity of complex 4 on human hepatocellular liver carcinoma HepG2 cell line implies the cell death through apoptosis.

  13. The Shimadzu CS 920 densitometer: illumination of thin layer chromatograms with a parallel light beam and its effects on quantification.

    PubMed

    Huf, F A

    1984-02-24

    The Shimadzu CS 920 has shown to be an easy to handle flying-spot densitometer that enables rapid quantification of thin layer chromatograms. Linear calibration curves with a relative standard deviation of 3 to 4% in the slope can be obtained for Sudan Yellow on Merck H60 plates. However, contrary to the statements in the instrument manual, the 'linearizer' performance is not in agreement with the Kubelka and Munk theory. Consequently, the CS 920 can only be used after empirically determined adjustment of the 'linearizer'. Furthermore, errors in analysis can increase up to 30% by using TLC-plates with fluctuating layer thickness.

  14. DNA-interaction and in vitro antimicrobial studies of some mixed-ligand complexes of cobalt(II) with fluoroquinolone antibacterial agent ciprofloxacin and some neutral bidentate ligands.

    PubMed

    Patel, M N; Chhasatia, M R; Gandhi, D S

    2009-05-15

    Six new mixed-ligand complexes of Co(II) with ciprofloxacin (Cip) and neutral bidentate ligands have been synthesized and characterized. Binding and cleavage of DNA with the complex were investigated using spectroscopic method, viscosity measurements and gel electrophoresis techniques. Antibacterial activity has been assayed against two Gram((-ve)) and three Gram((+ve)) microorganisms using the doubling dilution technique.

  15. Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy

    PubMed Central

    Chikira, Makoto; Ng, Chew Hee; Palaniandavar, Mallayan

    2015-01-01

    The interaction of simple and ternary Cu(II) complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II) complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR) spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements. PMID:26402668

  16. Strain-specific differentiation of lactococci in mixed starter culture populations using randomly amplified polymorphic DNA-derived probes.

    PubMed Central

    Erlandson, K; Batt, C A

    1997-01-01

    A hydrophobic grid membrane filtration (HGMF) colony hybridization assay was developed that allows strain-specific differentiation of defined bacterial populations. The randomly amplified polymorphic DNA (RAPD) fingerprinting technique was used to identify potential signature nucleic acid sequences unique to each member of a commercial cheese starter culture blend. The blend consisted of two closely related Lactococcus lactis subsp. cremoris strains, 160 and 331, and one L. lactis subsp. lactis strain, 210. Three RAPD primers (OPX 1, OPX 12, and OPX 15) generated a total of 32 products from these isolates, 20 of which were potential strain-specific markers. Southern hybridization analyses revealed, that the RAPD-generated signature sequences OPX15-0.95 and a 0.36-kb HaeIII fragment of OPX1-1.0b were specific for strains 331 and 210, respectively, within the context of the test starter culture blend. These strain-specific probes were used in a HGMF colony hybridization assay. Colony lysis, hybridization, and nonradioactive detection parameters were optimized to allow specific differentiation and quantitation of the target strains in the mixed starter culture population. When the 210 and 331 probes were tested at their optimal hybridization temperatures against single cultures, they detected 100% of the target strain CFUs, without cross-reactivity to the other strains. The probes for strains 210 and 331 also successfully detected their targets in blended cultures even with a high background of the other two strains. PMID:9212417

  17. Strain-specific differentiation of lactococci in mixed starter culture populations using randomly amplified polymorphic DNA-derived probes.

    PubMed

    Erlandson, K; Batt, C A

    1997-07-01

    A hydrophobic grid membrane filtration (HGMF) colony hybridization assay was developed that allows strain-specific differentiation of defined bacterial populations. The randomly amplified polymorphic DNA (RAPD) fingerprinting technique was used to identify potential signature nucleic acid sequences unique to each member of a commercial cheese starter culture blend. The blend consisted of two closely related Lactococcus lactis subsp. cremoris strains, 160 and 331, and one L. lactis subsp. lactis strain, 210. Three RAPD primers (OPX 1, OPX 12, and OPX 15) generated a total of 32 products from these isolates, 20 of which were potential strain-specific markers. Southern hybridization analyses revealed, that the RAPD-generated signature sequences OPX15-0.95 and a 0.36-kb HaeIII fragment of OPX1-1.0b were specific for strains 331 and 210, respectively, within the context of the test starter culture blend. These strain-specific probes were used in a HGMF colony hybridization assay. Colony lysis, hybridization, and nonradioactive detection parameters were optimized to allow specific differentiation and quantitation of the target strains in the mixed starter culture population. When the 210 and 331 probes were tested at their optimal hybridization temperatures against single cultures, they detected 100% of the target strain CFUs, without cross-reactivity to the other strains. The probes for strains 210 and 331 also successfully detected their targets in blended cultures even with a high background of the other two strains.

  18. DNA measurement and immunohistochemical characterization of epithelial and mesenchymal cells in canine mixed mammary tumours: putative evidence for a common histogenesis.

    PubMed

    Gärtner, F; Geraldes, M; Cassali, G; Rema, A; Schmitt, F

    1999-07-01

    DNA measurement by image cytometry, and a detailed immunohistochemical study using monoclonal antibodies directed against different human cytokeratin types, muscle-specific actin, vimentin and S100 protein were carried out on normal canine mammary tissue (n =4), benign canine mammary mixed tumours (n =20) and malignant canine mammary mixed tumours (n =13). The results showed that ductal and alveolar luminal cells in normal and neoplastic tissue were immunoreactive with CAM5.2 and AE1/AE3 antibodies recognizing human keratins.Basal/myoepithelial cells were clearly differentiated from ductal and alveolar epithelial cells, since the latter only expressed cytokeratins, whereas the former also expressed vimentin and muscle-specific actin. This immunohistochemical study showed that there is loss of expression of muscle-specific actin and cytokeratins in areas of myoepithelial proliferation, and enhanced expression of vimentin and S100 protein in proliferative areas with osseous and/or chondroid metaplasia. The ploidy studies revealed that 20% (4/20) of benign and 54% (7/13) of malignant mixed tumours of canine mammary gland were aneuploid and that the epithelial and myoepithelial components of the mixed tumours had identical DNA content. Our results reinforce the role of myoepithelial cells in mesenchymal metaplasia in mixed mammary tumours and suggest the possibility of a common origin of both components from a totipotential stem cell with capacity for divergent differentiation.

  19. 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)

  20. An automated Pearson's correlation change classification (APC3) approach for GC/MS metabonomic data using total ion chromatograms (TICs).

    PubMed

    Prakash, Bhaskaran David; Esuvaranathan, Kesavan; Ho, Paul C; Pasikanti, Kishore Kumar; Chan, Eric Chun Yong; Yap, Chun Wei

    2013-05-21

    A fully automated and computationally efficient Pearson's correlation change classification (APC3) approach is proposed and shown to have overall comparable performance with both an average accuracy and an average AUC of 0.89 ± 0.08 but is 3.9 to 7 times faster, easier to use and have low outlier susceptibility in contrast to other dimensional reduction and classification combinations using only the total ion chromatogram (TIC) intensities of GC/MS data. The use of only the TIC permits the possible application of APC3 to other metabonomic data such as LC/MS TICs or NMR spectra. A RapidMiner implementation is available for download at http://padel.nus.edu.sg/software/padelapc3.

  1. Glucose Tolerance, MTHFR C677T and NOS3 G894T Polymorphisms, and Global DNA Methylation in Mixed Ancestry African Individuals

    PubMed Central

    Mutize, Tinashe; Erasmus, Rajiv T.

    2016-01-01

    The aim of this study is to quantify global DNA methylation and investigate the relationship with diabetes status and polymorphisms in MTHFR C677T and NOS3 G894T genes in mixed ancestry subjects from South Africa. Global DNA methylation was measured, and MTHFR rs1801133 and NOS3 rs1799983 polymorphisms were genotyped using high throughput real-time polymerase chain reaction and direct DNA sequencing. Of the 564 participants, 158 (28%) individuals had T2DM of which 97 (17.2%) were screen-detected cases. Another 119 (21.1%) had prediabetes, that is, impaired fasting glucose, impaired glucose tolerance, or the combination of both, and the remainder 287 (50.9%) had normal glucose tolerance. Global DNA methylation was significantly higher in prediabetes and screen-detected diabetes than in normal glucose tolerance (both p ≤ 0.033) and in screen-detected diabetes compared to known diabetes on treatment (p = 0.019). There was no difference in global DNA methylation between known diabetes on treatment and normal glucose tolerance (p > 0.999). In multivariable linear regression analysis, only NOS3 was associated with increasing global DNA methylation (β = 0.943; 95% CI: 0.286 to 1.560). The association of global DNA methylation with screen-detected diabetes but not treated diabetes suggests that glucose control agents to some extent may be reversing DNA methylation. The association between NOS3 rs1799983 polymorphisms and DNA methylation suggests gene-epigenetic mechanisms through which vascular diabetes complications develop despite adequate metabolic control. PMID:27990443

  2. Quinoxaline based bio-active mixed ligand transition metal complexes: Synthesis, characterization, electrochemical, antimicrobial, DNA binding, cleavage, antioxidant and molecular docking studies.

    PubMed

    Dhanaraj, C Justin; Johnson, Jijo

    2015-10-01

    Co(II), Ni(II), Cu(II) and Zn(II) mixed ligand complexes have been synthesized from N(2), N(3)-bis(4-nitrophenyl)quinoxaline-2,3-diamine and 1,10-phenanthroline. The compounds were characterized by elemental analyses, molar conductance, magnetic susceptibility, IR, UV-Vis., (1)H NMR, mass and ESR spectra. Octahedral geometry has been assigned for Co(II), Ni(II) and Zn(II) complexes and distorted octahedral geometry for Cu(II) complex. Electrochemical behavior of the synthesized complexes was studied using cyclic voltammetry. Grain size and surface morphologies of the complexes were determined by powder XRD and SEM analyses. The mixed ligand metal complexes were screened for antimicrobial activity against bacterial species Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus; fungal species Aspergillus niger, and Candida albicans by disc diffusion method. The DNA binding and DNA cleavage activities of the compounds were determined using electronic absorption titration and agarose gel electrophoresis respectively. The superoxide radical scavenging and free radical scavenging activities of the Cu(II) complex was also evaluated. Molecular docking studies of the synthesized mixed ligand metal complexes were carried out against B-DNA dodecamer and the protein Plasmodium falciparum dihydrofolate reductase (pf DHFR).

  3. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations.

    PubMed

    Spacková, N; Berger, I; Sponer, J

    2001-04-11

    Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na(+) or K(+)). The simulations identify multiple nanosecond-scale stable arrangements of the thymidine loops present in the molecules investigated. In these thymidine loops, several structured pockets are identified capable of temporarily coordinating cations. However, no stable association of cations to a loop has been observed. The simulations reveal several paths through the thymidine loop regions that can be followed by the cations when exchanging between the central ion channel in the quadruplex stem and the surrounding solvent. We have carried out 20 independent simulations while the length of simulations reaches a total of 90 ns, rendering this study one of the most extensive MD investigations carried out on nucleic acids so far. The trajectories provide a largely converged characterization of the structural dynamics of these four-stranded G-DNA molecules.

  4. The catalytic A1 domains of cholera toxin and heat-labile enterotoxin are potent DNA adjuvants that evoke mixed Th1/Th17 cellular immune responses.

    PubMed

    Bagley, Kenneth; Xu, Rong; Ota-Setlik, Ayuko; Egan, Michael; Schwartz, Jennifer; Fouts, Timothy

    2015-01-01

    DNA encoded adjuvants are well known for increasing the magnitude of cellular and/or humoral immune responses directed against vaccine antigens. DNA adjuvants can also tune immune responses directed against vaccine antigens to better protect against infection of the target organism. Two potent DNA adjuvants that have unique abilities to tune immune responses are the catalytic A1 domains of Cholera Toxin (CTA1) and Heat-Labile Enterotoxin (LTA1). Here, we have characterized the adjuvant activities of CTA1 and LTA1 using HIV and SIV genes as model antigens. Both of these adjuvants enhanced the magnitude of antigen-specific cellular immune responses on par with those induced by the well-characterized cytokine adjuvants IL-12 and GM-CSF. CTA1 and LTA1 preferentially enhanced cellular responses to the intracellular antigen SIVmac239-gag over those for the secreted HIVBaL-gp120 antigen. IL-12, GM-CSF and electroporation did the opposite suggesting differences in the mechanisms of actions of these diverse adjuvants. Combinations of CTA1 or LTA1 with IL-12 or GM-CSF generated additive and better balanced cellular responses to both of these antigens. Consistent with observations made with the holotoxin and the CTA1-DD adjuvant, CTA1 and LTA1 evoked mixed Th1/Th17 cellular immune responses. Together, these results show that CTA1 and LTA1 are potent DNA vaccine adjuvants that favor the intracellular antigen gag over the secreted antigen gp120 and evoke mixed Th1/Th17 responses against both of these antigens. The results also indicate that achieving a balanced immune response to multiple intracellular and extracellular antigens delivered via DNA vaccination may require combining adjuvants that have different and complementary mechanisms of action.

  5. 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)

  6. ZRBA1, a Mixed EGFR/DNA Targeting Molecule, Potentiates Radiation Response Through Delayed DNA Damage Repair Process in a Triple Negative Breast Cancer Model

    SciTech Connect

    Heravi, Mitra; Kumala, Slawomir; Rachid, Zakaria; Jean-Claude, Bertrand J.; Radzioch, Danuta; Muanza, Thierry M.

    2015-06-01

    Purpose: ZRBA1 is a combi-molecule designed to induce DNA alkylating lesions and to block epidermal growth factor receptor (EGFR) TK domain. Inasmuch as ZRBA1 downregulates the EGFR TK-mediated antisurvival signaling and induces DNA damage, we postulated that it might be a radiosensitizer. The aim of this study was to further investigate the potentiating effect of ZRBA1 in combination with radiation and to elucidate the possible mechanisms of interaction between these 2 treatment modalities. Methods and Materials: The triple negative human breast MDA-MB-468 cancer cell line and mouse mammary cancer 4T1 cell line were used in this study. Clonogenic assay, Western blot analysis, and DNA damage analysis were performed at multiple time points after treatment. To confirm our in vitro findings, in vivo tumor growth delay assay was performed. Results: Our results show that a combination of ZRBA1 and radiation increases the radiation sensitivity of both cell lines significantly with a dose enhancement factor of 1.56, induces significant numbers of DNA strand breaks, prolongs higher DNA damage up to 24 hours after treatment, and significantly increases tumor growth delay in a syngeneic mouse model. Conclusions: Our data suggest that the higher efficacy of this combination could be partially due to increased DNA damage and delayed DNA repair process and to the inhibition of EGFR. The encouraging results of this combination demonstrated a significant improvement in treatment efficiency and therefore could be applicable in early clinical trial settings.

  7. Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross-correlation.

    PubMed

    Zhang, Mingjing; Wen, Ming; Zhang, Zhi-Min; Lu, Hongmei; Liang, Yizeng; Zhan, Dejian

    2015-03-01

    Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross-correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross-correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross-correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross-correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2.

  8. [Study on HPLC chromatograms of different processed Euphorbia ebracteolata products and content change of three chemical components].

    PubMed

    Zhuang, Guo; Li, Jun-Song; Cai, Bao-Chang

    2013-05-01

    To prepare processed products with different methods, in order to study the impact of auxiliary materials and temperature on chemical components of Euphorbia ebracteolata, and establish specific chromatograms of different processed products. Wel-chorm-C18 column (4.6 mm x 250 mm, 5 microm) was used and eluted with a gradient program, with acetonitrile (A)-water(B). The column temperature was 25 degrees C, and the detection wave length was set at 226 nm. The aim was to determine the content of effective components in different processed products--ebracteolata cpd B, ebracteolata cpd C and jolkinolide B and establish respective characteristic fingerprints to compare with similarity. The results showed that the content of ebracteolata cpd B, ebracteolata cpd C first increased and then decreased with the rise in temperature. Different processed products showed significant difference in HPLC spectrograms, with a low similarity. This study showed great impacts of auxiliary materials and temperature on chemical components of E. ebracteolata. As the vinegar processing method had higher attenuation and and synergistic effects than other methods, the auxiliary material vinegar cannot be replaced by chemical reagent acetic acid.

  9. EuroForMix: An open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts.

    PubMed

    Bleka, Øyvind; Storvik, Geir; Gill, Peter

    2016-03-01

    We have released a software named EuroForMix to analyze STR DNA profiles in a user-friendly graphical user interface. The software implements a model to explain the allelic peak height on a continuous scale in order to carry out weight-of-evidence calculations for profiles which could be from a mixture of contributors. Through a properly parameterized model we are able to do inference on mixture proportions, the peak height properties, stutter proportion and degradation. In addition, EuroForMix includes models for allele drop-out, allele drop-in and sub-population structure. EuroForMix supports two inference approaches for likelihood ratio calculations. The first approach uses maximum likelihood estimation of the unknown parameters. The second approach is Bayesian based which requires prior distributions to be specified for the parameters involved. The user may specify any number of known and unknown contributors in the model, however we find that there is a practical computing time limit which restricts the model to a maximum of four unknown contributors. EuroForMix is the first freely open source, continuous model (accommodating peak height, stutter, drop-in, drop-out, population substructure and degradation), to be reported in the literature. It therefore serves an important purpose to act as an unrestricted platform to compare different solutions that are available. The implementation of the continuous model used in the software showed close to identical results to the R-package DNAmixtures, which requires a HUGIN Expert license to be used. An additional feature in EuroForMix is the ability for the user to adapt the Bayesian inference framework by incorporating their own prior information.

  10. Diazido mixed-amine platinum(IV) anticancer complexes activatable by visible-light form novel DNA adducts.

    PubMed

    Zhao, Yao; Woods, Julie A; Farrer, Nicola J; Robinson, Kim S; Pracharova, Jitka; Kasparkova, Jana; Novakova, Olga; Li, Huilin; Salassa, Luca; Pizarro, Ana M; Clarkson, Guy J; Song, Lijiang; Brabec, Viktor; Sadler, Peter J

    2013-07-15

    Platinum diam(m)ine complexes, such as cisplatin, are successful anticancer drugs, but suffer from problems of resistance and side-effects. Photoactivatable Pt(IV) prodrugs offer the potential of targeted drug release and new mechanisms of action. We report the synthesis, X-ray crystallographic and spectroscopic properties of photoactivatable diazido complexes trans,trans,trans-[Pt(N3)2(OH)2(MA)(Py)] (1; MA=methylamine, Py=pyridine) and trans,trans,trans-[Pt(N3)2(OH)2(MA)(Tz)] (2; Tz=thiazole), and interpret their photophysical properties by TD-DFT modelling. The orientation of the azido groups is highly dependent on H bonding and crystal packing, as shown by polymorphs 1p and 1q. Complexes 1 and 2 are stable in the dark towards hydrolysis and glutathione reduction, but undergo rapid photoreduction with UVA or blue light with minimal amine photodissociation. They are over an order of magnitude more potent towards HaCaT keratinocytes, A2780 ovarian, and OE19 oesophageal carcinoma cells than cisplatin and show particular potency towards cisplatin-resistant human ovarian cancer cells (A2780cis). Analysis of binding to calf-thymus (CT), plasmids, oligonucleotide DNA and individual nucleotides reveals that photoactivated 1 and 2 form both mono- and bifunctional DNA lesions, with preference for G and C, similar to transplatin, but with significantly larger unwinding angles and a higher percentage of interstrand cross-links, with evidence for DNA strand cross-linking further supported by a comet assay. DNA lesions of 1 and 2 on a 50 bp duplex were not recognised by HMGB1 protein, in contrast to cisplatin-type lesions. The photo-induced platination reactions of DNA by 1 and 2 show similarities with the products of the dark reactions of the Pt(II) compounds trans-[PtCl2(MA)(Py)] (5) and trans-[PtCl2(MA)(Tz)] (6). Following photoactivation, complex 2 reacted most rapidly with CT DNA, followed by 1, whereas the dark reactions of 5 and 6 with DNA were comparatively slow

  11. Massive processing of pyro-chromatogram mass spectra (py-GCMS) of soil samples using the PARAFAC2 algorithm

    NASA Astrophysics Data System (ADS)

    Cécillon, Lauric; Quénéa, Katell; Anquetil, Christelle; Barré, Pierre

    2015-04-01

    Due to its large heterogeneity at all scales (from soil core to the globe), several measurements are often mandatory to get a meaningful value of a measured soil property. A large number of measurements can therefore be needed to study a soil property whatever the scale of the study. Moreover, several soil investigation techniques produce large and complex datasets, such as pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) which produces complex 3-way data. In this context, straightforward methods designed to speed up data treatments are needed to deal with large datasets. GC-MS pyrolysis (py-GCMS) is a powerful and frequently used tool to characterize soil organic matter (SOM). However, the treatment of the results of a py-GCMS analysis of soil sample is time consuming (number of peaks, co-elution, etc.) and the treatment of large data set of py-GCMS results is rather laborious. Moreover, peak position shifts and baseline drifts between analyses make the automation of GCMS programs data treatment difficult. These problems can be fixed using the Parallel Factor Analysis 2 (PARAFAC 2, Kiers et al., 1999; Bro et al., 1999). This algorithm has been applied frequently on chromatography data but has never been applied to analyses of SOM. We developed a Matlab routine based on existing Matlab packages dedicated to the simultaneous treatment of dozens of pyro-chromatograms mass spectra. We applied this routine on 40 soil samples. The benefits and expected improvements of our method will be discussed in our poster. References Kiers et al. (1999) PARAFAC2 - PartI. A direct fitting algorithm for the PARAFAC2 model. Journal of Chemometrics, 13: 275-294. Bro et al. (1999) PARAFAC2 - PartII. Modeling chromatographic data with retention time shifts. Journal of Chemometrics, 13: 295-309.

  12. Evaluation of environmental polychlorobiphenyls and DDE in terms of mixtures of commercial preparations from peak heights of packed-column gas chromatograms using a programmable calculator.

    PubMed

    Eder, G

    1976-06-23

    A method is proposed for evaluating gas chromatograms of multi-component PCB mixtures and superposed single components simultaneously. Apparent concentrations relative to a calibration mixture are assigned to a number of suitable peaks, and the apparent concentrations are related to the true concentrations by a set of linear equations, which are solved by least-squares approximation. The results are provided with an estimate of their confidence intervals.

  13. Combination of HPLC chromatogram and hypoglycemic effect identifies isoflavones as the principal active fraction of Belamcanda chinensis leaf extract in diabetes treatment.

    PubMed

    Chen, Yan; Wu, Chong-Ming; Dai, Rong-Ji; Li, Liang; Yu, Yu-Hong; Li, Yan; Meng, Wei-Wei; Zhang, Liang; Zhang, Yongqian; Deng, Yu-Lin

    2011-02-15

    In previous study, we demonstrated the hypoglycemic effect of aqueous extract of Belamcanda chinensis leaves in rats. Here, we separated the aqueous extract of B. chinensis leaves and investigated the spectrum-effect relationships between HPLC chromatograms and hypoglycemic activities of different isolates from B. chinensis leaf extract. Sequential solvent extraction with petroleum ether, chloroform, acetic ester and n-butanol provided several isolates showing similar hypoglycemic activities, making it difficult to discriminate the active fractions. Stepwise elution through HP20 macroporous resin by water, 40% and 95% ethanol provided isolates with distinct hypoglycemic activities, representing a simple, rapid and efficient preparative separation method. Combination of HPLC chromatogram and pharmacological effect targeted a hypoglycemic activity-related region in HPLC chromatogram. Each peak in this region was analyzed by UV spectrum scan. Most of them were flavonoids in which tectoridin and swertisin were known flavonoids with anti-diabetic activities. In together, this work provides a general model of combination of HPLC chromatography and pharmacological effect to study the spectrum-effect relationships of aqueous extract from B. chinensis leaves, which can be used to find principle components of B. chinensis on pharmacological activity.

  14. Fluorescent mixed ligand copper(II) complexes of anthracene-appended Schiff bases: studies on DNA binding, nuclease activity and cytotoxicity.

    PubMed

    Jaividhya, Paramasivam; Ganeshpandian, Mani; Dhivya, Rajkumar; Akbarsha, Mohammad Abdulkadher; Palaniandavar, Mallayan

    2015-07-14

    A series of mixed ligand copper(ii) complexes of the type [Cu(L)(phen)(ACN)](ClO4)21-5, where L is a bidentate Schiff base ligand (N(1)-(anthracen-10-ylmethylene)-N(2)-methylethane-1,2-diamine (L1), N(1)-(anthracen-10-ylmethylene)-N(2),N(2)-dimethylethane-1,2-diamine (L2), N(1)-(anthracen-10-yl-methylene)-N(2)-ethylethane-1,2-diamine (L3), N(1)-(anthracen-10-ylmethylene)-N(2),N(2)-diethylethane-1,2-diamine (L4) and N(1)-(anthracen-10-ylmethylene)-N(3)-methylpropane-1,3-diamine (L5)) and phen is 1,10-phenanthroline, have been synthesized and characterized by spectral and analytical methods. The X-ray crystal structure of 5 reveals that the coordination geometry around Cu(ii) is square pyramidal distorted trigonal bipyramidal (τ, 0.76). The corners of the trigonal plane of the geometry are occupied by the N2 nitrogen atom of phen, the N4 nitrogen atom of L5 and the N5 nitrogen of acetonitrile while the N1 nitrogen of phen and the N3 nitrogen of L5 occupy the axial positions with an N1-Cu1-N3 bond angle of 176.0(3)°. All the complexes display a ligand field band (600-705 nm) and three less intense anthracene-based bands (345-395 nm) in solution. The Kb values calculated from absorption spectral titration of the complexes (π→π*, 250-265 nm) with Calf Thymus (CT) DNA vary in the order 5 > 4 > 3 > 2 > 1. The fluorescence intensity of the complexes (520-525 nm) decreases upon incremental addition of CT DNA, which reveals the involvement of phen rather than the appended anthracene ring in partial DNA intercalation with the DNA base stack. The extent of quenching is in agreement with the DNA binding affinities and the relative increase in the viscosity of DNA upon binding to the complexes as well. Thus 5 interacts with DNA more strongly than 4 on account of the stronger involvement in hydrophobic DNA interaction of the anthracenyl moiety, which is facilitated by the propylene ligand backbone with chair conformation. The ability of complexes (100 μM) to cleave DNA (p

  15. Mixing of M Segment DNA Vaccines to Hantaan Virus and Puumala Virus Reduces Their Immunogenicity in Hamsters

    DTIC Science & Technology

    2008-01-01

    with renal syndrome (HFRS). In merica, several other hantaviruses cause hantavirus pulmonary yndrome (HPS) [1]. There are currently no U.S. licensed vac...online 25 April 2008 eywords: a b s t r a c t To determine if DNA vaccines for two hantaviruses causing hemorrhagic fever with renal syndrome, Hantaan...twoantaviruses emorrhagic fever with renal syndrome NA vaccines hantaviruses could be detected. In contrast, if the DNAs were given as separate vaccinations to

  16. Studies of the B-Z transition of DNA: The temperature dependence of the free-energy difference, the composition of the counterion sheath in mixed salt, and the preparation of a sample of the 5'-d[T-(m(5) C-G)12 -T] duplex in pure B-DNA or Z-DNA form.

    PubMed

    Guéron, Maurice; Plateau, Pierre; Filoche, Marcel

    2016-07-01

    It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution. Here, we analyze the non-electrostatic component of the free-energy difference between B-DNA and Z-DNA. We also compute the composition of the counterion sheath in a wide range of mixed-salt solutions and of temperatures: in contrast with the large difference of composition between the B-DNA and Z-DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed-salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small-Angle X-ray Scattering and complemented by (31) P NMR. With due consideration for the kinetics of the B-Z transition and for the capacity of generating at will the B or Z form in a single sample, the 5'-d[T-(m(5) C-G)12 -T] 26-mer emerges as a most suitable oligonucleotide for this study. Finally, the application of the finite element method to the resolution of the Poisson-Boltzmann equation is described in detail. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 369-384, 2016.

  17. Mixed ligand complexation of some transition metal ions in solution and solid state: Spectral characterization, antimicrobial, antioxidant, DNA cleavage activities and molecular modeling

    NASA Astrophysics Data System (ADS)

    Shobana, Sutha; Dharmaraja, Jeyaprakash; Selvaraj, Shanmugaperumal

    2013-04-01

    Equilibrium studies of Ni(II), Cu(II) and Zn(II) mixed ligand complexes involving a primary ligand 5-fluorouracil (5-FU; A) and imidazoles viz., imidazole (him), benzimidazole (bim), histamine (hist) and L-histidine (his) as co-ligands(B) were carried out pH-metrically in aqueous medium at 310 ± 0.1 K with I = 0.15 M (NaClO4). In solution state, the stoichiometry of MABH, MAB and MAB2 species have been detected. The primary ligand(A) binds the central M(II) ions in a monodentate manner whereas him, bim, hist and his co-ligands(B) bind in mono, mono, bi and tridentate modes respectively. The calculated Δ log K, log X and log X' values indicate higher stability of the mixed ligand complexes in comparison to binary species. Stability of the mixed ligand complex equilibria follows the Irving-Williams order of stability. In vitro biological evaluations of the free ligand(A) and their metal complexes by well diffusion technique show moderate activities against common bacterial and fungal strains. Oxidative cleavage interaction of ligand(A) and their copper complexes with CT DNA is also studied by gel electrophoresis method in the presence of oxidant. In vitro antioxidant evaluations of the primary ligand(A), CuA and CuAB complexes by DPPH free radical scavenging model were carried out. In solid, the MAB type of M(II)sbnd 5-FU(A)sbnd his(B) complexes were isolated and characterized by various physico-chemical and spectral techniques. Both the magnetic susceptibility and electronic spectral analysis suggest distorted octahedral geometry. Thermal studies on the synthesized mixed ligand complexes show loss of coordinated water molecule in the first step followed by decomposition of the organic residues subsequently. XRD and SEM analysis suggest that the microcrystalline nature and homogeneous morphology of MAB complexes. Further, the 3D molecular modeling and analysis for the mixed ligand MAB complexes have also been carried out.

  18. Molecular mechanism of promoter selection in gene transcription. I. Development of a rapid mixing-photocrosslinking technique to study the kinetics of Escherichia coli RNA polymerase binding to T7 DNA.

    PubMed

    Park, C S; Hillel, Z; Wu, C W

    1982-06-25

    A combined rapid mixing-photocrosslinking technique has been developed to investigate the kinetics of the interaction between Escherichia coli RNA polymerase and T7 DNA. The reactants were rapidly mixed in a modified Durrum stopped-flow apparatus, and the intermediates formed at different stages of the binding process were "frozen" by photocrosslinking with a UV light pulse of 10-mus duration at various times after mixing. The results indicate that the initial binding between RNA polymerase and T7 DNA is a diffusion-controlled reaction. Furthermore, the extents of initial contracts with DNA made with the beta, beta', and sigma subunits of RNA polymerase are roughly proportional to the sizes of these subunits, suggesting that complex formation occurs through random collision between the two reactants. After the initial complex formation, the rate of transfer of polymerase between individual DNA molecules is slow, implying that the polymerase molecules are undergoing predominantly intramolecular transfer during the promoter search. From the kinetic studies of subunit-DNA contacts during RNA polymerase binding to T7 DNA, it can be inferred that the beta, beta', and sigma subunits are directly participating in the promoter search process.

  19. Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

    PubMed Central

    Rubinstein, Nimrod D.; Feldstein, Tamar; Shenkar, Noa; Botero-Castro, Fidel; Griggio, Francesca; Mastrototaro, Francesco; Delsuc, Frédéric; Douzery, Emmanuel J.P.; Gissi, Carmela; Huchon, Dorothée

    2013-01-01

    Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia–Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate. PMID:23709623

  20. Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes.

    PubMed

    Rubinstein, Nimrod D; Feldstein, Tamar; Shenkar, Noa; Botero-Castro, Fidel; Griggio, Francesca; Mastrototaro, Francesco; Delsuc, Frédéric; Douzery, Emmanuel J P; Gissi, Carmela; Huchon, Dorothée

    2013-01-01

    Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.

  1. On-line coupled high performance liquid chromatography-gas chromatography for the analysis of contamination by mineral oil. Part 2: migration from paperboard into dry foods: interpretation of chromatograms.

    PubMed

    Biedermann, Maurus; Grob, Koni

    2012-09-14

    Mineral oil hydrocarbons are complex as well as varying mixtures and produce correspondingly complex chromatograms (on-line HPLC-GC-FID as described in Part 1): mostly humps of unresolved components are obtained, sometimes with sharp peaks on top. Chromatograms may also contain peaks of hydrocarbons from other sources which need to be subtracted from the mineral oil components. The review focuses on the interpretation and integration of chromatograms related to food contamination by mineral oil from paperboard boxes (off-set printing inks and recycled fibers), if possible distinguishing between various sources of mineral oil. Typical chromatograms are shown for relevant components and interferences as well as food samples encountered on the market. Details are pointed out which may provide relevant information. Integration is shown for examples of paperboard packaging materials as well as various foods. Finally the uncertainty of the analysis and limit of quantitation are discussed for specific examples. They primarily result from the interpretation of the chromatogram, manually placing the baseline and cuts for taking off extraneous components. Without previous enrichment, the limit of quantitation is between around 0.1 mg/kg for foods with a low fat content and 2.5 mg/kg for fats and oils. The measurement uncertainty can be kept clearly below 20% for most samples.

  2. Correlation between mixed-function oxidase enzyme induction and aflatoxin B/sub 1/-induced unscheduled DNA synthesis in the chick embryo, in vivo

    SciTech Connect

    Hamilton, J.W.; Bloom, S.E.

    1984-01-01

    The unscheduled DNA synthesis (UDS) technique has been adapted for use in the chick embryo, in vivo, to determine the relationship between induction of the mixed-function oxidase (MFO) enzyme system and genetic damage from an indirect-acting mutagen-carcinogen. Embryos were injected at 6 days of incubation (DI) with either phenobarbital (PB), a specific inducer of P-450-associated enzyme activities, or 3,4,3',4'-tetrachlorobiphenyl (TCB), a specific inducer of P/sub 1/-450-associated enzyme activities. Aflatoxin B/sub 1/ (AFB1) was injected 24 hr later (7 DI), followed by a 5-hr continuous /sup 3/H-thymidine exposure. The livers were removed, prepared for autoradiography, and hepatocytes were scored for an increase in grains/nucleus, indicative of UDS. Aflatoxin B/sub 1/ caused a dose-related increase in UDS in all control and induction groups. Phenobarbital-induced embryos had an increased UDS response while TCB-induced embryos had a decreased UDS response, relative to noninduced embryos, for each dosage of AFB1. This suggests that the genotoxicity of an indirect-acting mutagen-carcinogen can be either increased or decreased, in vivo, depending on the inducer used. The chick embryo provides an excellent system for studying the effect of MFO induction on the genotoxicity of promutagen-carcinogens in a developing system.

  3. Green turtles (Chelonia mydas) foraging at Arvoredo Island in Southern Brazil: Genetic characterization and mixed stock analysis through mtDNA control region haplotypes.

    PubMed

    Proietti, Maíra Carneiro; Lara-Ruiz, Paula; Reisser, Júlia Wiener; da Silva Pinto, Luciano; Dellagostin, Odir Antonio; Marins, Luis Fernando

    2009-07-01

    We analyzed mtDNA control region sequences of green turtles (Chelonia mydas) from Arvoredo Island, a foraging ground in southern Brazil, and identified eight haplotypes. Of these, CM-A8 (64%) and CM-A5 (22%) were dominant, the remainder presenting low frequencies (< 5%). Haplotype (h) and nucleotide (π) diversities were 0.5570 ± 0.0697 and 0.0021 ± 0.0016, respectively. Exact tests of differentiation and AMOVA Φ(ST) pairwise values between the study area and eight other Atlantic foraging grounds revealed significant differences in most areas, except Ubatuba and Rocas/Noronha, in Brazil (p > 0.05). Mixed Stock Analysis, incorporating eleven Atlantic and one Mediterranean rookery as possible sources of individuals, indicated Ascension and Aves islands as the main contributing stocks to the Arvoredo aggregation (68.01% and 22.96%, respectively). These results demonstrate the extensive relationships between Arvoredo Island and other Atlantic foraging and breeding areas. Such an understanding provides a framework for establishing adequate management and conservation strategies for this endangered species.

  4. Oxidative DNA damage of mixed copper(II) complexes with sulfonamides and 1,10-phenanthroline. Crystal structure of [Cu(N-quinolin-8-yl-p-toluenesulfonamidate)2(1,10-phenanthroline)].

    PubMed

    Macías, Benigno; García, Isabel; Villa, María V; Borrás, Joaquín; González-Alvarez, Marta; Castiñeiras, Alfonso

    2003-08-01

    Mixed coordination compounds of Cu(II) with sulfonamides and 1,10-phenanthroline as ligands have been prepared and characterised. Single crystal structural determination of the complex [Cu(N-quinolin-8-yl-p-toluenesulfonamidate)(2)(phen)] shows Cu(II) ions are located in a highly distorted octahedral environment, probably as a consequence of the Jahn-Teller effect. The FT-IR and electronic paramagnetic resonance (EPR) spectra are also discussed. The mixed complexes prepared undergo an extensive DNA cleavage in the presence of ascorbate and hydrogen peroxide. Two of the complexes have higher nucleolytic efficiency than the bis(o-phenanthroline)copper(II) complex.

  5. Characterization of the herb-derived components in rats following oral administration of Carthamus tinctorius extract by extracting diagnostic fragment ions (DFIs) in the MS(n) chromatograms.

    PubMed

    Chen, Jin-Feng; Song, Yue-Lin; Guo, Xiao-Yu; Tu, Peng-Fei; Jiang, Yong

    2014-12-21

    In this study, a new strategy named extracting diagnostic fragment ions (DFIs) in the MS(n) chromatograms [E(DFI)MS(n)Cs] was proposed to rapidly detect and identify the in vivo components derived from the extract of Carthamus tinctorius (ECT), using high performance liquid chromatography coupled with hybrid ion trap-time of flight mass spectrometry. In order to comprehensively summarize the DFIs for the global identification of in vivo constituents of ECT, chemical profiling was carried out, and then the typical metabolic pathways of the primary components were proposed according to their chemical categories, by orally administering representative reference compounds. Based on the proposed metabolic pathways and the fragmentation rules, a list of DFIs was constructed and adopted to differentiate and identify the metabolites from the endogenous substances in the MS(n) chromatograms of ECT-treated biological samples, in combination with the neutral loss scan mode as a supplement. As a result, a total of 156 compounds were tentatively assigned in vivo, including 63, 73, 50, and 17 components from rat plasma, urine, bile, and feces, respectively, following oral administration of ECT. Deglycosylation, oxidation, methylation, sulfonation, and glucuronidation were observed as the major metabolic pathways for the chemical constituents of ECT, and dehydroxylation was detected at the A-ring of flavones for the first time. The findings suggested that the E(DFI)MS(n)Cs-based strategy which integrated ideas from single compounds to herbal extracts and from extract chemical profiling to in vivo metabolite profiling, could be used as a reliable tool for rapidly discovering and identifying herb-related constituents in vivo.

  6. PEG-b-PPS-b-PEI micelles and PEG-b-PPS/PEG-b-PPS-b-PEI mixed micelles as non-viral vectors for plasmid DNA: tumor immunotoxicity in B16F10 melanoma.

    PubMed

    Velluto, Diana; Thomas, Susan N; Simeoni, Eleonora; Swartz, Melody A; Hubbell, Jeffrey A

    2011-12-01

    Cationic micelles formed from poly(ethylene glycol)-bl-poly(propylene sulfide)-bl-poly(ethylene imine) (PEG-b-PPS-b-PEI) and from mixtures of poly(ethylene glycol)-bl-poly(propylene sulfide) (PEG-b-PPS) with PEG-b-PPS-b-PEI were explored as non-viral vectors for plasmid DNA (pDNA) transfection in a tumor immunotoxicity model. Complexes with pDNA were found to be templated exclusively by the size of the pDNA-free micelles and ranged from 240 nm (for PEG-b-PPS-b-PEI) to 30 nm (for mixed micelles of PEG-b-PPS/PEG-b-PPS-b-PEI). Both formulations transfected melanoma cells well in vitro. As a model with a functional read-out of tumor cell death, one with likely only small bystander effects, tumors were transfected with an antigen transgene, using an antigen to which the recipient animals had been previously vaccinated with a Th1-biasing adjuvant. Reduction in tumor growth, increase in intratumoral infiltration of cytotoxic T lymphocytes and accumulation of Th1-biasing cytokines indicated that both micelle formulations transfected efficiently compared with naked pDNA and with low cytotoxicity.

  7. Synthesis, structure information, DNA/BSA binding affinity and in vitro cytotoxic studies of mixed ligand copper(II) complexes containing a phenylalanine derivative and diimine co-ligands.

    PubMed

    Annaraj, B; Balakrishnan, C; Neelakantan, M A

    2016-07-01

    Binary [Cu(PAIC)(H2O)2]·H2O (1) and mixed ligand [Cu(PAIC)(L)]·2H2O complexes, where PAIC=phenylalanine imidazole carboxylic acid, L=diimine coligands [2,2'-bipyridine (bpy) (2) and 1,10-phenanthroline (phen) (3)] have been synthesized and fully characterized by analytical and spectral techniques. The X-ray structure of [Cu(PAIC)(phen)]·2H2O (3) shows a N4O coordination with square pyramidal geometry around the copper (II) atom. The spin Hamiltonian parameters calculated for the complexes account for the distorted square planar structure and rules out the possibility of a trigonal bipyramidal structure. Interaction of the complexes (1-3) with calf thymus DNA (CT DNA) was studied by using different techniques (absorption titration, fluorescence quenching and thermal melting) and the studies suggest that these complexes bind to CT DNA through intercalation. The DNA-binding affinity of the complexes has further been explained by DFT computational results. Binding activity of Bovine serum albumin (BSA) reveals that the complexes can strongly quench the intrinsic fluorescence of BSA through a static quenching mechanism. DNA cleavage experiments using plasmid DNA pUC 19 show that the complexes exhibit efficient chemical nuclease activity even in the absence of any external additives. The cytotoxicity of the complexes against human normal cell line (HBL 100) and human breast cancer cell line (MCF-7) shows that metal complexation of the ligands results in a significant enhancement in the cell death of MCF-7. Finally, docking studies on DNA and protein binding interactions were performed.

  8. DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline.

    PubMed

    Mudasir; Yoshioka, N; Inoue, H

    1999-01-01

    Absorption spectroscopy and circular dichroism (CD) have been used to characterize the DNA binding of [Fe(phen)3]2+, [Fe(phen)2(DIP)]2+ and [Fe(phen)(DIP)2]2+ where phen and DIP stand for 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline, respectively. Both [Fe(phen)3]2+ and [Fe(phen)2(DIP)]2+ bind weakly to calf thymus DNA (CT-DNA) in an electrostatic mode, while [Fe(phen)(DIP)2]2+ binds more strongly to CT-DNA, possibly in an intercalation mode. The hypochromicity, red shift and Kb increase in the order [Fe(phen)3]2+ < [Fe(phen)2(DIP)]2+ < [Fe(phen)(DIP)2]2+ in accordance with the increase in size and hydrophobicity of the iron(II) complexes. The thermodynamic parameters obtained suggest that the DNA binding of both [Fe(phen)3]2+ and [Fe(phen)2(DIP)]2+ is entropically driven, while that of [Fe(phen)(DIP)2]2+ is enthalpically driven. A strong CD spectrum in the UV and visible region develops upon addition of CT-DNA into the racemate solution of each iron(II) complex (Pfeiffer effect). This has revealed that a shift in diastereomeric inversion equilibrium takes place in the solution to yield an excess of one of the DNA-complex diastereomers. The striking resemblance of the CD spectral profiles to those of the pure delta-enantiomer indicates that the delta-enantiomer of the iron(II) complexes is preferentially bound to CT-DNA. The mechanism of the development of Pfeiffer CD is proposed on the basis of kinetic studies on the DNA binding of the racemic iron(II) complexes.

  9. Determining the efficacy of microsatellite DNA-based mixed-stock analysis of Lake Michigan’s lake whitefish commercial fishery

    USGS Publications Warehouse

    VanDeHey, Justin A.; Sloss, Brian L.; Peeters, Paul J.; Sutton, Trent M.

    2009-01-01

    Management of commercially exploited fish should be conducted at the stock level. If a mixed stock fishery exists, a comprehensive mixed stock analysis is required for stock-based management. The lake whitefish Coregonus clupeaformis comprises the primary commercial fishery across the Great Lakes. Recent research resolved that six genetic stocks of lake whitefish were present in Lake Michigan, and long-term tagging data indicate that Lake Michigan's lake whitefish commercial fishery is a mixed stock fishery. The objective of this research was to determine the usefulness of microsatellite data for conducting comprehensive mixed stock analyses of the Lake Michigan lake whitefish commercial fishery. We used the individual assignment method as implemented in the program ONCOR to determine the accuracy level at which microsatellite data can reliably identify component populations or stocks. Self-assignment of lake whitefish to their population and stock of origin ranged from > 96% to 100%. Evaluation of genetic stock discreteness indicated a moderately high degree of correct assignment (average = 75%); simulations indicated supplementing baseline data by ∼ 50 to 100 individuals could increase accuracy by up to 4.5%. Simulated mixed stock commercial harvests with known stock composition showed a high degree of correct proportional assignment between observed and predicted harvest values. These data suggest that a comprehensive mixed stock analysis of Lake Michigan's lake whitefish commercial fishery is viable and would provide valuable information for improving management.

  10. Multiplex RT-PCR assays for the simultaneous detection of both RNA and DNA viruses infecting cassava and the common occurrence of mixed infections by two cassava brown streak viruses in East Africa.

    PubMed

    Abarshi, M M; Mohammed, I U; Jeremiah, S C; Legg, J P; Kumar, P Lava; Hillocks, R J; Maruthi, M N

    2012-01-01

    Uniplex and multiplex reverse transcription-polymerase chain reaction (RT-PCR) protocols were developed for the detection of cassava brown streak viruses (CBSVs) in single and mixed infections with cassava mosaic begomoviruses (CMBs) in a tropical crop plant, cassava (Manihot esculenta). CMBs contain ssDNA as their genome (genus Begomovirus, family Geminiviridae) while CBSVs are made up of positive sense ssRNA (genus Ipomovirus, family Potyviridae), and they cause the economically important cassava mosaic and cassava brown streak diseases, respectively, in sub-Saharan Africa. Diagnostic methodologies have long been available for CMBs but they are limited for CBSVs especially in mixed infections. In this study, the two CBSVs, Cassava brown streak virus (CBSV) and Cassava brown streak Uganda virus (CBSUV) occurring singly or in mixed infection with CMBs, African cassava mosaic virus and East African cassava mosaic virus were detected in a single RT-PCR using both previously described and newly designed virus-specific primers. These protocols were highly efficient for detecting CBSVs compared to the existing methods and have great potential to minimize sample handling and contamination. As well as improving the diagnosis of cassava viruses, the development of multiplex RT-PCR protocols have revealed the common occurrence of mixed infections by CBSV and CBSUV in cassava fields of Tanzania and Kenya, which was contrary to the common belief until recently that these two viruses have existed separately. These protocols have implications for diagnosis and epidemiological studies on cassava virus diseases in Eastern Africa.

  11. Salt-dependent binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine to calf thymus DNA.

    PubMed

    Mudasir; Wijaya, Karna; Tri Wahyuni, Endang; Yoshioka, Naoki; Inoue, Hidenari

    2006-04-20

    The salt-dependent binding of racemic iron(II) mixed-ligand complex containing 1,10-phenanthroline (phen) and dipyrido[3,2-a:2',3'-c]phenazine (dppz), [Fe(phen)2(dppz)]2+ to calf thymus DNA (ct-DNA) has been characterized by UV-VIS spectrophotometric titration. The equilibrium binding constant (Kb) of the iron(II) complex to ct-DNA decreases with the salt concentration in the solution. The slope, SK=(deltalog Kb/deltalog [Na2+]) has been found to be 0.49, suggesting that, in addition to intercalation, considerable electrostatic interaction is also involved in the ct-DNA binding of [Fe(phen)2(dppz)]2+. The calculation of non-electrostatic binding constant (Kt(o)) based on polyelectrolyte theory has revealed that the non-electrostatic contribution to the total binding constant (Kb) increases significantly with the increase in [Na+] and reaches 36% at 0.1 M NaCl. On the other hand, the contribution of the non-electrostatic binding free energy (DeltaGt(o)) to the total binding free energy change (DeltaGo) is considerably large, i.e. 87% at [Na+]=0.1 M, suggesting that the stabilization of the DNA binding is mostly due to the contribution of non-electrostatic process. Moreover, the effect of specific ligand substitutions on DeltaGo has been rigorously evaluated using the quantity DeltaDeltaGt(o), i.e. the difference in DeltaGt(o) relative to that of the parent iron(II) complex, [Fe(phen)3]2+, indicating that each substitution of phen by dip and dppz contributes 7.5 and 17.5 kJ mol(-1), respectively to more favorable ct-DNA binding.

  12. Enhancement of the cytotoxic potential of the mixed EGFR and DNA-targeting 'combi-molecule' ZRBA1 against human solid tumour cells by a bis-quinazoline-based drug design approach.

    PubMed

    Al-Safadi, Sherin; Domarkas, Juozas; Han, YingShan; Brahimi, Fouad; Jean-Claude, Bertrand J

    2012-06-01

    ZRBA1 is a quinazoline-based molecule termed 'combi-molecule' designed to block the epidermal growth factor receptor (EGFR) and further degrade to FD105, an EGFR inhibitor plus a DNA-alkylating agent. To augment the potency of ZRBA1, we designed JDE52, a bistriazene that, following degradation, was 'programmed' to yield higher concentrations of the free inhibitor FD105 and a more cytotoxic bifunctional DNA-damaging species. The results indicated that JDE52 was capable of inducing significant blockade of EGFR phosphorylation, DNA strand breaks and interstrand cross-links in human cells. The fluorescent property of FD105, the secondary inhibitor that both JDE52 and ZRBA1 are capable of releasing, has permitted the analysis of its levels in tumour cells by ultraviolet flow cytometry. It was found that JDE52 was indeed capable of significantly releasing higher levels of fluorescence (P<0.05) in human tumour cells when compared with ZRBA1. Apoptosis was triggered by JDE52 at a faster rate than ZRBA1 and led to higher levels of cell killing. The results in toto suggest that the superior potency of JDE52, when compared with ZRBA1, may be imputed to mechanisms associated with the generation of higher intracellular concentrations of FD105 and to the induction of DNA cross-links. These combined mechanisms (blockade of EGFR-tyrosine kinase and induction of cross-links) contributed to an accelerated rate of apoptosis by JDE52. This study conclusively demonstrated that designing molecules as prodrugs of high levels of quinazoline inhibitors of EGFR and bifunctional DNA cross-linking species is a valid strategy to enhance the potency of mixed EGFR-DNA-targeting combi-molecules.

  13. Comparison of dna-copying fidelity during repair and semiconservative synthesis by radioactive precursor distribution analysis

    SciTech Connect

    Nemirovskii, L.E.; Vasil'ev, V.K.

    1986-04-01

    The authors compare the fidelity of DNA copying during semiconservative and reparative synthesis under normal conditions and during cortisol-induced activation of free-radical processes, by examining the distribution of radioactivity among DNA pyrimidine isopliths. Radioactivity of nucleotide material in the isopliths was measured by counting in appropriate zones of the chromatograms in toluene scintillator. The investigation shows that injury to DNA of different organs, both directly and as a result of faulty repair, leads to shortening of the pyrimidine isopliths, i.e., to changes in the primary structure of DNA. These data help to explain the simultaneously cytostatic, carcinostatic, and mutagenic action of irradiation, cortisol and hydroxyurea.

  14. Synthesis, characterization, DNA interaction and cleavage, and in vitro cytotoxicity of copper(II) mixed-ligand complexes with 2-phenyl-3-hydroxy-4(1H)-quinolinone.

    PubMed

    Buchtík, Roman; Trávníček, Zdeněk; Vančo, Ján; Herchel, Radovan; Dvořák, Zdeněk

    2011-10-07

    A series of mixed-ligand complexes [Cu(qui)(L)]NO(3)·xH(2)O (1-6), where Hqui = 2-phenyl-3-hydroxy-4(1H)-quinolinone, L = 2,2'-bipyridine (bpy) (1), 1,10-phenanthroline (phen) (2), bis(2-pyridyl)amine (ambpy) (3), 5-methyl-1,10-phenanthroline (mphen) (4), 5-nitro-1,10-phenanthroline (nphen) (5) and bathophenanthroline (bphen) (6), have been synthesized and fully characterized. The X-ray structures of [Cu(qui)(phen)]NO(3)·H(2)O (2) and [Cu(qui)(ambpy)]NO(3) (3a) show a slightly distorted square-planar geometry in the vicinity of the central copper(II) atom. An in vitro cytotoxicity study of the complexes found significant activity against human osteosarcoma (HOS) and human breast adenocarcinoma (MCF7) cell lines, with the best results for complex 6, where IC(50) equals to 2.1 ± 0.2 μM, and 2.2 ± 0.4 μM, respectively. The strong interactions of the complexes with calf thymus DNA (CT-DNA) and high ability to cleave pUC19 DNA plasmid were found. A correlation has been found between the in vitro cytotoxicity and DNA cleavage studies of the complexes.

  15. Concept for facilitating analyst-mediated interpretation of qualitative chromatographic-mass spectral data: an alternative to manual examination of extracted ion chromatograms.

    PubMed

    Borges, Chad R

    2007-07-01

    A chemometrics-based data analysis concept has been developed as a substitute for manual inspection of extracted ion chromatograms (XICs), which facilitates rapid, analyst-mediated interpretation of GC- and LC/MS(n) data sets from samples undergoing qualitative batchwise screening for prespecified sets of analytes. Automatic preparation of data into two-dimensional row space-derived scatter plots (row space plots) eliminates the need to manually interpret hundreds to thousands of XICs per batch of samples while keeping all interpretation of raw data directly in the hands of the analyst-saving great quantities of human time without loss of integrity in the data analysis process. For a given analyte, two analyte-specific variables are automatically collected by a computer algorithm and placed into a data matrix (i.e., placed into row space): the first variable is the ion abundance corresponding to scan number x and analyte-specific m/z value y, and the second variable is the ion abundance corresponding to scan number x and analyte-specific m/z value z (a second ion). These two variables serve as the two axes of the aforementioned row space plots. In order to collect appropriate scan number (retention time) information, it is necessary to analyze, as part of every batch, a sample containing a mixture of all analytes to be tested. When pure standard materials of tested analytes are unavailable, but representative ion m/z values are known and retention time can be approximated, data are evaluated based on two-dimensional scores plots from principal component analysis of small time range(s) of mass spectral data. The time-saving efficiency of this concept is directly proportional to the percentage of negative samples and to the total number of samples processed simultaneously.

  16. Quantitative determination of transformed cells in a mixed population by stimultaneous fluorescence analysis of cell surface and DNA an individual cells.

    PubMed Central

    Hawkes, S P; Bartholomew, J C

    1977-01-01

    Cell-surface labeling with fluorescamine indicates that the fluorescence of Balb 3T3 A31 cells in considerably decreased after both viral and chemical transformation. This phenomenon, coupled with the technique of flow microfluorometry, enabled nontransformed and transformed cells to be distinguished. A second fluroescent probe, propidium iodide, which intercalates into DNA, was used in combination with fluorescamine in order to obtain a ratio of cell-surface labeling to DNA content. This manipulation allowed enhanced resolution of two populations and the detection of small numbers of transformants in a predominantly normal population. PMID:193110

  17. Small-Angle Neutron Scattering Studies on the Multilamellae Formed by Mixing Lamella-Forming Cationic Diblock Copolymers with Lipids and Their Interaction with DNA.

    PubMed

    Yang, Po-Wei; Lin, Tsang-Lang; Liu, I-Ting; Hu, Yuan; Jeng, U-Ser; Gilbert, Elliot Paul

    2016-02-23

    We demonstrate that the lamella-forming polystyrene-block-poly(N-methyl-4-vinylpyridinium iodine) (PS-b-P4VPQ), with similar sizes of the PS and P4VPQ blocks, can be dispersed in the aqueous solutions by forming lipid/PS-b-P4VPQ multilamellae. Using small-angle neutron scattering (SANS) and 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine (d62-DPPC) in D2O, a broad correlation peak is found in the scattering profile that signifies the formation of the loosely ordered d62-DPPC/PS-b-P4VPQ multilamellae. The thicknesses of the hydrophobic and hydrophilic layers of the d62-DPPC/PS-b-P4VPQ multilamellae are close to the PS layer and the condensed brush layer thicknesses as determined from previous neutron reflectometry studies on the PS-b-P4VPQ monolayer at the air-water interface. Such well-dispersed d62-DPPC/PS-b-P4VPQ multilamellae are capable of forming multilamellae with DNA in aqueous solution. It is found that the encapsulation of DNA in the hydrophilic layer of the d62-DPPC/PS-b-P4VPQ multilamellae slightly increases the thickness of the hydrophilic layer. Adding CaCl2 can enhance the DNA adsorption in the hydrophilic brush layer, and it is similar to that observed in the neutron reflectometry study of the DNA adsorption by the PS-b-P4VPQ monolayer.

  18. Ruthenium(II) and osmium(II) mixed chelates based on pyrenyl-pyridylimidazole and 2,2'-bipyridine ligands as efficient DNA intercalators and anion sensors.

    PubMed

    Mardanya, Sourav; Karmakar, Srikanta; Maity, Dinesh; Baitalik, Sujoy

    2015-01-20

    We report herein the synthesis and characterization of two monometallic ruthenium(II) and osmium(II) complexes of composition [(bpy)2M(HImzPPy)] (ClO4)2 derived from pyrenylimidazole-10-pyridin-2-yl-9H-9,11-diazacyclopenta[e]pyrene (HImzPPy) and 2,2'-bipyridine (bpy) ligands. X-ray crystallographic study shows that both crystals belong to the triclinic system having space group P1̅. The photophysical properties of 1 and 2 in acetonitrile indicate that the metal-to-ligand charge-transfer excited state is mainly centered in the [M(bpy)2](2+) moiety of the complexes and slightly affected by the extended conjugation of the pyrenylimidazole moiety. Both complexes display one-electron reversible metal-centered oxidative processes and a number of quasi-reversible reductive processes. The binding affinities of the complexes toward calf-thymus DNA (CT-DNA) were thoroughly studied through different methods such as absorption, emission, excited-state lifetime, circular dichroism, and thermal denaturation of DNA and a relative DNA binding study using ethidium bromide. All of these experiments account for the intercalative nature of both 1 and 2 toward CT-DNA as well as their light-switch behavior. The anion recognition study through different spectroscopic techniques reveals that both complexes act as "turn-on" luminescence sensors for H2PO4(-) and "turn-off" sensors toward F(-) and AcO(-). The imidazole N-H proton of the receptors gets deprotonated with the excessive addition of F(-) and AcO(-), while it interacts with H2PO4(-) through hydrogen-bonding interaction. Theoretical calculations (DFT and TD-DFT) were also performed to understand the photophysical properties of the metalloreceptors.

  19. Synthesis, characterization, X-ray crystal structure, DFT calculation, DNA binding, and antimicrobial assays of two new mixed-ligand copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Mohamadi, Maryam; Suarez, Sebastian; Baggio, Ricardo; Khaleghi, Moj; Torkzadeh-Mahani, Masoud; Mostafavi, Ali

    2015-05-01

    Two new Cu(II) complexes, [Cu(L)(phen)] (1), [Cu(L)(bipy)] (2), where L2- = (3-methoxy-2oxidobenzylidene)benzohydrazidato, phen = 1,10 phenanthroline, and bipy = 2,2‧ bipyridine, were prepared and fully characterized using elemental analyses, FT-IR, molar conductivity, and electronic spectra. The structures of both complexes were also determined by X-ray diffraction. It was found that, both complexes possessed square pyramidal coordination environment in which, Cu(II) ions were coordinated by donor atoms of HL and two nitrogens of heterocyclic bases. Computational studies were performed using DFT calculations at B3LYP/6-311+G(d,p) level of theory. DNA binding activities of these complexes were also investigated using electronic absorption, competitive fluorescence titration and cyclic voltammetry studies. The obtained results indicated that binding of the complexes to DNA was of intercalative mode. Furthermore, antimicrobial activities of these compounds were screened against microorganisms.

  20. In vitro DNA and BSA-binding, cell imaging and anticancer activity against human carcinoma cell lines of mixed ligand copper(II) complexes.

    PubMed

    Anjomshoa, Marzieh; Torkzadeh-Mahani, Masoud

    2015-01-01

    Binding studies of two water soluble copper(II) complexes of the type [Cu(phen-dion)(diimine)Cl]Cl, where phen-dione is 1,10-phenanthroline-5,6-dione and diimine is 1,10-phenanthroline (1) and 2,2'-bipyridine (2), with fish sperm DNA (FS-DNA) and bovine serum albumin (BSA) have been examined under physiological conditions by a series of experimental methods (UV-Vis absorption, fluorescence, viscosity, cyclic voltammetry (CV) and circular dichroism (CD) spectroscopic techniques). The experimental results indicate that the complexes interact with FS-DNA by electrostatic and partial insertion of pyridyl rings between the base stacks of double-stranded DNA. The complexes could quench the intrinsic fluorescence of BSA with the binding constants (Kbin) of 32×10(5) M(-1) (1) and 1.7×10(5) M(-1) (2) at 290 K. The quenching mechanism, thermodynamic parameters, the number of binding sites and the effect of the Cu(II) complexes on the secondary structure of BSA have been explored. The in vitro anticancer chemotherapeutic potential of two copper(II) complexes against the three human carcinoma cell lines (MCF-7, A-549, and HT-29) and one normal cell line (DPSC) were evaluated by MTT assay. The results of in vitro cytotoxicity indicate that the complex (1) has greater cytotoxicity activity against all of the cell lines, especially HT-29 with IC50 values of 1.8 μM. Based on the IC50 values, these complexes did not display an apparent cyto-selective profile, because it would appear that two complexes are toxic to all four model cell lines. The microscopic analyses of the cancer cells confirm results of cytotoxicity.

  1. An electrochemical DNA biosensor for evaluating the effect of mix anion in cellular fluid on the antioxidant activity of CeO2 nanoparticles.

    PubMed

    Zhai, Yanwu; Zhang, Yan; Qin, Fei; Yao, Xin

    2015-08-15

    CeO2 nanoparticles are of particular interest as a novel antioxidant for scavenging free radicals. However, some studies showed that they could cause cell damage or death by generating reactive oxygen species (ROS). Up to now, it is not well understood about these paradoxical phenomena. Therefore, many attentions have been paid to the factors that could affect the antioxidant activity of CeO2 nanoparticles. CeO2 nanoparticles would inevitably encounter body fluid environment for its potential medical application. In this work the antioxidant activity behavior of CeO2 nanoparticles is studied in simulated cellular fluid, which contains main body anions (HPO4(2-), HCO3(-), Cl(-) and SO4(2-)), by a method of electrochemical DNA biosensor. We found that in the solution of Cl(-) and SO4(2-), CeO2 nanoparticles can protect DNA from damage by hydroxyl radicals, while in the presence of HPO4(2-) and HCO3(-), CeO2 nanoparticles lose the antioxidant activity. This can be explained by the cerium phosphate and cerium carbonate formed on the surface of the nanoparticles, which interfere with the redox cycling between Ce(3+) and Ce(4+). These results not only add basic knowledge to the antioxidant activity of CeO2 nanoparticles under different situations, but also pave the way for practical applications of nanoceria. Moreover, it also shows electrochemical DNA biosensor is an effective method to explore the antioxidant activity of CeO2 nanoparticles.

  2. Cationized gelatin hydrogels mixed with plasmid DNA induce stronger and more sustained gene expression than atelocollagen at calvarial bone defects in vivo.

    PubMed

    Komatsu, K; Shibata, T; Shimada, A; Ideno, H; Nakashima, K; Tabata, Y; Nifuji, A

    2016-01-01

    Gene transduction of exogenous factors at local sites in vivo is a promising approach to promote regeneration of tissue defects owing to its simplicity and capacity for expression of a variety of genes. Gene transduction by viral vectors is highly efficient; however, there are safety concerns associated with viruses. As a method for nonviral gene transduction, plasmid DNA delivery is safer and simpler, but requires an efficient carrier substance. Here, we aimed to develop a simple, efficient method for bone regeneration by gene transduction and to identify optimal conditions for plasmid DNA delivery at bone defect sites. We focused on carrier substances and compared the efficiencies of two collagen derivatives, atelocollagen, and gelatin hydrogel, as substrates for plasmid DNA delivery in vivo. To assess the efficiencies of these substrates, we examined exogenous expression of green fluorescence protein (GFP) by fluorescence microscopy, polymerase chain reaction, and immunohistochemistry. GFP expression at the bone defect site was higher when gelatin hydrogel was used as a substrate to deliver plasmids than when atelocollagen was used. Moreover, the gelatin hydrogel was almost completely absorbed at the defect site, whereas some atelocollagen remained. When a plasmid harboring bone morphogenic protein 2 was delivered with the substrate to bony defect sites, more new bone formation was observed in the gelatin group than in the atelocollagen group. These results suggested that the gelatin hydrogel was more efficient than atelocollagen as a substrate for local gene delivery and may be a superior material for induction of bone regeneration.

  3. DNA binding, cytotoxicity and apoptosis induction activity of a mixed-ligand copper(II) complex with taurine Schiff base and imidazole

    NASA Astrophysics Data System (ADS)

    Li, Mei; kong, Lin Lin; Gou, Yi; Yang, Feng; Liang, Hong

    2014-07-01

    A novel binuclear copper(II) complex (complex 1) with taurine Schiff base and imidazole has been synthesized and structurally characterized by single crystal X-ray diffraction, elemental analysis, ESI-MS spectrometry, UV-vis and IR spectroscopy. Single-crystal analysis revealed that 1 displays the sulfonate-bridged dinuclear copper(II) centers. Both copper atoms are five-coordinated and exhibit slightly distorted square pyramidal geometries. Each of copper atom is surrounded by three oxygen atoms and one nitrogen atom from different taurine Schiff base ligands, and one nitrogen atom from one imidazole ligand. The interaction between 1 and calf thymus DNA (CT-DNA) was investigated by UV-vis, fluorescence, circular dichroism (CD) spectra and agarose gel electrophoresis. The experimental results indicated that 1 could bind to CT-DNA via an intercalative mode and show efficient cleavage activity. In addition, 1 showed an antitumor effect on cell cycle and apoptosis. Flow cytometric analysis revealed that MGC-803 cells were arrested in the S phase after treatment with 1. Fluorescence microscopic observation indicated that 1 could induce apoptosis of MGC-803 cells.

  4. Synthesis and Evaluation of In Vitro DNA/Protein Binding Affinity, Antimicrobial, Antioxidant and Antitumor Activity of Mononuclear Ru(II) Mixed Polypyridyl Complexes.

    PubMed

    Putta, Venkat Reddy; Chintakuntla, Nagamani; Mallepally, Rajender Reddy; Avudoddi, Srishailam; K, Nagasuryaprasad; Nancherla, Deepika; V V N, Yaswanth; R S, Prakasham; Surya, Satyanarayana Singh; Sirasani, Satyanarayana

    2016-01-01

    The four novel Ru(II) complexes [Ru(phen)2MAFIP](2+) (1) [MAFIP = 2-(5-(methylacetate)furan-2-yl)-1 H-imidazo[4,5-f] [1, 10]phenanthroline, phen = 1,10-Phenanthroline], [Ru(bpy)2MAFIP](2+) (2) (bpy = 2,2'-bipyridine) and [Ru(dmb)2MAFIP](2+) (3) (dmb = 4,4'-dimethyl-2,2'-bipyridine) and [Ru(hdpa)2MAFIP](2+) (4) (hdpa = 2,2-dipyridylamine) have been synthesized and fully characterized via elemental analysis, NMR spectroscopy, EI-MS and FT-IR spectroscopy. In addition, the DNA-binding behaviors of the complexes 1-4 with calf thymus DNA were investigated by UV-Vis absorption, fluorescence studies and viscosity measurement. The DNA-binding experiments showed that the complexes 1-4 interact with CT-DNA through an intercalative mode. BSA protein binding affinity of synthesized complexes was determined by UV/Vis absorption and fluorescence emission titrations. The binding affinity of ruthenium complexes was supported by molecular docking. The photoactivated cleavage of plasmid pBR322 DNA by ruthenium complexes 1-4 was investigated. All the synthesized compounds were tested for antimicrobial activity by using three Gram-negative (Escherichia coli, Salmonella typhi and Pseudomonas aeruginosa) and three Gram-positive (Micrococcus luteus, Bacillus subtilis and Bacillus megaterium) organisms, these results indicated that complex 3 was more activity compared to other complexes against all tested microbial strains while moderate antimicrobial activity profile was noticed for complex 4. The antioxidant activity experiments show that the complexes exhibit moderate antioxidant activity. The cytotoxicity of synthesized complexes on HeLa cell lines has been examined by MTT assay. The apoptosis assay was carried out with Acridine Orange (AO) staining methods and the results indicate that complexes can induce the apoptosis of HeLa cells. The cell cycle arrest investigated by flow cytometry and these results indicate that complexes 1-4 induce the cell cycle arrest at G0/G1

  5. Multiplexed Sequence Encoding: A Framework for DNA Communication

    PubMed Central

    Zakeri, Bijan; Carr, Peter A.; Lu, Timothy K.

    2016-01-01

    Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication—data encoding, data transfer & data extraction—and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system—Multiplexed Sequence Encoding (MuSE)—that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA. PMID:27050646

  6. Mixed ligand copper(II) complexes of 1,10-phenanthroline with tridentate phenolate/pyridyl/(benz)imidazolyl Schiff base ligands: covalent vs non-covalent DNA binding, DNA cleavage and cytotoxicity.

    PubMed

    Rajarajeswari, Chandrasekaran; Ganeshpandian, Mani; Palaniandavar, Mallayan; Riyasdeen, Anvarbatcha; Akbarsha, Mohammad Abdulkadher

    2014-11-01

    A series of copper(II) complexes of the types [Cu(L)(phen)](ClO4) 1-2, where HL is a tridentate ligand with two nitrogen and one oxygen donor atoms (2NO) such as 2-(2-(1H-benzimidazol-2-yl)ethyliminomethyl)phenol (HL1) and 2-(2-(1H-benzimidazol-2-yl)ethyl-imino)methyl)-4-methylphenol (HL2), phen is 1,10-phenanthroline and [Cu(L)(phen)](ClO4)23-6, where L is a tridentate ligand with three nitrogen donor atoms (3N) such as (2-pyridin-2-ylethyl)pyridin-2-ylmethyleneamine (L3), 2-(1H-benzimidazol-2-yl)ethyl)-pyridin-2-yl-methyleneamine (L4), 2-(1H-benzimidazol-2-yl)ethyl)(1H-imidazol-2-ylmethylene)-amine (L5) and 2-(1H-benzimidazol-2-yl)ethyl)(4,4a-dihydroquinolin-2-ylmethylene)amine (L6), has been isolated and characterized by different spectral techniques. In single crystal X-ray structures, 1 possesses square pyramidal distorted trigonal bipyramidal (SPDTBP), geometry whereas 3 and 4 possess trigonal bipyramidal distorted square pyramidal (TBDSP) geometry. UV-Vis and fluorescence spectral studies reveal that the complexes 1-6 bind non-covalently to calf thymus DNA more strongly than the corresponding covalently bound chlorido complexes [Cu(2NO)Cl] 1a-2a and [Cu(3N)Cl2] 3a-6a. On prolonged incubation, all the complexes 1-6 exhibit double strand cleavage of supercoiled (SC) plasmid DNA in the absence of an activator. Also, they exhibit cytotoxicity against human breast cancer cell lines (HBL-100) more potent than their corresponding chlorido complexes 1a-6a, and have the potential to act as efficient cytotoxic drugs.

  7. Development of a ligase detection reaction/CGE method using a LIF dual-channel detection system for direct identification of allelic composition of mutated DNA in a mixed population of excess wild-type DNA.

    PubMed

    Hamada, Mariko; Shimase, Koji; Noda, Keiichi; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

    2013-05-01

    We developed an inexpensive LIF dual-channel detection system and applied it to a ligase detection reaction (LDR)/CGE method to identify the allelic composition of low-abundance point mutations in a large excess of wild-type DNA in a single reaction with a high degree of certainty. Ligation was performed in a tube with a nonlabeled common primer and multiplex discriminating primers, each labeled with a different standard fluorophore. The discriminating primers were directed against three mutant variations in codon 12 of the K-ras oncogene that have a high diagnostic value for colorectal cancer. LDR products generated from a particular K-ras mutation through successful ligation events were separated from remaining discriminating primers by CGE, followed by LIF detection using the new system, which consists of two photomultiplier tubes, each with a unique optical filter. Each fluorophore label conjugated to the corresponding LDR product produced a distinct fluorescence signal intensity ratio from the two detection channels, allowing spectral discrimination of the three labels. The ability of this system to detect point mutations in a wild-type sequence-dominated population, and to disclose their allelic composition, was thus demonstrated successfully.

  8. Mixed Dementia

    MedlinePlus

    ... with Lewy bodies , What Is Alzheimer's? NIA-Funded Memory & Aging Project Reveals Mixed Dementia Common Data from ... commonly with Alzheimer's disease. For example, in the Memory and Aging Project study involving long-term cognitive ...

  9. GenoMass - a computer software for automated identification of oligonucleotide DNA adducts from LC-MS analysis of DNA digests

    PubMed Central

    Liao, Qing; Shen, Chang; Vouros, Paul

    2009-01-01

    In the investigation of oligonucleotides, DNA and their adducts by LC-MS, a myriad of data are generated that make manual data processing quite difficult. This paper describes a ‘reversed pseudo-combinatorial’ approach for fragment identification and the software implementation of this approach. Combinatorial isomer libraries are generated in silico to represent the digestion products of oligonucleotides, DNA or DNA adducts of various sizes. The software automatically calculates ion masses of each isomeric segment of the library, searches for them in complicated LC-MS data, lists their intensities and plots extracted ion chromatograms (EIC). This customized new data analysis tool has enabled a study of the enzymatic behavior of a nuclease system in the digestion of normal and adducted DNA, and in the recognition of oligomers containing a carcinogen bound to a nucleobase. The software program potentially can be further expanded to postulate unknown DNA sequences and recognize the adduction sites. PMID:19053159

  10. Age dependency of base modification in rabbit liver DNA

    NASA Technical Reports Server (NTRS)

    Yamamoto, O.; Fuji, I.; Yoshida, T.; Cox, A. B.; Lett, J. T.

    1988-01-01

    Age-related modifications of DNA bases have been observed in the liver of the New Zealand white (NZW) rabbit (Oryctolagus cuniculus), a lagomorph with a median life span in captivity of 5-7 yr. The ages of the animals studied ranged from 6 wk to 9 yr. After the DNA had been extracted from the liver cell nuclei and hydrolyzed with acid, the bases were analyzed by column chromatography with Cellulofine gels (GC-15-m). Two peaks in the chromatogram, which eluted before the four DNA bases, contained modified bases. Those materials, which were obtained in relatively large amounts from old animals, were highly fluorescent, and were shown to be crosslinked base products by mass spectrometry. The yield of crosslinked products versus rabbit age (greater than 0.5 yr) can be fitted by an exponential function (correlation coefficient: 0.76 +/- 0.09).

  11. Ion mixing

    NASA Technical Reports Server (NTRS)

    Matteson, S.; Nicolet, M.-A.

    1983-01-01

    Recent experimental studies of the ion-mixing phenomenon are summarized. Ion mixing is differentiated from ion implantation and shown to be a useful technique for overcoming the sputter-dependent limitations of implantation processes. The fundamental physical principles of ion/solid interactions are explored. The basic experimental configurations currently in use are characterized: bilayered samples, multilayered samples, and samples with a thin marker layer. A table listing the binary systems (metal-semiconductor or metal-metal) which have been investigated using each configuration is presented. Results are discussed, and some sample data are plotted. The prospects for future application of ion mixing to the alteration of solid surface properties are considered. Practical applications are seen as restricted by economic considerations to the production of small, expensive components or to fields (such as the semiconductor industry) which already have facilities for ion implantation.

  12. Determination of dioxin-like polychlorinated biphenyls in 1 mL whole blood using programmable temperature vaporization large volume injection coupled to gas chromatogram and high-resolution mass spectrometry.

    PubMed

    Shen, Haitao; Guan, Rongfa; Li, Jingguang; Zhang, Lei; Ren, Yiping; Xu, Xiaomin; Song, Yang; Zhao, Yunfeng; Han, Jianlong; Wu, Yongning

    2013-03-12

    A sensitive method based on programmable temperature vaporization large volume injection coupled to gas chromatogram and high-resolution mass spectrometry (PTV-GC-HRMS) has been developed for the determination of ultra trace levels of dioxin-like polychlorinated biphenyls (DL PCBs) in small amounts of human blood. Blood samples (1mL) were first extracted by column extraction and then purified with column chromatorgraphies. Final extracts (20μL) were introduced to the PTV injector under the solvent vent mode and detected by GC-HRMS (SIM mode). PTV parameters were observed by changing one factor at a time (practical conditions: vent flow: 50mLmin(-1), vent pressure: 0kPa and vent time: 0.1min), recoveries of most PCB congeners ranged from 55.1% to 108%, and method detection limits were in the range of 0.11-1.63pgg(-1).

  13. Average mass scan of the total ion chromatograms: a new gas chromatography-mass spectrometry derived variable for fast and reliable multivariate statistical treatment of essential oil compositional data.

    PubMed

    Radulović, Niko S; Blagojević, Polina D

    2013-08-02

    Plant volatiles have been repeatedly shown to provide valuable insight into the evolutionary relationships among plant taxa on various taxonomical levels. The number of variables available from GC-MS analyses of these plant metabolites usually represents a large data set. The comparison of such data sets requires the use of multivariate statistical analyses (MSA) but with several serious shortcomings. In order to make multivariate statistical comparison of essential oils more applicable, reliable and faster, this work was set to explore the suitability of a complementary use of relative abundances of m/z values of the average mass scan of the total GC chromatograms instead of the traditionally used variables-percentages (peak areas) of individual oil constituents. To achieve this, essential oils extracted from 12 different Artemisia species were analyzed using GC-FID and GC-MS. Almost 500 different constituents were successfully identified. Average mass scans of the total GC chromatograms (AMS) and chemical compositions (relative percentages) of the analyzed oils were separately compared using two MSA methods: agglomerative hierarchical cluster analysis and principal component analysis. This approach was applied to an additional set of essential oil compositional data (representatives of a number of different genera/families; data from the literature) using both types of variables. The obtained results strongly suggest that MSA of complex volatile mixtures, using the corresponding directly obtainable AMS, could be considered as a promising time saving tool for easy and reliable comparison purposes. The AMS approach gives comparable or even better results than the traditional method - it reflected the natural relationships between observations within both studied groups of oils.

  14. Lateral Mixing

    DTIC Science & Technology

    2013-09-30

    apl.uw.edu/dasaro LONG-TERM GOALS I seek to understand the processes controlling lateral mixing in the ocean, particularly at the submesoscale ...APPROACH During AESOP, Lee and D’Asaro pioneered an innovative approach to measuring submesoscale structure in strong fronts. An adaptive measurement...injection of potential vorticity and scalars is predicted to create an intense ‘ submesoscale soup’ of high small-scale variance. The combination of small

  15. Lateral Mixing

    DTIC Science & Technology

    2012-11-08

    to mesoscale forcing. APPROACH Figure 1: MVP system deployed from stern of R/V Endeavor in Sargasso Sea . 1 DISTRIBUTION STATEMENT A. Approved for...integrative efforts with other sea -going investigators and numerical modelers. The Lateral Mixing Experiment project was an ideal opportunity to...2011 I also participated in the sea -going part of this project, taking my group on the R/V Endeavor in June 2011. Our role was to sample around the

  16. Lateral Mixing

    DTIC Science & Technology

    2011-09-30

    ocean as it responds to mesoscale forcing. APPROACH Figure 1: MVP system deployed from stern of R/V Endeavor in Sargasso Sea . My approach for...therefore requires integrative efforts with other sea -going investigators and numerical modelers. The Lateral Mixing Experiment project was an ideal...also participated in the sea -going part of this project, taking my group on the R/V Endeavor in June 2011. Our role was to sample around the center of

  17. Successful isolation and PCR amplification of DNA from National Institute of Standards and Technology herbal dietary supplement standard reference material powders and extracts.

    PubMed

    Cimino, Matthew T

    2010-03-01

    Twenty-four herbal dietary supplement powder and extract reference standards provided by the National Institute of Standards and Technology (NIST) were investigated using three different commercially available DNA extraction kits to evaluate DNA availability for downstream nucleotide-based applications. The material included samples of Camellia, Citrus, Ephedra, Ginkgo, Hypericum, Serenoa, And Vaccinium. Protocols from Qiagen, MoBio, and Phytopure were used to isolate and purify DNA from the NIST standards. The resulting DNA concentration was quantified using SYBR Green fluorometry. Each of the 24 samples yielded DNA, though the concentration of DNA from each approach was notably different. The Phytopure method consistently yielded more DNA. The average yield ratio was 22 : 3 : 1 (ng/microL; Phytopure : Qiagen : MoBio). Amplification of the internal transcribed spacer II region using PCR was ultimately successful in 22 of the 24 samples. Direct sequencing chromatograms of the amplified material suggested that most of the samples were comprised of mixtures. However, the sequencing chromatograms of 12 of the 24 samples were sufficient to confirm the identity of the target material. The successful extraction, amplification, and sequencing of DNA from these herbal dietary supplement extracts and powders supports a continued effort to explore nucleotide sequence-based tools for the authentication and identification of plants in dietary supplements.

  18. Results of External Quality Assessment for Proviral DNA Testing of HIV Tropism in the Maraviroc Switch Collaborative Study

    PubMed Central

    Land, Sally; Pett, Sarah; Emery, Sean; Marks, Kat; Kelleher, Anthony D.; Kaye, Steve; Kaiser, Rolf; Schuelter, Eugene; Harrigan, Richard

    2013-01-01

    The Maraviroc Switch collaborative study (MARCH) is a study in aviremic patients on stable antiretroviral therapy and utilizes population-based sequencing of proviral DNA to determine HIV tropism and susceptibility to maraviroc. An external quality assessment (EQA) program was implemented to ensure competency in assessing the tropism of clinical samples conducted by MARCH laboratories (n = 14). The MARCH EQA has three prestudy phases assessing V3 loop sequencing and tropism determination using the bioinformatic algorithm geno2pheno, which generates a false-positive rate (FPR). DNA sequences with low FPRs are more likely to be from CXCR4-using (X4) viruses. Phase 1 of the EQA involved chromatogram interpretation. Phases 2, 2/3, and 3 involved patient and clonal samples. Clinical samples used in these phases were from treatment-experienced HIV-infected volunteers; 18/20 had viral loads of <50 copies/ml, and 10/15 were CXCR4-tropic on prior phenotyping. All samples were tested in triplicate, and any replicate with a geno2pheno FPR of <10% was designated X4. Performance was deemed adequate if ≤2 R5 and ≤1 X4 specimens were miscalled. For several clinical samples in the EQA, triplicate testing revealed marked DNA variability (FPR range, 0 to 96.7%). Therefore, a consensus-based approach was employed for each sample, i.e., a median FPR across laboratories was used to define sample tropism. Further sequencing analysis showed mixed viral populations in the clinical samples, explaining the differences in tropism predictions. All laboratories passed the EQA after achieving predefined competence thresholds in either of the phase 2 rounds. The use of clinical samples from patients resembling those who were likely to be screened in the MARCH, coupled with triplicate testing, revealed inherent DNA variability that might have been missed if single or duplicate testing and/or clonal samples alone were used. These data highlight the importance of intensive EQA of tropism

  19. Results of external quality assessment for proviral DNA testing of HIV tropism in the Maraviroc Switch collaborative study.

    PubMed

    Tu, Elise; Swenson, Luke C; Land, Sally; Pett, Sarah; Emery, Sean; Marks, Kat; Kelleher, Anthony D; Kaye, Steve; Kaiser, Rolf; Schuelter, Eugene; Harrigan, Richard

    2013-07-01

    The Maraviroc Switch collaborative study (MARCH) is a study in aviremic patients on stable antiretroviral therapy and utilizes population-based sequencing of proviral DNA to determine HIV tropism and susceptibility to maraviroc. An external quality assessment (EQA) program was implemented to ensure competency in assessing the tropism of clinical samples conducted by MARCH laboratories (n = 14). The MARCH EQA has three prestudy phases assessing V3 loop sequencing and tropism determination using the bioinformatic algorithm geno2pheno, which generates a false-positive rate (FPR). DNA sequences with low FPRs are more likely to be from CXCR4-using (X4) viruses. Phase 1 of the EQA involved chromatogram interpretation. Phases 2, 2/3, and 3 involved patient and clonal samples. Clinical samples used in these phases were from treatment-experienced HIV-infected volunteers; 18/20 had viral loads of <50 copies/ml, and 10/15 were CXCR4-tropic on prior phenotyping. All samples were tested in triplicate, and any replicate with a geno2pheno FPR of <10% was designated X4. Performance was deemed adequate if ≤2 R5 and ≤1 X4 specimens were miscalled. For several clinical samples in the EQA, triplicate testing revealed marked DNA variability (FPR range, 0 to 96.7%). Therefore, a consensus-based approach was employed for each sample, i.e., a median FPR across laboratories was used to define sample tropism. Further sequencing analysis showed mixed viral populations in the clinical samples, explaining the differences in tropism predictions. All laboratories passed the EQA after achieving predefined competence thresholds in either of the phase 2 rounds. The use of clinical samples from patients resembling those who were likely to be screened in the MARCH, coupled with triplicate testing, revealed inherent DNA variability that might have been missed if single or duplicate testing and/or clonal samples alone were used. These data highlight the importance of intensive EQA of tropism

  20. DNA profiling of trace DNA recovered from bedding.

    PubMed

    Petricevic, Susan F; Bright, Jo-Anne; Cockerton, Sarah L

    2006-05-25

    Trace DNA is often detected on handled items and worn clothing examined in forensic laboratories. In this study, the potential transfer of trace DNA to bedding by normal contact, when an individual sleeps in a bed, is examined. Volunteers slept one night on a new, lower bed sheet in their own bed and one night in a bed foreign to them. Samples from the sheets were collected and analysed by DNA profiling. The results indicate that the DNA profile of an individual can be obtained from bedding after one night of sleeping in a bed. The DNA profile of the owner of the bed could also be detected in the foreign bed experiments. Since mixed DNA profiles can be obtained from trace DNA on bedding, caution should be exercised when drawing conclusions from DNA profiling results obtained from such samples. This transfer may have important repercussions in sexual assault investigations.

  1. Source identification of petroleum hydrocarbons in soil and sediments from Iguaçu River Watershed, Paraná, Brazil using the CHEMSIC method (CHEMometric analysis of Selected Ion Chromatograms).

    PubMed

    Gallotta, Fabiana D C; Christensen, Jan H

    2012-04-27

    A chemometric method based on principal component analysis (PCA) of pre-processed and combined sections of selected ion chromatograms (SICs) is used to characterise the hydrocarbon profiles in soil and sediment from Araucária, Guajuvira, General Lúcio and Balsa Nova Municipalities (Iguaçu River Watershed, Paraná, Brazil) and to indicate the main sources of hydrocarbon pollution. The study includes 38 SICs of polycyclic aromatic compounds (PACs) and four of petroleum biomarkers in two separate analyses. The most contaminated samples are inside the Presidente Getúlio Vargas Refinery area. These samples represent a petrogenic pattern and different weathering degrees. Samples from outside the refinery area are either less or not contaminated, or contain mixtures of diagenetic, pyrogenic and petrogenic inputs where different proportions predominate. The locations farthest away from industrial activity (Balsa Nova) contains the lowest levels of PAC contamination. There are no evidences to conclude positive matches between the samples from outside the refinery area and the Cusiana spilled oil.

  2. Rigorous buoyancy driven bubble mixing for centrifugal microfluidics.

    PubMed

    Burger, S; Schulz, M; von Stetten, F; Zengerle, R; Paust, N

    2016-01-21

    We present batch-mode mixing for centrifugal microfluidics operated at fixed rotational frequency. Gas is generated by the disk integrated decomposition of hydrogen peroxide (H2O2) to liquid water (H2O) and gaseous oxygen (O2) and inserted into a mixing chamber. There, bubbles are formed that ascent through the liquid in the artificial gravity field and lead to drag flow. Additionaly, strong buoyancy causes deformation and rupture of the gas bubbles and induces strong mixing flows in the liquids. Buoyancy driven bubble mixing is quantitatively compared to shake mode mixing, mixing by reciprocation and vortex mixing. To determine mixing efficiencies in a meaningful way, the different mixers are employed for mixing of a lysis reagent and human whole blood. Subsequently, DNA is extracted from the lysate and the amount of DNA recovered is taken as a measure for mixing efficiency. Relative to standard vortex mixing, DNA extraction based on buoyancy driven bubble mixing resulted in yields of 92 ± 8% (100 s mixing time) and 100 ± 8% (600 s) at 130g centrifugal acceleration. Shake mode mixing yields 96 ± 11% and is thus equal to buoyancy driven bubble mixing. An advantage of buoyancy driven bubble mixing is that it can be operated at fixed rotational frequency, however. The additional costs of implementing buoyancy driven bubble mixing are low since both the activation liquid and the catalyst are very low cost and no external means are required in the processing device. Furthermore, buoyancy driven bubble mixing can easily be integrated in a monolithic manner and is compatible to scalable manufacturing technologies such as injection moulding or thermoforming. We consider buoyancy driven bubble mixing an excellent alternative to shake mode mixing, in particular if the processing device is not capable of providing fast changes of rotational frequency or if the low average rotational frequency is challenging for the other integrated fluidic operations.

  3. Mixed cryoglobulinemia

    PubMed Central

    Ferri, Clodoveo

    2008-01-01

    Mixed cryoglobulinemia (MC), type II and type III, refers to the presence of circulating cryoprecipitable immune complexes in the serum and manifests clinically by a classical triad of purpura, weakness and arthralgias. It is considered to be a rare disorder, but its true prevalence remains unknown. The disease is more common in Southern Europe than in Northern Europe or Northern America. The prevalence of 'essential' MC is reported as approximately 1:100,000 (with a female-to-male ratio 3:1), but this term is now used to refer to a minority of MC patients only. MC is characterized by variable organ involvement including skin lesions (orthostatic purpura, ulcers), chronic hepatitis, membranoproliferative glomerulonephritis, peripheral neuropathy, diffuse vasculitis, and, less frequently, interstitial lung involvement and endocrine disorders. Some patients may develop lymphatic and hepatic malignancies, usually as a late complication. MC may be associated with numerous infectious or immunological diseases. When isolated, MC may represent a distinct disease, the so-called 'essential' MC. The etiopathogenesis of MC is not completely understood. Hepatitis C virus (HCV) infection is suggested to play a causative role, with the contribution of genetic and/or environmental factors. Moreover, MC may be associated with other infectious agents or immunological disorders, such as human immunodeficiency virus (HIV) infection or primary Sjögren's syndrome. Diagnosis is based on clinical and laboratory findings. Circulating mixed cryoglobulins, low C4 levels and orthostatic skin purpura are the hallmarks of the disease. Leukocytoclastic vasculitis involving medium- and, more often, small-sized blood vessels is the typical pathological finding, easily detectable by means of skin biopsy of recent vasculitic lesions. Differential diagnoses include a wide range of systemic, infectious and neoplastic disorders, mainly autoimmune hepatitis, Sjögren's syndrome, polyarthritis, and B

  4. Mixed infection by Legionella pneumophila in outbreak patients.

    PubMed

    Coscollá, Mireia; Fernández, Carmen; Colomina, Javier; Sánchez-Busó, Leonor; González-Candelas, Fernando

    2014-05-01

    During the molecular epidemiological study of a legionellosis outbreak, we obtained sequence based typing (SBT) profiles from uncultured respiratory samples of 15 affected patients. We detected several distinct allelic profiles some of which were a mixture of alleles present in the more common profiles. Chromatograms from the sequences of one patient with mixed profile showed polymorphisms in several positions, which could result from the simultaneous presence of different Legionella variants in the sample. In order to test this possibility, we cloned PCR amplification products from six loci for two patients with a mixed profile and a patient with a pure profile. After obtaining around 20 sequences for each locus of three patients, we detected several variants in two of them and two variants in the third one. In summary, the three analyzed patients showed evidence of more than one Legionella variant during the acute infection. These results indicate that probably some patients were infected by more than one strain, which could be due to co-infection from the same environmental source or, alternatively, to independent infections in a very short period of time. Although our data cannot discriminate between these hypotheses, these results suggest that Legionella infection patterns can be more complex than previously assumed. None of the environmental samples analyzed during this outbreak was even similar to any of the clinical ones.

  5. Base-specific and enantioselective studies for the DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2- a:2',3'- c]phenazine

    NASA Astrophysics Data System (ADS)

    Mudasir; Wijaya, Karna; Wahyuni, Endang Tri; Inoue, Hidenari; Yoshioka, Naoki

    2007-01-01

    Base specificity and enantioselectivity for the DNA binding of [Fe(phen) 2(dppz)] 2+ (phen = 1,10-phenanthroline and dppz = dipyrido[3,2- a:2',3'- c]phenazine) have been studied by determining the equilibrium binding constant ( Kb) of the iron(II) complex to calf thymus DNA (ct-DNA), poly[(dA-dT) 2], poly[(dG-dC) 2] and poly[(dI-dC) 2] using spectrophotometric titration and by monitoring the CD spectral profile of the iron(II) complex in the presence and absence of different types of DNA using circular dichroism (CD) spectroscopy, respectively. It has been shown that [Fe(phen) 2(dppz)] 2+ prefers to intercalate into the A-T and I-C sequences of poly[(dA-dT) 2] and poly[(dI-dC) 2] rather than into the G-C sequences of poly[(dG-dC) 2] or into the base pairs of ct-DNA. In contrast to previous reports, it is a surprising observation that the enantioselectivity of the DNA binding for [Fe(phen) 2(dppz)] 2+ is base-dependent in nature. The Δ-enantiomer of [Fe(phen) 2(dppz)] 2+ is preferentially intercalated into the base pairs of poly[(dG-dC) 2] or ct-DNA as indicated by its CD spectral profiles. On the other hand, the Λ-enantiomer of [Fe(phen) 2(dppz)] 2+ is favorably intercalated into poly[(dA-dT) 2] or poly[(dI-dC) 2] as suggested by the opposite CD spectral profile. This preferential binding of Λ-[Fe(phen) 2(dppz)] 2+ for the A-T sequence may be attributed to the fact that the binding site for the A-T sequence is relatively facile and thus the steric effect caused by the ancillary (non-intercalated) phen ligands is alleviated. The degree of enantioselectivity represented by inversion constants ( Kinv) decreases as the salt concentration in the solution increases, indicating that electrostatic interaction is also operating in the ct-DNA-binding events of the iron (II) complex.

  6. Base-specific and enantioselective studies for the DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine.

    PubMed

    Mudasir; Wijaya, Karna; Wahyuni, Endang Tri; Inoue, Hidenari; Yoshioka, Naoki

    2007-01-01

    Base specificity and enantioselectivity for the DNA binding of [Fe(phen)2(dppz)]2+ (phen=1,10-phenanthroline and dppz=dipyrido[3,2-a:2',3'-c]phenazine) have been studied by determining the equilibrium binding constant (Kb) of the iron(II) complex to calf thymus DNA (ct-DNA), poly[(dA-dT)2], poly[(dG-dC)2] and poly[(dI-dC)2] using spectrophotometric titration and by monitoring the CD spectral profile of the iron(II) complex in the presence and absence of different types of DNA using circular dichroism (CD) spectroscopy, respectively. It has been shown that [Fe(phen)2(dppz)]2+ prefers to intercalate into the A-T and I-C sequences of poly[(dA-dT)2] and poly[(dI-dC)2] rather than into the G-C sequences of poly[(dG-dC)2] or into the base pairs of ct-DNA. In contrast to previous reports, it is a surprising observation that the enantioselectivity of the DNA binding for [Fe(phen)2(dppz)]2+ is base-dependent in nature. The Delta-enantiomer of [Fe(phen)2(dppz)]2+ is preferentially intercalated into the base pairs of poly[(dG-dC)2] or ct-DNA as indicated by its CD spectral profiles. On the other hand, the Lambda-enantiomer of [Fe(phen)2(dppz)]2+ is favorably intercalated into poly[(dA-dT)2] or poly[(dI-dC)2] as suggested by the opposite CD spectral profile. This preferential binding of Lambda-[Fe(phen)2(dppz)]2+)for the A-T sequence may be attributed to the fact that the binding site for the A-T sequence is relatively facile and thus the steric effect caused by the ancillary (non-intercalated) phen ligands is alleviated. The degree of enantioselectivity represented by inversion constants (Kinv) decreases as the salt concentration in the solution increases, indicating that electrostatic interaction is also operating in the ct-DNA-binding events of the iron (II) complex.

  7. Reliable screening and confirmation of 156 multi-class illegal adulterants in dietary supplements based on extracted common ion chromatograms by ultra-high-performance liquid chromatography-quadrupole/time of flight-mass spectrometry.

    PubMed

    Kim, Eun Hye; Seo, Hee Seung; Ki, Nam Yong; Park, Na-Hyun; Lee, Wonwoong; Do, Jung Ah; Park, Sungkwan; Baek, Sun Young; Moon, Bongjin; Oh, Han Bin; Hong, Jongki

    2017-03-31

    An analytical method for the reliable screening and confirmation of 156 illegal drugs (58 erectile dysfunction drugs, 49 synthetic steroids, 26 anabolic steroids, and 23 anti-histamine drugs) in supplementary diets using ultra-high-performance liquid chromatography coupled with quadrupole/time-of-flight mass spectrometry (UHPLC-Q/TOF-MS) was developed. Various types of supplements (liquid, capsule, powder, pill and tablet) with complicated matrices were pretreated by simple liquid-liquid extraction. The wide scope of 156 target compounds was effectively determined within 15min in the positive ion mode, detecting the compounds at a sub-ppb level. Their MS/MS spectra were preferentially investigated to find diagnostic common ions according to the structural similarity of diverse adulterants. For the rapid screening of multiple classes of the target adulterants, extracted common ion chromatograms (ECICs) based on specific fragments of similar molecular moieties were attempted. A database including the elemental compositions, retention times, and MS/MS spectra was built for the confirmation of adulterants. The established method was validated in terms of the linearity, limits of detection (LOD), precision, and accuracy. The linear correlation coefficient and limit of detection ranged from 0.9880 to 1 and from 0.02 to 16.04ng/mL, respectively. The precision and accuracy of intra- and inter-day experiments for the spiked samples at the range of 0.2 and 16.0ng/mL were from 0.16 to 13.50% and 0.19-11.48%, respectively, with relative standard deviation. Mean recoveries ranged from 81.6 to 124.7%, and relative standard deviation was less than 9.20%. The screening and confirmation method demonstrated the usefulness of UHPLC-Q/TOF-MS combined with ECICs as a promising approach for the analysis of multi-class adulterants. Finally, the established method was successfully applied for the monitoring of several types of dietary supplements in routine analysis.

  8. 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.

  9. 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)

  10. 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.

  11. New mixed ligand palladium(II) complexes based on the antiepileptic drug sodium valproate and bioactive nitrogen-donor ligands: Synthesis, structural characterization, binding interactions with DNA and BSA, in vitro cytotoxicity studies and DFT calculations

    NASA Astrophysics Data System (ADS)

    Tabrizi, Leila; Chiniforoshan, Hossein; Tavakol, Hossein

    2015-04-01

    The complexes [Pd(valp)2(imidazole)2] (1), [Pd(valp)2(pyrazine)2] (2) (valp is sodium valproate) have been synthesized and characterized using IR, 1H NMR, 13C{1H} NMR and UV-Vis spectrometry. The interaction of complexes with CT-DNA has been investigated using spectroscopic tools and viscosity measurement. In each case, the association constant (Kb) was deduced from the absorption spectral study and the number of binding sites (n) and the binding constant (K) were calculated from relevant fluorescence quenching data. As a result, a non-covalent interaction between the metal complex and DNA was suggested, which could be assigned to an intercalative binding. In addition, the interaction of 1 and 2 was ventured with bovine serum albumin (BSA) with the help of absorption and fluorescence spectroscopy measurements. Through these techniques, the apparent association constant (Kapp) and the binding constant (K) could be calculated for each complex. Evaluation of cytotoxic activity of the complexes against four different cancer cell lines proved that the complexes exhibited cytotoxic specificity and significant cancer cell inhibitory rate. Moreover, density functional theory (DFT) calculations were employed to provide more evidence about the observed data. The majority of trans isomers were supported not only by energies, but also by the similarity of its calculated IR frequencies, UV adsorptions and NMR chemical shifts to the experimental values.

  12. Mixing in astrophysics

    SciTech Connect

    Fryer, Christopher Lee

    2011-01-07

    Turbulent mixing plays a vital role in many fields in astronomy. Here I review a few of these sites, discuss the importance of this turbulent mixing and the techniques used by astrophysicists to solve these problems.

  13. Mixing in explosions

    SciTech Connect

    Kuhl, A.L.

    1993-12-01

    Explosions always contain embedded turbulent mixing regions, for example: boundary layers, shear layers, wall jets, and unstable interfaces. Described here is one particular example of the latter, namely, the turbulent mixing occurring in the fireball of an HE-driven blast wave. The evolution of the turbulent mixing was studied via two-dimensional numerical simulations of the convective mixing processes on an adaptive mesh. Vorticity was generated on the fireball interface by baroclinic effects. The interface was unstable, and rapidly evolved into a turbulent mixing layer. Four phases of mixing were observed: (1) a strong blast wave phase; (2) and implosion phase; (3) a reshocking phase; and (4) an asymptotic mixing phase. The flowfield was azimuthally averaged to evaluate the mean and r.m.s. fluctuation profiles across the mixing layer. The vorticity decayed due to a cascade process. This caused the corresponding enstrophy parameter to increase linearly with time -- in agreement with homogeneous turbulence calculations of G.K. Batchelor.

  14. Improvements in Mixing Time and Mixing Uniformity in Devices Designed for Studies of Protein Folding Kinetics

    SciTech Connect

    Yao, Shuhuai; Bakajin, Olgica

    2007-08-01

    Using a microfluidic laminar flow mixer designed for studies of protein folding kinetics, we demonstrate a mixing time of 1 +/- 1 micros with sample consumption on the order of femtomoles. We recognize two limitations of previously proposed designs: (1) size and shape of the mixing region, which limits mixing uniformity and (2) the formation of Dean vortices at high flow rates, which limits the mixing time. We address these limitations by using a narrow shape-optimized nozzle and by reducing the bend of the side channel streamlines. The final design, which combines both of these features, achieves the best performance. We quantified the mixing performance of the different designs by numerical simulation of coupled Navier-Stokes and convection-diffusion equations and experiments using fluorescence resonance energy-transfer (FRET)-labeled DNA.

  15. Mixed methods research.

    PubMed

    Halcomb, Elizabeth; Hickman, Louise

    2015-04-08

    Mixed methods research involves the use of qualitative and quantitative data in a single research project. It represents an alternative methodological approach, combining qualitative and quantitative research approaches, which enables nurse researchers to explore complex phenomena in detail. This article provides a practical overview of mixed methods research and its application in nursing, to guide the novice researcher considering a mixed methods research project.

  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. DNA microarray-based mutation discovery and genotyping.

    PubMed

    Gresham, David

    2011-01-01

    DNA microarrays provide an efficient means of identifying single-nucleotide polymorphisms (SNPs) in DNA samples and characterizing their frequencies in individual and mixed samples. We have studied the parameters that determine the sensitivity of DNA probes to SNPs and found that the melting temperature (T (m)) of the probe is the primary determinant of probe sensitivity. An isothermal-melting temperature DNA microarray design, in which the T (m) of all probes is tightly distributed, can be implemented by varying the length of DNA probes within a single DNA microarray. I describe guidelines for designing isothermal-melting temperature DNA microarrays and protocols for labeling and hybridizing DNA samples to DNA microarrays for SNP discovery, genotyping, and quantitative determination of allele frequencies in mixed samples.

  18. Molecular Cloning of the Bovine Liver ADPRT cDNA

    DTIC Science & Technology

    1988-12-13

    of the DNA was - 0.5 micrograms. The 209 bp fragment from SV40 was mixed with pUC19 DNA in equal amounts and ligated ovenight at 12*C using T4 DNA ... ligase . The ligation mixture was used to transform Ecoli JM109 (1). Transformanrs were selected on LB plates cont- aining X-gal + FF0 + ampicillin (1

  19. 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.

  20. /sup 32/P-postlabeling analysis of DNA adducts in liver of wild English sole (Parophrys vetulus) and winter flounder (Pseudopleuronectes americanus)

    SciTech Connect

    Varanasi, U.; Reichert, W.L.; Stein, J.E.

    1989-03-01

    The 1-butanol adduct enhancement version of the 32P-postlabeling assay was used to measure the levels of hepatic DNA adducts in the marine flatfish, English sole (Parophrys vetulus), sampled from the Duwamish Waterway and Eagle Harbor, Puget Sound, WA, where they are exposed to high concentrations of sediment-associated chemical contaminants and exhibit an elevated prevalence of hepatic neoplasms. Hepatic DNA was also analyzed from English sole from a reference area (Useless Bay, WA) and from reference English sole treated with organic-solvent extracts of sediments from the two contaminated sites. Autoradiograms of thin-layer chromatograms of 32P-labeled hepatic DNA digests from English sole from the contaminated sites exhibited up to three diagonal radioactive zones, which were not present in autoradiograms of thin-layer chromatogram maps of 32P-labeled DNA digests from English sole from the reference site. These diagonal radioactive zones contained several distinct spots as well as what appeared to be multiple overlapping adduct spots. The levels (nmol of adducts/mol of nucleotides) of total DNA adducts for English sole from Duwamish Waterway and Eagle Harbor were 26 +/- 28 (DS) and 17 +/- 9.6, respectively. All autoradiograms of DNA from fish from the contaminated sites exhibited a diagonal radioactive zone where DNA adducts of chrysene, benzo(a)pyrene, and dibenz(a,h)anthracene, formed in vitro using English sole hepatic microsomes, were shown to chromatograph. English sole treated with extracts of the contaminated sediments had adduct profiles generally similar to those for English sole from the respective contaminated sites.

  1. Sorting fluorescent nanocrystals with DNA

    SciTech Connect

    Gerion, Daniele; Parak, Wolfgang J.; Williams, Shara C.; Zanchet, Daniela; Micheel, Christine M.; Alivisatos, A. Paul

    2001-12-10

    Semiconductor nanocrystals with narrow and tunable fluorescence are covalently linked to oligonucleotides. These biocompounds retain the properties of both nanocrystals and DNA. Therefore, different sequences of DNA can be coded with nanocrystals and still preserve their ability to hybridize to their complements. We report the case where four different sequences of DNA are linked to four nanocrystal samples having different colors of emission in the range of 530-640 nm. When the DNA-nanocrystal conjugates are mixed together, it is possible to sort each type of nanoparticle using hybridization on a defined micrometer -size surface containing the complementary oligonucleotide. Detection of sorting requires only a single excitation source and an epifluorescence microscope. The possibility of directing fluorescent nanocrystals towards specific biological targets and detecting them, combined with their superior photo-stability compared to organic dyes, opens the way to improved biolabeling experiments, such as gene mapping on a nanometer scale or multicolor microarray analysis.

  2. Stabbing simulations and DNA transfer.

    PubMed

    Samie, Lydie; Hicks, Tacha; Castella, Vincent; Taroni, Franco

    2016-05-01

    Technical developments have made it possible to analyze very low amounts of DNA. This has many advantages, but the drawback of this technological progress is that interpretation of the results becomes increasingly complex: the number of mixed DNA profiles increased relatively to single source DNA profiles and stochastic effects in the DNA profile, such as drop-in and drop-out, are more frequently observed. Moreover, the relevance of low template DNA material regarding the activities alleged is not as straightforward as it was a few years ago, when for example large quantities of blood were recovered. The possibility of secondary and tertiary transfer is now becoming an issue. The purpose of this research is twofold: first, to study the transfer of DNA from the handler and secondly, to observe if handlers would transfer DNA from persons closely connected to them. We chose to mimic cases where the offender would attack a person with a knife. As a first approach, we envisaged that the defense would not give an alternative explanation for the origin of the DNA. In our transfer experiments (4 donors, 16 experiments each, 64 traces), 3% of the traces were single DNA profiles. Most of the time, the DNA profile of the person handling the knife was present as the major profile: in 83% of the traces the major contributor profile corresponded to the stabber's DNA profile (in single stains and mixtures). Mixture with no clear major/minor fraction (12%) were observed. 5% of the traces were considered of insufficient quality (more than 3 contributors, presence of a few minor peaks). In that case, we considered that the stabber's DNA was absent. In our experiments, no traces allowed excluding the stabber, however it must be noted that precautions were taken to minimize background DNA as knives were cleaned before the experiments. DNA profiles of the stabber's colleagues were not observed. We hope that this study will allow for a better understanding of the transfer mechanism and

  3. 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.

  4. Mixed oxide solid solutions

    DOEpatents

    Magno, Scott; Wang, Ruiping; Derouane, Eric

    2003-01-01

    The present invention is a mixed oxide solid solution containing a tetravalent and a pentavalent cation that can be used as a support for a metal combustion catalyst. The invention is furthermore a combustion catalyst containing the mixed oxide solid solution and a method of making the mixed oxide solid solution. The tetravalent cation is zirconium(+4), hafnium(+4) or thorium(+4). In one embodiment, the pentavalent cation is tantalum(+5), niobium(+5) or bismuth(+5). Mixed oxide solid solutions of the present invention exhibit enhanced thermal stability, maintaining relatively high surface areas at high temperatures in the presence of water vapor.

  5. Cement mixing with vibrator

    SciTech Connect

    Allen, T.E.

    1991-07-09

    This patent describes a method of cementing a casing string in a bore hole of a well. It comprises introducing water and dry cement material into a mixing vessel; mixing the water and dry cement material in the mixing vessel to form a cement slurry, the slurry including lumps of the dry cement material, the mixing including steps of: agitating the slurry; and while agitating the slurry, transmitting vibrational energy into the slurry and thereby aiding disintegration and subsequent wetting of the lumps of the dry cement material in the slurry; and pumping the slurry into an annulus between the casing string and the bore hole.

  6. Mixed waste minimization/mixed waste avoidance

    SciTech Connect

    Todisco, L.R.

    1994-12-31

    This presentation describes methods for the minimization and volume reduction of low-level radioactive and mixed wastes. Many methods are presented including: source reduction, better waste monitoring activities, waste segregation, recycling, administrative controls, and optimization of waste-generating processes.

  7. 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)

  8. 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.

  9. Dilution Zone Mixing

    NASA Technical Reports Server (NTRS)

    Holdeman, J. D.

    1983-01-01

    Studies to characterize dilution zone mixing; experiments on the effects of free-stream turbulence on a jet in crossflow; and the development of an interactive computer code for the analysis of the mixing of jets with a confined crossflow are reviewed.

  10. Screening of hydrophobic DNA adducts in flounder (Platichthys flesus) from the Baltic Sea.

    PubMed

    Malmström, C; Konn, M; Bogovski, S; Lang, T; Lönnström, L-G; Bylund, G

    2009-12-01

    Neoplasia and other histopathological lesions in flounder (Platichthys flesus) liver have been investigated in several European sea areas, including the Baltic Sea. Several studies have been able to link neoplasm epizootics in fish with the exposure to genotoxins such as polycyclic aromatic hydrocarbons (PAHs). The level of hydrophobic DNA adducts in tissue DNA reflects the exposure of the organism to PAHs. Using hydrophobic DNA adduct levels as biomarkers, possible PAH exposure was assessed in flounder from 10 different sites in the Baltic Sea, collected during the years 1995-1997. The results show that the overall levels of hepatic DNA adducts were low and, in general, the chromatograms appeared clean. The highest levels of DNA adducts were found at two sites in the southern Baltic Sea. There were no statistically significant differences in adduct levels between the sites. Our results indicate that flounder from studied off shore sites of the Baltic Sea had not been exposed to a greater extent to large polycyclic hydrophobic hydrocarbons in their environment.

  11. Interference of Co-amplified nuclear mitochondrial DNA sequences on the determination of human mtDNA heteroplasmy by Using the SURVEYOR nuclease and the WAVE HS system.

    PubMed

    Yen, Hsiu-Chuan; Li, Shiue-Li; Hsu, Wei-Chien; Tang, Petrus

    2014-01-01

    High-sensitivity and high-throughput mutation detection techniques are useful for screening the homoplasmy or heteroplasmy status of mitochondrial DNA (mtDNA), but might be susceptible to interference from nuclear mitochondrial DNA sequences (NUMTs) co-amplified during polymerase chain reaction (PCR). In this study, we first evaluated the platform of SURVEYOR Nuclease digestion of heteroduplexed DNA followed by the detection of cleaved DNA by using the WAVE HS System (SN/WAVE-HS) for detecting human mtDNA variants and found that its performance was slightly better than that of denaturing high-performance liquid chromatography (DHPLC). The potential interference from co-amplified NUMTs on screening mtDNA heteroplasmy when using these 2 highly sensitive techniques was further examined by using 2 published primer sets containing a total of 65 primer pairs, which were originally designed to be used with one of the 2 techniques. We confirmed that 24 primer pairs could amplify NUMTs by conducting bioinformatic analysis and PCR with the DNA from 143B-ρ0 cells. Using mtDNA extracted from the mitochondria of human 143B cells and a cybrid line with the nuclear background of 143B-ρ0 cells, we demonstrated that NUMTs could affect the patterns of chromatograms for cell DNA during SN-WAVE/HS analysis of mtDNA, leading to incorrect judgment of mtDNA homoplasmy or heteroplasmy status. However, we observed such interference only in 2 of 24 primer pairs selected, and did not observe such effects during DHPLC analysis. These results indicate that NUMTs can affect the screening of low-level mtDNA variants, but it might not be predicted by bioinformatic analysis or the amplification of DNA from 143B-ρ0 cells. Therefore, using purified mtDNA from cultured cells with proven purity to evaluate the effects of NUMTs from a primer pair on mtDNA detection by using PCR-based high-sensitivity methods prior to the use of a primer pair in real studies would be a more practical strategy.

  12. Metabolite Profiling and Classification of DNA-Authenticated Licorice Botanicals.

    PubMed

    Simmler, Charlotte; Anderson, Jeffrey R; Gauthier, Laura; Lankin, David C; McAlpine, James B; Chen, Shao-Nong; Pauli, Guido F

    2015-08-28

    Raw licorice roots represent heterogeneous materials obtained from mainly three Glycyrrhiza species. G. glabra, G. uralensis, and G. inflata exhibit marked metabolite differences in terms of flavanones (Fs), chalcones (Cs), and other phenolic constituents. The principal objective of this work was to develop complementary chemometric models for the metabolite profiling, classification, and quality control of authenticated licorice. A total of 51 commercial and macroscopically verified samples were DNA authenticated. Principal component analysis and canonical discriminant analysis were performed on (1)H NMR spectra and area under the curve values obtained from UHPLC-UV chromatograms, respectively. The developed chemometric models enable the identification and classification of Glycyrrhiza species according to their composition in major Fs, Cs, and species specific phenolic compounds. Further key outcomes demonstrated that DNA authentication combined with chemometric analyses enabled the characterization of mixtures, hybrids, and species outliers. This study provides a new foundation for the botanical and chemical authentication, classification, and metabolomic characterization of crude licorice botanicals and derived materials. Collectively, the proposed methods offer a comprehensive approach for the quality control of licorice as one of the most widely used botanical dietary supplements.

  13. MHD turbulent mixing layers

    SciTech Connect

    Esquivel, A.; Lazarian, A.; Benjamin, R.A.; Cho, J.; Leitner, S.N.

    2005-09-28

    Turbulent mixing layers have been proposed to explain observations of line ratios of highly ionized elements in the interstellar medium. We present preliminary results of numerical simulations of turbulent mixing layers in a magnetized medium. We developed a MHD code with radiative cooling. The magnetic field is expected to be a controlling factor by suppressing instabilities that lead to the turbulent mixing. Our results suggest that the difference in turbulent mixing in the unmagnetized case as compared to the case of a weak magnetic field, {beta} = Pgas/Pmag {approx} 10, is insignificant. With a more thorough exploration of parameter space, this work will provide more reliable diagnostics of turbulent mixing layers than those available today.

  14. Microfluidic Mixing: A Review

    PubMed Central

    Lee, Chia-Yen; Chang, Chin-Lung; Wang, Yao-Nan; Fu, Lung-Ming

    2011-01-01

    The aim of microfluidic mixing is to achieve a thorough and rapid mixing of multiple samples in microscale devices. In such devices, sample mixing is essentially achieved by enhancing the diffusion effect between the different species flows. Broadly speaking, microfluidic mixing schemes can be categorized as either “active”, where an external energy force is applied to perturb the sample species, or “passive”, where the contact area and contact time of the species samples are increased through specially-designed microchannel configurations. Many mixers have been proposed to facilitate this task over the past 10 years. Accordingly, this paper commences by providing a high level overview of the field of microfluidic mixing devices before describing some of the more significant proposals for active and passive mixers. PMID:21686184

  15. ADVANCED MIXING MODELS

    SciTech Connect

    Lee, S; Richard Dimenna, R; David Tamburello, D

    2008-11-13

    The process of recovering the waste in storage tanks at the Savannah River Site (SRS) typically requires mixing the contents of the tank with one to four dual-nozzle jet mixers located within the tank. The typical criteria to establish a mixed condition in a tank are based on the number of pumps in operation and the time duration of operation. To ensure that a mixed condition is achieved, operating times are set conservatively long. This approach results in high operational costs because of the long mixing times and high maintenance and repair costs for the same reason. A significant reduction in both of these costs might be realized by reducing the required mixing time based on calculating a reliable indicator of mixing with a suitably validated computer code. The work described in this report establishes the basis for further development of the theory leading to the identified mixing indicators, the benchmark analyses demonstrating their consistency with widely accepted correlations, and the application of those indicators to SRS waste tanks to provide a better, physically based estimate of the required mixing time. Waste storage tanks at SRS contain settled sludge which varies in height from zero to 10 ft. The sludge has been characterized and modeled as micron-sized solids, typically 1 to 5 microns, at weight fractions as high as 20 to 30 wt%, specific gravities to 1.4, and viscosities up to 64 cp during motion. The sludge is suspended and mixed through the use of submersible slurry jet pumps. To suspend settled sludge, water is added to the tank as a slurry medium and stirred with the jet pump. Although there is considerable technical literature on mixing and solid suspension in agitated tanks, very little literature has been published on jet mixing in a large-scale tank. If shorter mixing times can be shown to support Defense Waste Processing Facility (DWPF) or other feed requirements, longer pump lifetimes can be achieved with associated operational cost and

  16. 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 ...

  17. ADVANCED MIXING MODELS

    SciTech Connect

    Lee, S; Dimenna, R; Tamburello, D

    2011-02-14

    The process of recovering and processing High Level Waste (HLW) the waste in storage tanks at the Savannah River Site (SRS) typically requires mixing the contents of the tank with one to four mixers (pumps) located within the tank. The typical criteria to establish a mixed condition in a tank are based on the number of pumps in operation and the time duration of operation. To ensure that a mixed condition is achieved, operating times are typically set conservatively long. This approach results in high operational costs because of the long mixing times and high maintenance and repair costs for the same reason. A significant reduction in both of these costs might be realized by reducing the required mixing time based on calculating a reliable indicator of mixing with a suitably validated computer code. The focus of the present work is to establish mixing criteria applicable to miscible fluids, with an ultimate goal of addressing waste processing in HLW tanks at SRS and quantifying the mixing time required to suspend sludge particles with the submersible jet pump. A single-phase computational fluid dynamics (CFD) approach was taken for the analysis of jet flow patterns with an emphasis on the velocity decay and the turbulent flow evolution for the farfield region from the pump. Literature results for a turbulent jet flow are reviewed, since the decay of the axial jet velocity and the evolution of the jet flow patterns are important phenomena affecting sludge suspension and mixing operations. The work described in this report suggests a basis for further development of the theory leading to the identified mixing indicators, with benchmark analyses demonstrating their consistency with widely accepted correlations. Although the indicators are somewhat generic in nature, they are applied to Savannah River Site (SRS) waste tanks to provide a better, physically based estimate of the required mixing time. Waste storage tanks at SRS contain settled sludge which varies in

  18. 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.

  19. 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

  20. The mixing of fluids

    SciTech Connect

    Ottino, J.M.

    1989-01-01

    What do the eruption of Krakatau, the manufacture of puff pastry and the brightness of stars have in common Each involves some aspect of mixing. Mixing also plays a critical role in modern technology. Chemical engineers rely on mixing to ensure that substances react properly, to produce polymer blends that exhibit unique properties and to disperse drag-reducing agents in pipelines. Yet in spite of its of its ubiquity in nature and industry, mixing is only imperfectly under-stood. Indeed, investigators cannot even settle on a common terminology: mixing is often referred to as stirring by oceanographers and geophysicists, as blending by polymer engineers and as agitation by process engineers. Regardless of what the process is called, there is little doubt that it is exceedingly complex and is found in a great variety of systems. In constructing a theory of fluid mixing, for example, one has to take into account fluids that can be miscible or partially miscible and reactive or inert, and flows that are slow and orderly or very fast and turbulent. It is therefore not surprising that no single theory can explain all aspect of mixing in fluids and that straightforward computations usually fail to capture all the important details. Still, both physical experiments and computer simulations can provide insight into the mixing process. Over the past several years the authors and his colleague have taken both approaches in an effort to increase understanding of various aspect of the process-particularly of mixing involving slow flows and viscous fluids such as oils.

  1. Plasmonic Metallurgy Enabled by DNA

    DOE PAGES

    Ross, Michael B.; Ku, Jessie C.; Lee, Byeongdu; ...

    2016-02-05

    In this study, mixed silver and gold plasmonic nanoparticle architectures are synthesized using DNA-programmable assembly, unveiling exquisitely tunable optical properties that are predicted and explained both by effective thin-film models and explicit electrodynamic simulations. These data demonstrate that the manner and ratio with which multiple metallic components are arranged can greatly alter optical properties, including tunable color and asymmetric reflectivity behavior of relevance for thin-film applications.

  2. Plasmonic Metallurgy Enabled by DNA.

    PubMed

    Ross, Michael B; Ku, Jessie C; Lee, Byeongdu; Mirkin, Chad A; Schatz, George C

    2016-04-13

    Mixed silver and gold plasmonic nanoparticle architectures are synthesized using DNA-programmable assembly, unveiling exquisitely tunable optical properties that are predicted and explained both by effective thin-film models and explicit electrodynamic simulations. These data demonstrate that the manner and ratio with which multiple metallic components are arranged can greatly alter optical properties, including tunable color and asymmetric reflectivity behavior of relevance for thin-film applications.

  3. Mixing method and apparatus

    DOEpatents

    Green, Norman W.

    1982-06-15

    Method of mixing particulate materials comprising contacting a primary source and a secondary source thereof whereby resulting mixture ensues; preferably at least one of the two sources has enough motion to insure good mixing and the particulate materials may be heat treated if desired. Apparatus for such mixing comprising an inlet for a primary source, a reactor communicating therewith, a feeding means for supplying a secondary source to the reactor, and an inlet for the secondary source. Feeding means is preferably adapted to supply fluidized materials.

  4. Nearly discontinuous chaotic mixing

    SciTech Connect

    Sharp, David Howland; Lim, Hyun K; Yu, Yan; Glimm, James G

    2009-01-01

    A new scientific approach is presented for a broad class of chaotic problems involving a high degree of mixing over rapid time scales. Rayleigh-Taylor and Richtmyer-Meshkov unstable flows are typical of such problems. Microscopic mixing properties such as chemical reaction rates for turbulent mixtures can be obtained with feasible grid resolution. The essential dependence of (some) fluid mixing observables on transport phenomena is observed. This dependence includes numerical as well as physical transport and it includes laminar as well as turbulent transport. A new approach to the mathematical theory for the underlying equations is suggested.

  5. Bacterial identification and subtyping using DNA microarray and DNA sequencing.

    PubMed

    Al-Khaldi, Sufian F; Mossoba, Magdi M; Allard, Marc M; Lienau, E Kurt; Brown, Eric D

    2012-01-01

    The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

  6. Lipid phase control of DNA delivery

    SciTech Connect

    Koynova, Rumiana; Wang, Li; Tarahovsky, Yury; MacDonald, Robert C.

    2010-01-18

    Cationic lipids form nanoscale complexes (lipoplexes) with polyanionic DNA and can be utilized to deliver DNA to cells for transfection. Here we report the correlation between delivery efficiency of these DNA carriers and the mesomorphic phases they form when interacting with anionic membrane lipids. Specifically, formulations that are particularly effective DNA carriers form phases of highest negative interfacial curvature when mixed with anionic lipids, whereas less effective formulations form phases of lower curvature. Structural evolution of the carrier lipid/DNA complexes upon interaction with cellular lipids is hence suggested as a controlling factor in lipid-mediated DNA delivery. A strategy for optimizing lipofection is deduced. The behavior of a highly effective lipoplex formulation, DOTAP/DOPE, is found to conform to this 'efficiency formula'.

  7. Detection of Quadruplex DNA by Gold Nanoparticles

    PubMed Central

    Crouse, Heather F.; Doudt, Alex; Zerbe, Cassie; Basu, Swarna

    2012-01-01

    Gold nanoparticles have been used as a probe to detect low (<10 ppb) concentrations of quadruplex DNA. These nanoparticles display a tendency to form aggregates in the presence of certain quadruplex forms, as observed via enhanced plasmon resonance light scattering (PRLS) signals. These nanoparticles showed differing degrees of interactions with different types of quadruplex and mixed sequences but no interaction with duplex DNA. Enhancement of PRLS signals greater than 50% was observed at nanomolar DNA concentration, and a lower limit of detection of 2.1 nM was established for three different quadruplex DNA sequences, including the thrombin-inhibiting single-stranded 15 mer aptamer DNA, d(GGTTGGTGTGGTTGG), and the double-stranded 12 mer DNA, d(G4T4G4). Two different sample preparation protocols were used for the PRLS experiments, and they yielded similar results. PMID:22567555

  8. Applications of DNA fingerprinting in pediatric practice.

    PubMed

    McCabe, E R

    1992-04-01

    Pediatric cases have played historic and precedent-setting roles in DNA forensics. DNA fingerprinting is a powerful tool for the pediatrician in cases of physical and sexual abuse and when issues arise regarding identification and familial relationships. If this technology is to be utilized effectively, the physician must know how to collect and document specimens. The pediatrician needs to be cautious in making referrals for commercial DNA banking. Whereas well-maintained and protected DNA repositories can be extremely valuable when there are medical and other appropriate indications, there are very real concerns about commercial DNA banking solely for purposes of identification. Pediatricians should recognize that this technology can be applied in novel but important new ways in their practices. For example, at the first indication of a possible mix-up of babies in the nursery, this should be acknowledged and rapidly resolved through DNA profiling of the parents and the neonates.

  9. Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma

    PubMed Central

    Zhang, Ruoyu; Nakahira, Kiichi; Guo, Xiaoxian; Choi, Augustine M.K.; Gu, Zhenglong

    2016-01-01

    Cell free DNA (cfDNA) has received increasing attention and has been studied in a broad range of clinical conditions. However, few studies have focused on mitochondrial DNA (mtDNA) in the cell free form. We optimized DNA isolation and sequencing library preparation protocols to better retain short DNA fragments from plasma, and applied these optimized methods to plasma samples from patients with sepsis. Our methods can retain substantially shorter DNA, resulting in an average of 11.5 fold increase in short DNA fragments yield (DNA <100bp). We report that cf-mtDNA in plasma is highly enriched in short-size cfDNA (30~60 bp). Motivated by this unique size distribution, we size-selected short cfDNA, which further increased the mtDNA recovery rate by an average of 10.4 fold. We then detected mtDNA heteroplasmy in plasma from 3 patients. In one patient who previously received bone marrow transplantation, different minor allele frequencies were observed between plasma and leukocytes at heteroplasmic sites, consistent with mixed-tissue origin for cfDNA. For the other two patients, the heteroplasmy pattern is also different between plasma and leukocyte. Our study shed new lights into the architecture of the cfDNA, and mtDNA heteroplasmy identified in plasma provides new potential for biomarker discovery. PMID:27811968

  10. Guidelines for mixed waste minimization

    SciTech Connect

    Owens, C.

    1992-02-01

    Currently, there is no commercial mixed waste disposal available in the United States. Storage and treatment for commercial mixed waste is limited. Host States and compacts region officials are encouraging their mixed waste generators to minimize their mixed wastes because of management limitations. This document provides a guide to mixed waste minimization.

  11. How to make DNA count: DNA-based diagnostic tools in veterinary parasitology.

    PubMed

    Hunt, P W; Lello, J

    2012-05-04

    Traditional methods for the diagnosis of parasitic helminth infections of livestock have a number of limitations, such as the inability to distinguish mixed-species infections, a heavy reliance on technical experience and also sub-sampling errors. Some of these limitations may be overcome through the development of rapid and accurate DNA-based tests. For example, DNA-based tests can specifically detect individual species in a mixed infection at either the larval or egg stages, in the absence of morphological differences among species. Even so, some diagnostic problems remain the same, irrespective of whether a DNA-based or traditional method is used. For example, sub-sampling errors from an aggregated distribution are likely to persist. It is proposed, however, that DNA-based diagnostic technologies offer an opportunity to expand diagnostic capabilities, and are discussed in the current review. The future introduction of DNA-based diagnostic technologies into routine diagnostic settings will also be discussed.

  12. Artificial upwelling and mixing

    SciTech Connect

    Not Available

    1989-01-01

    The authors present results related to artificial upwelling and coastal mariculture using deep ocean water and mixing in coastal waters. They discuss the application of research results for marine waste disposal.

  13. Mixed-Media Owls

    ERIC Educational Resources Information Center

    Schultz, Kathy

    2010-01-01

    The fun of creating collages is there are unlimited possibilities for the different kinds of materials one can use. In this article, the author describes how her eighth-grade students created an owl using mixed media.

  14. Asymmetric antiproton debuncher: No bad mixing, more good mixing

    SciTech Connect

    Visnjic, V.

    1994-07-01

    An asymmetric lattice for the Fermilab Antiproton Debuncher is designed. The lattice has zero mixing between the pickups and the kickers (bad mixing) while the mixing in the rest of the machine (good mixing) can be varied (even during the operation of the machine) in order to optimize the stochastic cooling. As an example, a lattice with zero bad mixing and twice the good mixing is presented. The betatron cooling rate in this lattice is twice its present value.

  15. 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)

  16. 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)

  17. 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

  18. Mixing of Supersonic Streams

    NASA Technical Reports Server (NTRS)

    Hawk, C. W.; Landrum, D. B.; Muller, S.; Turner, M.; Parkinson, D.

    1998-01-01

    The Strutjet approach to Rocket Based Combined Cycle (RBCC) propulsion depends upon fuel-rich flows from the rocket nozzles and turbine exhaust products mixing with the ingested air for successful operation in the ramjet and scramjet modes. It is desirable to delay this mixing process in the air-augmented mode of operation present during low speed flight. A model of the Strutjet device has been built and is undergoing test to investigate the mixing of the streams as a function of distance from the Strutjet exit plane during simulated low speed flight conditions. Cold flow testing of a 1/6 scale Strutjet model is underway and nearing completion. Planar Laser Induced Fluorescence (PLIF) diagnostic methods are being employed to observe the mixing of the turbine exhaust gas with the gases from both the primary rockets and the ingested air simulating low speed, air augmented operation of the RBCC. The ratio of the pressure in the turbine exhaust duct to that in the rocket nozzle wall at the point of their intersection is the independent variable in these experiments. Tests were accomplished at values of 1.0, 1.5 and 2.0 for this parameter. Qualitative results illustrate the development of the mixing zone from the exit plane of the model to a distance of about 10 rocket nozzle exit diameters downstream. These data show the mixing to be confined in the vertical plane for all cases, The lateral expansion is more pronounced at a pressure ratio of 1.0 and suggests that mixing with the ingested flow would be likely beginning at a distance of 7 nozzle exit diameters downstream of the nozzle exit plane.

  19. Mixing of Supersonic Streams

    NASA Technical Reports Server (NTRS)

    Hawk, C. W.; Landrum, D. B.; Muller, S.; Turner, M.; Parkinson, D.

    1998-01-01

    The Strutjet approach to Rocket Based Combined Cycle (RBCC) propulsion depends upon fuel-rich flows from the rocket nozzles and turbine exhaust products mixing with the ingested air for successful operation in the ramjet and scramjet modes. It is desirable to delay this mixing process in the air-augmented mode of operation present during low speed flight. A model of the Strutjet device has been built and is undergoing test to investigate the mixing of the streams as a function of distance from the Strutjet exit plane during simulated low speed flight conditions. Cold flow testing of a 1/6 scale Strutjet model is underway and nearing completion. Planar Laser Induced Fluorescence (PLIF) diagnostic methods are being employed to observe the mixing of the turbine exhaust gas with the gases from both the primary rockets and the ingested air simulating low speed, air augmented operation of the RBCC. The ratio of the pressure in the turbine exhaust duct to that in the rocket nozzle wall at the point of their intersection is the independent variable in these experiments. Tests were accomplished at values of 1.0, 1.5 and 2.0 for this parameter. Qualitative results illustrate the development of the mixing zone from the exit plane of the model to a distance of about 19 equivalent rocket nozzle exit diameters downstream. These data show the mixing to be confined in the vertical plane for all cases, The lateral expansion is more pronounced at a pressure ratio of 1.0 and suggests that mixing with the ingested flow would be likely beginning at a distance of 7 nozzle exit diameters downstream of the nozzle exit plane.

  20. Enhanced solubilization of curcumin in mixed surfactant vesicles.

    PubMed

    Kumar, Arun; Kaur, Gurpreet; Kansal, S K; Chaudhary, Ganga Ram; Mehta, S K

    2016-05-15

    Self-assemblies of equimolar double and single chain mixed ionic surfactants, with increasing numbers of carbon atoms of double chain surfactant, were analyzed on the basis of fluorescence and conductivity results. Attempts were also made to enhance the solubilization of curcumin in aqueous equimolar mixed surfactant systems. Mixed surfactant assembly was successful in retarding the degradation of curcumin in alkaline media (only 25-28 40% degraded in 10h at pH 13). Fluorescence spectroscopy and fluorescence quenching methods were employed to predict the binding position and mechanism of curcumin with self-assemblies. Results indicate that the interactions take place according to both dynamic and static quenching mechanisms and curcumin was distributed in a palisade layer of mixed aggregates. Antioxidant activity (using DPPH radical) and biocompatibility (using calf-thymus DNA) of curcumin-loaded mixed surfactant formulations were also evaluated. The prepared systems improved the stability, solubility and antioxidant activity of curcumin and additionally are biocompatible.

  1. Mixed waste management options

    SciTech Connect

    Owens, C.B.; Kirner, N.P.

    1991-12-31

    Disposal fees for mixed waste at proposed commercial disposal sites have been estimated to be $15,000 to $40,000 per cubit foot. If such high disposal fees are imposed, generators may be willing to apply extraordinary treatment or regulatory approaches to properly dispose of their mixed waste. This paper explores the feasibility of several waste management scenarios and attempts to answer the question: Can mixed waste be managed out of existence? Existing data on commercially generated mixed waste streams are used to identify the realm of mixed waste known to be generated. Each waste stream is evaluated from both a regulatory and technical perspective in order to convert the waste into a strictly low-level radioactive or a hazardous waste. Alternative regulatory approaches evaluated in this paper include a delisting petition, no migration petition, and a treatability variance. For each waste stream, potentially available treatment options are identified that could lead to these variances. Waste minimization methodology and storage for decay are also considered. Economic feasibility of each option is discussed broadly.

  2. 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.

  3. Mixed waste: Proceedings

    SciTech Connect

    Moghissi, A.A.; Blauvelt, R.K.; Benda, G.A.; Rothermich, N.E.

    1993-12-31

    This volume contains the peer-reviewed and edited versions of papers submitted for presentation a the Second International Mixed Waste Symposium. Following the tradition of the First International Mixed Waste Symposium, these proceedings were prepared in advance of the meeting for distribution to participants. The symposium was organized by the Mixed Waste Committee of the American Society of Mechanical Engineers. The topics discussed at the symposium include: stabilization technologies, alternative treatment technologies, regulatory issues, vitrification technologies, characterization of wastes, thermal technologies, laboratory and analytical issues, waste storage and disposal, organic treatment technologies, waste minimization, packaging and transportation, treatment of mercury contaminated wastes and bioprocessing, and environmental restoration. Individual abstracts are catalogued separately for the data base.

  4. Natural convective mixing flows

    NASA Astrophysics Data System (ADS)

    Ramos, Eduardo; de La Cruz, Luis; del Castillo, Luis

    1998-11-01

    Natural convective mixing flows. Eduardo Ramos and Luis M. de La Cruz, National University of Mexico and Luis Del Castillo San Luis Potosi University. The possibility of mixing a fluid with a natural convective flow is analysed by solving numerically the mass, momentum and energy equations in a cubic container. Two opposite vertical walls of the container are assumed to have temperatures that oscillate as functions of time. The phase of the oscillations is chosen in such a way that alternating corrotating vortices are formed in the cavity. The mixing efficiency of this kind of flow is examined with a Lagrangian tracking technique. This work was partially financed by CONACyT-Mexico project number GE0044

  5. Remotely controllable mixing system

    NASA Technical Reports Server (NTRS)

    Belew, Robert R. (Inventor)

    1987-01-01

    A remotely controllable mixing system (210) in which a plurality of mixing assemblies (10a-10e) are arranged in an annular configuration, and wherein each assembly (10) employs a central chamber (16) and two outer, upper and lower, chambers (12, 14). Valves (18, 20) are positioned between chambers, and these valves (18, 20) for a given mixing assembly (10) are operated by upper and lower control rotors (29), which in turn are driven by upper and lower drive rotors (270, 270b). Additionally, a hoop (278) is compressed around upper control rotors (29) and a hoop (278b) is compressed around lower control rotors (29) to thus insure constant frictional engagement between all control rotors (29) and drive rotors (270, 270b). The drive rollers (270, 270b) are driven by a motor (213).

  6. Dilution jet mixing program

    NASA Technical Reports Server (NTRS)

    Srinivasan, R.; Coleman, E.; Johnson, K.

    1984-01-01

    Parametric tests were conducted to quantify the mixing of opposed rows of jets (two-sided injection) in a confined cross flow. Results show that jet penetrations for two sided injections are less than that for single-sided injections, but the jet spreading rates are faster for a given momentum ratio and orifice plate. Flow area convergence generally enhances mixing. Mixing characteristics with asymmetric and symmetric convergence are similar. For constant momentum ratio, the optimum S/H(0) with in-line injections is one half the optimum value for single sided injections. For staggered injections, the optimum S/H(0) is twice the optimum value for single-sided injection. The correlations developed predicted the temperature distributions within first order accuracy and provide a useful tool for predicting jet trajectory and temperature profiles in the dilution zone with two-sided injections.

  7. Mixing navigation on networks

    NASA Astrophysics Data System (ADS)

    Zhou, Tao

    2008-05-01

    In this article, we propose a mixing navigation mechanism, which interpolates between random-walk and shortest-path protocol. The navigation efficiency can be remarkably enhanced via a few routers. Some advanced strategies are also designed: For non-geographical scale-free networks, the targeted strategy with a tiny fraction of routers can guarantee an efficient navigation with low and stable delivery time almost independent of network size. For geographical localized networks, the clustering strategy can simultaneously increase efficiency and reduce the communication cost. The present mixing navigation mechanism is of significance especially for information organization of wireless sensor networks and distributed autonomous robotic systems.

  8. Atomization and mixing study

    NASA Technical Reports Server (NTRS)

    Ferrenberg, A.; Jaqua, V. W.

    1983-01-01

    The state of the art in atomization and mixing for triplet, pentad, and coaxial injectors is described. Injectors that are applicable for LOX/hydrocarbon propellants and main chamber and fuel rich preburner/gas generator mixture ratios are of special interest. Various applicable correlating equations and parameters as well as test data found in the literature are presented. The validity, utility, and important aspects of these data and correlations are discussed and the measurement techniques used are evaluated. Propellant mixing tests performed are described and summarized, results are reported, and tentative conclusions are included.

  9. Mixed crystal organic scintillators

    DOEpatents

    Zaitseva, Natalia P; Carman, M Leslie; Glenn, Andrew M; Hamel, Sebastien; Hatarik, Robert; Payne, Stephen A; Stoeffl, Wolfgang

    2014-09-16

    A mixed organic crystal according to one embodiment includes a single mixed crystal having two compounds with different bandgap energies, the organic crystal having a physical property of exhibiting a signal response signature for neutrons from a radioactive source, wherein the signal response signature does not include a significantly-delayed luminescence characteristic of neutrons interacting with the organic crystal relative to a luminescence characteristic of gamma rays interacting with the organic crystal. According to one embodiment, an organic crystal includes bibenzyl and stilbene or a stilbene derivative, the organic crystal having a physical property of exhibiting a signal response signature for neutrons from a radioactive source.

  10. Atomization and Mixing Study

    NASA Technical Reports Server (NTRS)

    Ferrenberg, A.; Hunt, K.; Duesberg, J.

    1985-01-01

    The primary objective was the obtainment of atomization and mixing performance data for a variety of typical liquid oxygen/hydrocarbon injector element designs. Such data are required to establish injector design criteria and to provide critical inputs to liquid rocket engine combustor performance and stability analysis, and computational codes and methods. Deficiencies and problems with the atomization test equipment were identified, and action initiated to resolve them. Test results of the gas/liquid mixing tests indicated that an assessment of test methods was required. A series of 71 liquid/liquid tests were performed.

  11. 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.

  12. Specific triplex binding capacity of mixed base sequence duplex nucleic acids used for single-nucleotide polymorphism detection.

    PubMed

    Daksis, Jasmine I; Erikson, Glen H

    2005-01-01

    Specific base recognition and binding between native double-stranded DNA (dsDNA) and complementary single-stranded DNA (ssDNA) of mixed base sequence is presented. Third-strand binding, facilitated and stabilized by a DNA intercalator, YOYO-1, occurs within 5 min at room temperature. This triplex binding capability has been used to develop a homogeneous assay that accurately detects 1-, 2-, or 3-bp mutations or deletions in the dsDNA target. Every type of 1-bp mismatch can be identified. The assay can reliably distinguish homozygous from heterozygous polymerase chain reaction (PCR)-amplified genomic dsDNA, thus providing a highly sensitive clinical diagnostic assay.

  13. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

  14. Sylgard® Mixing Study

    SciTech Connect

    Bello, Mollie; Welch, Cynthia F.; Goodwin, Lynne Alese; Keller, Jennie

    2014-08-22

    Sylgard® 184 and Sylgard® 186 silicone elastomers form Dow Corning® are used as potting agents across the Nuclear Weapons Complex. A standardized mixing procedure is required for filled versions of these products. The present study is a follow-up to a mixing study performed by MST-7 which established the best mixing procedure to use when adding filler to either 184 or 186 base resins. The most effective and consistent method of mixing resin and curing agent for three modified silicone elastomer recipes is outlined in this report. For each recipe, sample size, mixing type, and mixing time was varied over 10 separate runs. The results show that the THINKY™ Mixer gives reliable mixing over varying batch sizes and mixing times. Hand Mixing can give improved mixing, as indicated by reduced initial viscosity; however, this method is not consistent.

  15. Mixing and Transport.

    ERIC Educational Resources Information Center

    Ditmars, John D.

    1978-01-01

    Presents a literature review of longitudinal dispersion, mixing and transport in streams, rivers, lakes, reservoirs, estuaries, and oceans. This review covers also: (1) fluid-solid mixtures and (2) oil spill behavior. A list of 189 references published in 1976 and 1977 is presented. (HM)

  16. Mixed-Initiative Clustering

    ERIC Educational Resources Information Center

    Huang, Yifen

    2010-01-01

    Mixed-initiative clustering is a task where a user and a machine work collaboratively to analyze a large set of documents. We hypothesize that a user and a machine can both learn better clustering models through enriched communication and interactive learning from each other. The first contribution or this thesis is providing a framework of…

  17. Stabilizer for mixed fuels

    SciTech Connect

    Yamamura, M.; Igarashi, T.; Ukigai, T.

    1984-03-13

    A stabilizer for mixed fuels containing a reaction product obtained by reacting (1) a polyol having at least 3 hydroxyl groups in the molecule and a molecular weight of 400-10,000 with (2) an epihalohydrin, as the principal component.

  18. True Anonymity Without Mixes

    NASA Astrophysics Data System (ADS)

    Molina-Jimenez, C.; Marshall, L.

    2002-04-01

    Anonymizers based on mix computers interposed between the sender and the receiver of an e-mail message have been used in the Internet for several years by senders of e-mail messages who do not wish to disclose their identity. Unfortunately, the degree of anonymity provided by this paradigm is limited and fragile. First, the messages sent are not truly anonymous but pseudo-anonymous since one of the mixes, at least, always knows the sender's identity. Secondly, the strength of the system to protect the sender's identity depends on the ability and the willingness of the mixes to keep the secret. If the mixes fail, the sender/'s anonymity is reduced to pieces. In this paper, we propose a novel approach for sending truly anonymous messages over the Internet where the anonymous message is sent from a PDA which uses dynamically assigned temporary, non-personal, random IP and MAC addresses. Anonymous E-cash is used to pay for the service.

  19. Radial Mixing in Turbomachines

    DTIC Science & Technology

    1991-03-31

    Belgium March 31, 1991 Final Scientific Report June 1, 1989 - July 31, 1990 VUB -STR -17 Approved for public release; distribution unlimited. - Prepared ...secondary flows and turbulence as sources of mixing was investigated by conducting experiments using hot-wire anemometry and ehtylene tracer gas

  20. DNA logic gates.

    PubMed

    Okamoto, Akimitsu; Tanaka, Kazuo; Saito, Isao

    2004-08-04

    A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine ((MD)A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an (MD)A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite (MD)A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through (MD)A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple (MD)A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.

  1. 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.

  2. Mixing by individual swimmers

    NASA Astrophysics Data System (ADS)

    Pushkin, Dmitri; Shum, Henry; Yeomans, Julia

    2012-11-01

    Despite their evolutionary and technological importance, different biomixing mechanisms, their effectiveness and universality remain poorly understood. In this talk we focus on the Lagrangian transport of the surrounding fluid by swimmers. Low Re passive tracers advected by swimmers move in loops that are, in general, almost closed. We analyze the reasons for this behavior and, as non-closedness of the loops is a natural requirement for an efficient mixing, propose a classification of possible mechanisms for biogenic mixing. Next, we discuss the universal (common to all swimmers) and the swimmer-dependent features of the resulting tracer displacements and analyze the Darwin drift, the total fluid volume displaced by a swimmer passing from and to infinity. We show that the Darwin drift is finite for force-free swimmers and can be decomposed into a universal and a swimmer-dependent part. We illustrate our consideration with examples for model swimmers and biological data.

  3. Experiments in mixed reality

    NASA Astrophysics Data System (ADS)

    Krum, David M.; Sadek, Ramy; Kohli, Luv; Olson, Logan; Bolas, Mark

    2010-01-01

    As part of the Institute for Creative Technologies and the School of Cinematic Arts at the University of Southern California, the Mixed Reality lab develops technologies and techniques for presenting realistic immersive training experiences. Such experiences typically place users within a complex ecology of social actors, physical objects, and collections of intents, motivations, relationships, and other psychological constructs. Currently, it remains infeasible to completely synthesize the interactivity and sensory signatures of such ecologies. For this reason, the lab advocates mixed reality methods for training and conducts experiments exploring such methods. Currently, the lab focuses on understanding and exploiting the elasticity of human perception with respect to representational differences between real and virtual environments. This paper presents an overview of three projects: techniques for redirected walking, displays for the representation of virtual humans, and audio processing to increase stress.

  4. Magnetically driven surface mixing

    NASA Astrophysics Data System (ADS)

    Belkin, M.; Snezhko, A.; Aranson, I. S.; Kwok, W.-K.

    2009-07-01

    Magnetic microparticles suspended on the surface of liquid and energized by vertical alternating magnetic field exhibit complex collective behavior. Various immobile and self-propelled self-assembled structures have been observed. Here, we report on experimental studies of mixing and surface diffusion processes in this system. We show that the pattern-induced surface flows have properties of quasi-two-dimensional turbulence. Correspondingly, the surface advection of tracer particle exhibits properties of Brownian diffusion.

  5. Flows, Turbulence, and Mixing

    NASA Astrophysics Data System (ADS)

    Lazarian, Alex

    2003-07-01

    HST and FUSE spectra of distant UV-bright sources reveal interstellar absorption lines of high stages of ionization {O VI, C IV, N V, Si IV} arising in many different astrophysical environments such as superbubbles, interstellar chimneys, high-velocity clouds, galaxy halos and cosmic filaments. Turbulence, always present in the magnetized ISM, must mix the hot { 10^6 K} gas with cooler gas within "turbulent mixing layers". Present theory, based on 1D steady-state flows, suggest the line ratios in these layers differ significantly from photoionized gas, radiative shocks, cooling zones, or conduction fronts. These models are use to infer mass and energy fluxes important to understanding the ISM. We propose to develop a suite of 3D time-dependent models that properly calculate turbulent mixing. We will produce synthetic UV absorption lines and optical emission lines directly relevant to HST observations that use GHRS, STIS, and eventually, COS. These models will allow us to explore the sensitivity of the spectral diagnostics to magnetic field strength, turbulence intensity, and relative velocity of the hot and cold gas. We will publish the resulting grid of spectral diagnostics and make them available through the Web.

  6. Stochastic neutrino mixing mechanism

    NASA Astrophysics Data System (ADS)

    Guzzo, M. M.; de Holanda, P. C.; Peres, O. L. G.; Zavanin, E. M.

    2013-05-01

    We propose a mechanism which provides an explanation of the Gallium and antineutrino reactor anomalies. Differently from original Pontecorvo’s hypothesis, this mechanism is based on the phenomenological assumption in which the admixture of neutrino mass eigenstates in the moments of neutrino creation and detection can assume different configurations around the admixture parametrized by the usual values of the mixing angles θ12, θ23, and θ13. For simplicity, we assume a Gaussian distribution for the mixing angles in such a way that the average value of this distribution is given by the usual values of the mixing angles, and the width of the Gaussian is denoted by α. We show that the proposed mechanism provides a possible explanation for very short-baseline neutrino disappearance, necessary to accommodate Gallium and antineutrino reactor anomalies, which is not allowed in usual neutrino oscillations based on Pontecorvo’s original hypotheses. We also can describe high-energy oscillation experiments, like LSND, Fermi, and NuTeV, assuming a weakly energy dependent width parameter, α(E), that nicely fits all experimental results.

  7. Mixing kaons with mixed action chiral perturbation theory

    NASA Astrophysics Data System (ADS)

    Aubin, Christopher

    2006-12-01

    We calculate the neutral kaon mixing parameter, BK , to next-to-leading order in mixed action (domain-wall valence with staggered sea quarks) chiral perturbation theory. We find the expres- sion for BK in this mixed-action case only differs from the continuum partially quenched expres- sion by an additional analytic term. Additionally, in preparation for a lattice calculation of BK with a mixed action, we discuss quantitatively the effects of the taste violations as well as finite volume effects.

  8. Heteroplasmy of chloroplast DNA in Medicago.

    PubMed

    Johnson, L B; Palmer, J D

    1989-01-01

    Two chloroplast DNA (cpDNA) regions exhibiting a high frequency of intra- or inter-species variation were identified in 12 accessions of the genus Medicago. Restriction maps of both regions were prepared for alfalfa, and the probable nature of the events causing the DNA differences was identified. Specific DNA fragments were then cloned for use in identification of variants in each region. Two each of M. sativa ssp. varia and ssp. caerulea and one of six M. sativa ssp. sativa single plants examined possessed cpDNA heterogeneity as identified by screening extracts for fragments generated by the presence and absence of a specific Xba I restriction site. Three plants of M. sativa ssp. sativa, two of each of sspp. varia and caerulea, and three M. scutellata were also examined for single-plant cpDNA heterogeneity at a hypervariable region where differences resulted from small insertion-deletion events. A single M. scutellata plant with mixed cpDNAs was identified. Sorting out was seen when one spp. sativa plant with mixed plastid types identifiable by the Xba I restriction site difference was vegetatively propagated. This indicated that the initial stock plant was heteroplastidic. Controlled crosses will be required in order to test whether heteroplasmy results from chloroplast transmission in the pollen and to examine the dynamic of sorting out. However, heteroplasmy is apparently not a rare situation in Medicago.

  9. Rapid and Sensitive PCR-Dipstick DNA Chromatography for Multiplex Analysis of the Oral Microbiota

    PubMed Central

    Niwa, Kousuke; Kawase, Mitsuo; Tanner, Anne C. R.; Takahashi, Nobuhiro

    2014-01-01

    A complex of species has been associated with dental caries under the ecological hypothesis. This study aimed to develop a rapid, sensitive PCR-dipstick DNA chromatography assay that could be read by eye for multiplex and semiquantitative analysis of plaque bacteria. Parallel oligonucleotides were immobilized on a dipstick strip for multiplex analysis of target DNA sequences of the caries-associated bacteria, Streptococcus mutans, Streptococcus sobrinus, Scardovia wiggsiae, Actinomyces species, and Veillonella parvula. Streptavidin-coated blue-colored latex microspheres were to generate signal. Target DNA amplicons with an oligonucleotide-tagged terminus and a biotinylated terminus were coupled with latex beads through a streptavidin-biotin interaction and then hybridized with complementary oligonucleotides on the strip. The accumulation of captured latex beads on the test and control lines produced blue bands, enabling visual detection with the naked eye. The PCR-dipstick DNA chromatography detected quantities as low as 100 pg of DNA amplicons and demonstrated 10- to 1000-fold higher sensitivity than PCR-agarose gel electrophoresis, depending on the target bacterial species. Semiquantification of bacteria was performed by obtaining a series of chromatograms using serial 10-fold dilution of PCR-amplified DNA extracted from dental plaque samples. The assay time was less than 3 h. The semiquantification procedure revealed the relative amounts of each test species in dental plaque samples, indicating that this disposable device has great potential in analysis of microbial composition in the oral cavity and intestinal tract, as well as in point-of-care diagnosis of microbiota-associated diseases. PMID:25485279

  10. MixSIAR: advanced stable isotope mixing models in R

    EPA Science Inventory

    Background/Question/Methods The development of stable isotope mixing models has coincided with modeling products (e.g. IsoSource, MixSIR, SIAR), where methodological advances are published in parity with software packages. However, while mixing model theory has recently been ex...

  11. 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.

  12. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    PubMed Central

    Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R; Amaral-Zettler, Linda; Gilbert, Jack A; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-Serra, Philippe; Sterk, Peter; Arumugam, Manimozhiyan; Bailey, Mark; Baumgartner, Laura; Birren, Bruce W; Blaser, Martin J; Bonazzi, Vivien; Booth, Tim; Bork, Peer; Bushman, Frederic D; Buttigieg, Pier Luigi; Chain, Patrick S G; Charlson, Emily; Costello, Elizabeth K; Huot-Creasy, Heather; Dawyndt, Peter; DeSantis, Todd; Fierer, Noah; Fuhrman, Jed A; Gallery, Rachel E; Gevers, Dirk; Gibbs, Richard A; Gil, Inigo San; Gonzalez, Antonio; Gordon, Jeffrey I; Guralnick, Robert; Hankeln, Wolfgang; Highlander, Sarah; Hugenholtz, Philip; Jansson, Janet; Kau, Andrew L; Kelley, Scott T; Kennedy, Jerry; Knights, Dan; Koren, Omry; Kuczynski, Justin; Kyrpides, Nikos; Larsen, Robert; Lauber, Christian L; Legg, Teresa; Ley, Ruth E; Lozupone, Catherine A; Ludwig, Wolfgang; Lyons, Donna; Maguire, Eamonn; Methé, Barbara A; Meyer, Folker; Muegge, Brian; Nakielny, Sara; Nelson, Karen E; Nemergut, Diana; Neufeld, Josh D; Newbold, Lindsay K; Oliver, Anna E; Pace, Norman R; Palanisamy, Giriprakash; Peplies, Jörg; Petrosino, Joseph; Proctor, Lita; Pruesse, Elmar; Quast, Christian; Raes, Jeroen; Ratnasingham, Sujeevan; Ravel, Jacques; Relman, David A; Assunta-Sansone, Susanna; Schloss, Patrick D; Schriml, Lynn; Sinha, Rohini; Smith, Michelle I; Sodergren, Erica; Spor, Aymé; Stombaugh, Jesse; Tiedje, James M; Ward, Doyle V; Weinstock, George M; Wendel, Doug; White, Owen; Whiteley, Andrew; Wilke, Andreas; Wortman, Jennifer R; Yatsunenko, Tanya; Glöckner, Frank Oliver

    2012-01-01

    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere. PMID:21552244

  13. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

    PubMed

    Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R; Amaral-Zettler, Linda; Gilbert, Jack A; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-Serra, Philippe; Sterk, Peter; Arumugam, Manimozhiyan; Bailey, Mark; Baumgartner, Laura; Birren, Bruce W; Blaser, Martin J; Bonazzi, Vivien; Booth, Tim; Bork, Peer; Bushman, Frederic D; Buttigieg, Pier Luigi; Chain, Patrick S G; Charlson, Emily; Costello, Elizabeth K; Huot-Creasy, Heather; Dawyndt, Peter; DeSantis, Todd; Fierer, Noah; Fuhrman, Jed A; Gallery, Rachel E; Gevers, Dirk; Gibbs, Richard A; San Gil, Inigo; Gonzalez, Antonio; Gordon, Jeffrey I; Guralnick, Robert; Hankeln, Wolfgang; Highlander, Sarah; Hugenholtz, Philip; Jansson, Janet; Kau, Andrew L; Kelley, Scott T; Kennedy, Jerry; Knights, Dan; Koren, Omry; Kuczynski, Justin; Kyrpides, Nikos; Larsen, Robert; Lauber, Christian L; Legg, Teresa; Ley, Ruth E; Lozupone, Catherine A; Ludwig, Wolfgang; Lyons, Donna; Maguire, Eamonn; Methé, Barbara A; Meyer, Folker; Muegge, Brian; Nakielny, Sara; Nelson, Karen E; Nemergut, Diana; Neufeld, Josh D; Newbold, Lindsay K; Oliver, Anna E; Pace, Norman R; Palanisamy, Giriprakash; Peplies, Jörg; Petrosino, Joseph; Proctor, Lita; Pruesse, Elmar; Quast, Christian; Raes, Jeroen; Ratnasingham, Sujeevan; Ravel, Jacques; Relman, David A; Assunta-Sansone, Susanna; Schloss, Patrick D; Schriml, Lynn; Sinha, Rohini; Smith, Michelle I; Sodergren, Erica; Spo, Aymé; Stombaugh, Jesse; Tiedje, James M; Ward, Doyle V; Weinstock, George M; Wendel, Doug; White, Owen; Whiteley, Andrew; Wilke, Andreas; Wortman, Jennifer R; Yatsunenko, Tanya; Glöckner, Frank Oliver

    2011-05-01

    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

  14. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

    SciTech Connect

    Yilmaz, P.; Kottmann, R.; Field, D.; Knight, R.; Cole, J. R.; Amaral-Zettler, L.; Gilbert, J. A.

    2011-05-01

    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences - the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

  15. Error Estimates for Mixed Methods.

    DTIC Science & Technology

    1979-03-01

    This paper presents abstract error estimates for mixed methods for the approximate solution of elliptic boundary value problems. These estimates are...then applied to obtain quasi-optimal error estimates in the usual Sobolev norms for four examples: three mixed methods for the biharmonic problem and a mixed method for 2nd order elliptic problems. (Author)

  16. Magnetically coupled system for mixing

    SciTech Connect

    Miller, III, Harlan; Meichel, George; Legere, Edward; Malkiel, Edwin; Woods, Robert Paul; Ashley, Oliver; Katz, Joseph; Ward, Jason; Petersen, Paul

    2014-04-01

    The invention provides a mixing system comprising a magnetically coupled drive system and a foil for cultivating algae, or cyanobacteria, in an open or enclosed vessel. The invention provides effective mixing, low energy usage, low capital expenditure, and ease of drive system component maintenance while maintaining the integrity of a sealed mixing vessel.

  17. Magnetically coupled system for mixing

    DOEpatents

    Miller, III, Harlan; Meichel, George; Legere, Edward; Malkiel, Edwin; Woods, Robert Paul; Ashley, Oliver; Katz, Joseph; Ward, Jason; Petersen, Paul

    2015-09-22

    The invention provides a mixing system comprising a magnetically coupled drive system and a foil for cultivating algae, or cyanobacteria, in an open or enclosed vessel. The invention provides effective mixing, low energy usage, low capital expenditure, and ease of drive system component maintenance while maintaining the integrity of a sealed mixing vessel.

  18. 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.

  19. B Lifetimes and Mixing

    SciTech Connect

    Evans, Harold G.; /Indiana U.

    2009-05-01

    The Tevatron experiments, CDF and D0, have produced a wealth of new B-physics results since the start of Run II in 2001. We've observed new B-hadrons, seen new effects, and increased many-fold the precision with which we know the properties of b-quark systems. In these proceedings, we will discuss two of the most fruitful areas in the Tevatron B-physics program: lifetimes and mixing. We'll examine the experimental issues driving these analyses, present a summary of the latest results, and discuss prospects for the future.

  20. 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

  1. 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.

  2. Detection and mapping of homologous, repeated and amplified DNA sequences by DNA renaturation in agarose gels.

    PubMed Central

    Roninson, I B

    1983-01-01

    A new molecular hybridization approach to the analysis of complex genomes has been developed. Tracer and driver DNAs were digested with the same restriction enzyme(s), and tracer DNA was labeled with 32P using T4 DNA polymerase. Tracer DNA was mixed with an excess amount of driver, and the mixture was electrophoresed in an agarose gel. Following electrophoresis, DNA was alkali-denatured in situ and allowed to reanneal in the gel, so that tracer DNA fragments could hybridize to the driver only when homologous driver DNA sequences were present at the same place in the gel, i.e. within a restriction fragment of the same size. After reannealing, unhybridized single-stranded DNA was digested in situ with S1 nuclease. The hybridized tracer DNA was detected by autoradiography. The general applicability of this technique was demonstrated in the following experiments. The common EcoRI restriction fragments were identified in the genomes of E. coli and four other species of bacteria. Two of these fragments are conserved in all Enterobacteriaceae. In other experiments, repeated EcoRI fragments of eukaryotic DNA were visualized as bands of various intensity after reassociation of a total genomic restriction digest in the gel. The situation of gene amplification was modeled by the addition of varying amounts of lambda phage DNA to eukaryotic DNA prior to restriction enzyme digestion. Restriction fragments of lambda DNA were detectable at a ratio of 15 copies per chicken genome and 30 copies per human genome. This approach was used to detect amplified DNA fragments in methotrexate (MTX)-resistant mouse cells and to identify commonly amplified fragments in two independently derived MTX-resistant lines. Images PMID:6310499

  3. 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.

  4. 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.

  5. Collisional atomic mixing

    NASA Astrophysics Data System (ADS)

    Biersack, Jochen P.

    The collisional mixing of thin metal markers in silicon is investigated with the computer program TRIM-DYNAMIC (T-DYN). This code assumes that at high dose irradiation, the substrate Si or Ge, will get fully amorphized, and the recoil atom can stop in any position after slowing down below a certain final energy Ef (taken here as 3 eV). In order to avoid chemical effects, the system Au marker in a silicon matrix was chosen for the TRIM simulation. The results are in good agreement with the experimental findings, as compiled in the review article by Paine and Averback. Similar collisional mixing effects occur in the process of SIMS or Auger electron depth profiling, and cannot be avoided. An example is given here for a thin layer of arsenic vapor deposited on Si and covered by amorphous silicon. The analysing ion beam in this case was 14.5 keV Cs+ incident at 37° towards the surface normal. In comparison with the SIMS measurements by modern depth profiling equipment, again good agreement was found between the T-DYN results and the experiment.

  6. Transition mixing study

    NASA Technical Reports Server (NTRS)

    Reynolds, R.; White, C.

    1986-01-01

    A computer model capable of analyzing the flow field in the transition liner of small gas turbine engines is developed. A FORTRAN code has been assembled from existing codes and physical submodels and used to predict the flow in several test geometries which contain characteristics similar to transition liners, and for which experimental data was available. Comparisons between the predictions and measurements indicate that the code produces qualitative results but that the turbulence models, both K-E and algebraic Reynolds Stress, underestimate the cross-stream diffusion. The code has also been used to perform a numerical experiment to examine the effect of a variety of parameters on the mixing process in transition liners. Comparisons illustrate that geometries with significant curvature show a drift of the jet trajectory toward the convex wall and weaker wake region vortices and decreased penetration for jets located on the convex wall of the liner, when compared to jets located on concave walls. Also shown were the approximate equivalency of angled slots and round holes and a technique by which jet mixing correlations developed for rectangular channels can be used for can geometries.

  7. Wave mixing spectroscopy

    SciTech Connect

    Smith, R.W.

    1980-08-01

    Several new aspects of nonlinear or wave mixing spectroscopy were investigated utilizing the polarization properties of the nonlinear output field and the dependence of this field upon the occurrence of multiple resonances in the nonlinear susceptibility. First, it is shown theoretically that polarization-sensitive detection may be used to either eliminate or controllably reduce the nonresonant background in coherent anti-Stokes Raman spectroscopy, allowing weaker Raman resonances to be studied. The features of multi-resonant four-wave mixing are examined in the case of an inhomogeneously broadened medium. It is found that the linewidth of the nonlinear output narrows considerably (approaching the homogeneous width) when the quantum mechanical expressions for the doubly- and triply-resonant susceptibilities are averaged over a Doppler or strain broadened profile. Experimental studies of nonlinear processes in Pr/sup +3/:LaF/sub 3/ verify this linewidth narrowing, but indicate that this strain broadened system cannot be treated with a single broadening parameter as in the case of Doppler broadening in a gas. Several susceptibilities are measured from which are deduced dipole matrix elements and Raman polarizabilities related to the /sup 3/H/sub 4/, /sup 3/H/sub 6/, and /sup 3/P/sub 0/ levels of the praseodymium ions.

  8. Solute-solvent interactions in micellar electrokinetic chromatography. 6. Optimization of the selectivity of lithium dodecyl sulfate-lithium perfluorooctanesulfonate mixed micellar buffers.

    PubMed

    Fuguet, Elisabet; Ràfols, Clara; Torres-Lapasió, José Ramón; García-Alvarez-Coque, María Celia; Bosch, Elisabeth; Rosés, Martí

    2002-09-01

    The optimization of the composition of mixed surfactants used as micellar electrokinetic chromatography (MEKC) pseudostationary phases is proposed as an effective method for the separation of complex mixtures of analytes. The solvation parameter model is used to select two surfactants (lithium dodecyl sulfate, LDS, and lithium perfluorooctanesulfonate, LPFOS) with contrasting solvation properties. Combination of these two surfactants allows variations of the solvation properties of MEKC pseudostationary phase along a wide range. Thus, the convenient variation of the proportion of both surfactants allows an effective control of the selectivity in such systems. An algorithm that predicts the overall resolution of a given mixture of compounds is described and applied to optimize the composition of the mixed surfactant for the separation of the mixture. The algorithm is based on the calculation of peak purities on simulated chromatograms as a function of the composition of the mixed LDS/LPFOS micellar buffer from data at several micellar buffer compositions. Successful separations were achieved for mixtures containing up to 20 compounds, in less than 12 min.

  9. 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.

  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. [Application of fingerprint chromatogram in quality assessment of apple cider].

    PubMed

    Xu, Kangzhen; Song, Jirong; Ren, Yinghui; Ma, Haixia; Huang, Jie; Du, Xiaodan

    2007-01-01

    Fingerprints of 14 apple cider samples from different manufacturers were studied using high performance liquid chromatography (HPLC) with an electrochemical detector (ECD). The analysis was carried out on a Zorbax SB-C18 column at 30 degrees C with 2% (v/v) methanol aqueous solution-4% (v/v) acetic acid aqueous solution as mobile phase at a flow rate of 0.8 mL/min. The electrochemical detector was set at 0.7 V. By calculating the relative retention times of certain peaks with chlorogenic acid as the reference standard, 8 common peaks in the samples were analyzed. Relative retention times for the common peaks of various samples were calculated, and the similarities of all the samples were figured out through each peak area with the vectorial angle cosine method and correlative coefficient method. The results indicated that apple cider products of the same manufacturer have good similarity, with the similarities greater than 92.7%. According to this experiment, effectual microcosmic information for apple cider analysis was gained through HPLC and ECD. Moreover, this test method will help the analysis and the control of product quality, the development of new products and the establishment of trade standard.

  13. 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

  14. Mixed methods, mixed methodology health services research in practice.

    PubMed

    Johnstone, P Lynne

    2004-02-01

    Mixed methods, mixed methodology research is a little documented but increasingly accepted approach employed to investigate organizational phenomena. The author presents a synthesis of literature that informed the decision to adopt a mixed methods, mixed methodology, dominantly naturalistic study approach to health services research in which she explored the process and organizational consequences of new artifact adoption in surgery. She describes the way whereby a collective case study involving five Australian hospitals yielded quantitative and qualitative data that were analyzed using inductive and/or deductive reasoning. She goes beyond the theoretical rational for employing a mixed methods, mixed methodology approach to present a summative conceptual model of the research process and describe the structural aspects of the dissertation in which the research was reported that should benefit researchers contemplating the value of such an approach.

  15. Separation of Short Single- and Double-Stranded DNA Based on Their Adsorption Kinetics Difference on Graphene Oxide

    PubMed Central

    Huang, Po-Jung Jimmy; Liu, Juewen

    2013-01-01

    Separation of short single- and double-stranded DNA typically requires gel electrophoresis followed by DNA extraction, which is a time consuming process. Graphene oxide adsorbs single-stranded DNA more quickly than double-stranded ones, allowing for selective removal of the former with a simple mixing and centrifugation operation. The effect of DNA length and salt on adsorption selectivity has been characterized and its application in DNA melting curve measurement has been demonstrated.

  16. Mixed Mode Matrix Multiplication

    SciTech Connect

    Meng-Shiou Wu; Srinivas Aluru; Ricky A. Kendall

    2004-09-30

    In modern clustering environments where the memory hierarchy has many layers (distributed memory, shared memory layer, cache,...), an important question is how to fully utilize all available resources and identify the most dominant layer in certain computations. When combining algorithms on all layers together, what would be the best method to get the best performance out of all the resources we have? Mixed mode programming model that uses thread programming on the shared memory layer and message passing programming on the distributed memory layer is a method that many researchers are using to utilize the memory resources. In this paper, they take an algorithmic approach that uses matrix multiplication as a tool to show how cache algorithms affect the performance of both shared memory and distributed memory algorithms. They show that with good underlying cache algorithm, overall performance is stable. When underlying cache algorithm is bad, superlinear speedup may occur, and an increasing number of threads may also improve performance.

  17. Radioactive mixed waste disposal

    SciTech Connect

    Jasen, W.G.; Erpenbeck, E.G.

    1993-02-01

    Various types of waste have been generated during the 50-year history of the Hanford Site. Regulatory changes in the last 20 years have provided the emphasis for better management of these wastes. Interpretations of the Atomic Energy Act of 1954 (AEA), the Resource Conservation and Recovery Act of 1976 (RCRA), and the Hazardous and Solid Waste Amendments (HSWA) have led to the definition of radioactive mixed wastes (RMW). The radioactive and hazardous properties of these wastes have resulted in the initiation of special projects for the management of these wastes. Other solid wastes at the Hanford Site include low-level wastes, transuranic (TRU), and nonradioactive hazardous wastes. This paper describes a system for the treatment, storage, and disposal (TSD) of solid radioactive waste.

  18. Biogenic inputs to ocean mixing.

    PubMed

    Katija, Kakani

    2012-03-15

    Recent studies have evoked heated debate about whether biologically generated (or biogenic) fluid disturbances affect mixing in the ocean. Estimates of biogenic inputs have shown that their contribution to ocean mixing is of the same order as winds and tides. Although these estimates are intriguing, further study using theoretical, numerical and experimental techniques is required to obtain conclusive evidence of biogenic mixing in the ocean. Biogenic ocean mixing is a complex problem that requires detailed understanding of: (1) marine organism behavior and characteristics (i.e. swimming dynamics, abundance and migratory behavior), (2) mechanisms utilized by swimming animals that have the ability to mix stratified fluids (i.e. turbulence and fluid drift) and (3) knowledge of the physical environment to isolate contributions of marine organisms from other sources of mixing. In addition to summarizing prior work addressing the points above, observations on the effect of animal swimming mode and body morphology on biogenic fluid transport will also be presented. It is argued that to inform the debate on whether biogenic mixing can contribute to ocean mixing, our studies should focus on diel vertical migrators that traverse stratified waters of the upper pycnocline. Based on our understanding of mixing mechanisms, body morphologies, swimming modes and body orientation, combined with our knowledge of vertically migrating populations of animals, it is likely that copepods, krill and some species of gelatinous zooplankton and fish have the potential to be strong sources of biogenic mixing.

  19. Fluid mixing in stratified gravity currents: the Prandtl mixing length.

    PubMed

    Odier, P; Chen, J; Rivera, M K; Ecke, R E

    2009-04-03

    Shear-induced vertical mixing in a stratified flow is a key ingredient of thermohaline circulation. We experimentally determine the vertical flux of momentum and density of a forced gravity current using high-resolution velocity and density measurements. A constant eddy-viscosity model provides a poor description of the physics of mixing, but a Prandtl mixing length model relating momentum and density fluxes to mean velocity and density gradients works well. For the average gradient Richardson number Ri(g) approximately 0.08 and a Taylor Reynolds number Re(lambda) approximately 100, the mixing lengths are fairly constant, about the same magnitude, comparable to the turbulent shear length.

  20. On the correlation between phase evolution of lipoplexes/anionic lipid mixtures and DNA release

    NASA Astrophysics Data System (ADS)

    Caracciolo, Giulio; Pozzi, Daniela; Caminiti, Ruggero; Marchini, Cristina; Montani, Maura; Amici, Augusto; Amenitsch, Heinz

    2007-10-01

    We investigated the structural evolution of three lipoplex formulations when interacting with anionic lipids by synchrotron small angle x-ray diffraction, while the extent of DNA release from lipoplexes by anionic lipids was evaluated by gel electrophoresis. Lipoplexes formed lamellar phases when mixed with anionic dioleoylphosphatidylglycerol (DOPG), while promoting the formation of nonbilayer structures when mixed with anionic dioleoylphosphatidic acid (DOPA). However, lipoplexes exhibited a virtually identical extent of DNA release when mixed with DOPG or DOPA. Thus, the recently proposed correlation between the formation of nonlamellar phases in lipoplex/anionic lipid mixtures and the increase of DNA release does not seem to exist.

  1. The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme of escherichia coli.

    PubMed Central

    Burgers, P M; Kornberg, A; Sakakibara, Y

    1981-01-01

    An Escherichia coli mutant, dnaN59, stops DNA synthesis promptly upon a shift to a high temperature; the wild-type dnaN gene carried in a transducing phage encodes a polypeptide of about 41,000 daltons [Sakakibara, Y. & Mizukami, T. (1980) Mol. Gen. Genet. 178, 541-553; Yuasa, S. & Sakakibara, Y. (1980) Mol. Gen. Genet. 180, 267-273]. We now find that the product of dnaN gene is the beta subunit of DNA polymerase III holoenzyme, the principal DNA synthetic multipolypeptide complex in E. coli. The conclusion is based on the following observations: (i) Extracts from dnaN59 cells were defective in phage phi X174 and G4 DNA synthesis after the mutant cells had been exposed to the increased temperature. (ii) The enzymatic defect was overcome by addition of purified beta subunit but not by other subunits of DNA polymerase III holoenzyme or by other replication proteins required for phi X174 DNA synthesis. (iii) Partially purified beta subunit from the dnaN mutant, unlike that from the wild type, was inactive in reconstituting the holoenzyme when mixed with the other purified subunits. (iv) Increased dosage of the dnaN gene provided by a plasmid carrying the gene raised cellular levels of the beta subunit 5- to 6-fold. PMID:6458041

  2. The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme of escherichia coli.

    PubMed

    Burgers, P M; Kornberg, A; Sakakibara, Y

    1981-09-01

    An Escherichia coli mutant, dnaN59, stops DNA synthesis promptly upon a shift to a high temperature; the wild-type dnaN gene carried in a transducing phage encodes a polypeptide of about 41,000 daltons [Sakakibara, Y. & Mizukami, T. (1980) Mol. Gen. Genet. 178, 541-553; Yuasa, S. & Sakakibara, Y. (1980) Mol. Gen. Genet. 180, 267-273]. We now find that the product of dnaN gene is the beta subunit of DNA polymerase III holoenzyme, the principal DNA synthetic multipolypeptide complex in E. coli. The conclusion is based on the following observations: (i) Extracts from dnaN59 cells were defective in phage phi X174 and G4 DNA synthesis after the mutant cells had been exposed to the increased temperature. (ii) The enzymatic defect was overcome by addition of purified beta subunit but not by other subunits of DNA polymerase III holoenzyme or by other replication proteins required for phi X174 DNA synthesis. (iii) Partially purified beta subunit from the dnaN mutant, unlike that from the wild type, was inactive in reconstituting the holoenzyme when mixed with the other purified subunits. (iv) Increased dosage of the dnaN gene provided by a plasmid carrying the gene raised cellular levels of the beta subunit 5- to 6-fold.

  3. 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.

  4. 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

  5. Low-energy plasma immersion ion implantation to induce DNA transfer into bacterial E. coli

    NASA Astrophysics Data System (ADS)

    Sangwijit, K.; Yu, L. D.; Sarapirom, S.; Pitakrattananukool, S.; Anuntalabhochai, S.

    2015-12-01

    Plasma immersion ion implantation (PIII) at low energy was for the first time applied as a novel biotechnology to induce DNA transfer into bacterial cells. Argon or nitrogen PIII at low bias voltages of 2.5, 5 and 10 kV and fluences ranging from 1 × 1012 to 1 × 1017 ions/cm2 treated cells of Escherichia coli (E. coli). Subsequently, DNA transfer was operated by mixing the PIII-treated cells with DNA. Successes in PIII-induced DNA transfer were demonstrated by marker gene expressions. The induction of DNA transfer was ion-energy, fluence and DNA-size dependent. The DNA transferred in the cells was confirmed functioning. Mechanisms of the PIII-induced DNA transfer were investigated and discussed in terms of the E. coli cell envelope anatomy. Compared with conventional ion-beam-induced DNA transfer, PIII-induced DNA transfer was simpler with lower cost but higher efficiency.

  6. Estimating beta-mixing coefficients

    PubMed Central

    McDonald, Daniel J.; Shalizi, Cosma Rohilla; Schervish, Mark

    2015-01-01

    The literature on statistical learning for time series assumes the asymptotic independence or “mixing” of the data-generating process. These mixing assumptions are never tested, and there are no methods for estimating mixing rates from data. We give an estimator for the beta-mixing rate based on a single stationary sample path and show it is L1-risk consistent. PMID:26279742

  7. Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

    DOEpatents

    Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

    2010-05-04

    A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

  8. Optimal broadcasting of mixed states

    SciTech Connect

    Dang Guifang; Fan Heng

    2007-08-15

    The N to M (M{>=}N) universal quantum broadcasting of mixed states {rho}{sup xN} is proposed for a qubit system. The broadcasting of mixed states is universal and optimal in the sense that the shrinking factor is independent of the input state and achieves the upper bound. The quantum broadcasting of mixed qubits is a generalization of the universal quantum cloning machine for identical pure input states. A pure state decomposition of the identical mixed qubits {rho}{sup xN} is obtained.

  9. Overview of Neutrino Mixing Models and Their Mixing Angle Predictions

    SciTech Connect

    Albright, Carl H.

    2009-11-01

    An overview of neutrino-mixing models is presented with emphasis on the types of horizontal flavor and vertical family symmetries that have been invoked. Distributions for the mixing angles of many models are displayed. Ways to differentiate among the models and to narrow the list of viable models are discussed.

  10. Mixed voltage VLSI design

    NASA Technical Reports Server (NTRS)

    Panwar, Ramesh; Rennels, David; Alkalaj, Leon

    1993-01-01

    A technique for minimizing the power dissipated in a Very Large Scale Integration (VLSI) chip by lowering the operating voltage without any significant penalty in the chip throughput even though low voltage operation results in slower circuits. Since the overall throughput of a VLSI chip depends on the speed of the critical path(s) in the chip, it may be possible to sustain the throughput rates attained at higher voltages by operating the circuits in the critical path(s) with a high voltage while operating the other circuits with a lower voltage to minimize the power dissipation. The interface between the gates which operate at different voltages is crucial for low power dissipation since the interface may possibly have high static current dissipation thus negating the gains of the low voltage operation. The design of a voltage level translator which does the interface between the low voltage and high voltage circuits without any significant static dissipation is presented. Then, the results of the mixed voltage design using a greedy algorithm on three chips for various operating voltages are presented.

  11. Mixed oxide fuel development

    SciTech Connect

    Leggett, R.D.; Omberg, R.P.

    1987-05-08

    This paper describes the success of the ongoing mixed-oxide fuel development program in the United States aimed at qualifying an economical fuel system for liquid metal cooled reactors. This development has been the cornerstone of the US program for the past 20 years and has proceeded in a deliberate and highly disciplined fashion with high emphasis on fuel reliability and operational safety as major features of an economical fuel system. The program progresses from feature testing in EBR-II to qualifying full size components in FFTF under fully prototypic conditions to establish a basis for extending allowable lifetimes. The development program started with the one year (300 EFPD) core, which is the FFTF driver fuel, continued with the demonstration of a two year (600 EFPD) core and is presently evaluating a three year (900 EFPD) fuel system. All three of these systems, consistent with other LMR fuel programs around the world, use fuel pellets gas bonded to a cladding tube that is assembled into a bundle and fitted into a wrapper tube or duct for ease of insertion into a core. The materials of construction progressed from austenitic CW 316 SS to lower swelling austenitic D9 to non swelling ferritic/martensitic HT9. 6 figs., 2 tabs.

  12. In vitro transfection of plasmid DNA by cationized gelatin prepared from different amine compounds.

    PubMed

    Kushibiki, Toshihiro; Tomoshige, Ryuji; Iwanaga, Kazunori; Kakemi, Masawo; Tabata, Yasuhiko

    2006-01-01

    The objective of this paper is to compare the in vitro transfection efficiency of a luciferase plasmid DNA using cationized gelatin prepared from different amine compounds. The compounds used here were ethylenediamine, putrescine, spermidine and spermine, chemically introduced to the carboxyl group of gelatin for the cationization. Complexation of the cationized gelatin with the plasmid DNA was performed by simply mixing the two materials at various N+/P- mixing ratios (the molar number ratio of amino groups of gelatin to the phosphate groups of DNA) in aqueous solution. Gel retardation studies revealed that the formation of cationized-gelatin-plasmid DNA complexes depended on the N+/P- mixing ratio. The stronger interaction of plasmid DNA with the cationized gelatin of spermine compared to the other cationized gelatins was observed by an ethidium bromide intercalation assay and Scatchard binding analysis. When the transfection efficiency of plasmid DNA complexed with the various cationized gelatins at different N+/P- mixing ratios was evaluated for mouse L929 fibroblasts, the highest transfection efficiency was observed for the complex prepared from the cationized gelatin of spermine at a N+/P- mixing ratio of 2. The present study indicates that there is an optimal N+/P- mixing ratio and a type of amine compound or cationization extent of cationized gelatin to enhance the transfection efficiency of plasmid DNA.

  13. Flavonoid-DNA binding studies and thermodynamic parameters

    NASA Astrophysics Data System (ADS)

    Janjua, Naveed Kausar; Shaheen, Amber; Yaqub, Azra; Perveen, Fouzia; Sabahat, Sana; Mumtaz, Misbah; Jacob, Claus; Ba, Lalla Aicha; Mohammed, Hamdoon A.

    2011-09-01

    Interactional studies of new flavonoid derivatives (Fl) with chicken blood ds.DNA were investigated spectrophotometrically in DMSO-H 2O (9:1 v/v) at various temperatures. Spectral parameters suggest considerable binding between the flavonoid derivatives studied and ds.DNA. The binding constant values lie in the enhanced-binding range. Thermodynamic parameters obtained from UV studies also point to strong spontaneous binding of Fl with ds.DNA. Viscometric studies complimented the UV results where a small linear increase in relative viscosity of the DNA solution was observed with added optimal flavonoid concentration. An overall mixed mode of interaction (intercalative plus groove binding) is proposed between DNA and flavonoids. Conclusively, investigated flavonoid derivatives are found to be strong DNA binders and seem to be promising drug candidates like their natural analogues.

  14. DNA analysis of fingernail clippings: an unusual case report.

    PubMed

    Song, Fangming; Liu, Yanjun; He, Qun; Hou, Wenmin; Wei, Feng; Liu, Liang

    2014-06-01

    The case of an unusual DNA analysis of fingernail clippings is described. A 20-year-old woman died of strangulation, and her former boyfriend entered the police's sight as suspect through rapid investigation and inspection. Genomic DNA from debris scraped underneath the suspect's fingernail was extracted 2 days after the incident using the modified DNA pretreatment method. Finally, mixed DNA profiles were observed from the suspect's fingernail clippings, one of them originating from the victim, which is consistent with the result of criminal investigation. With the support of strong evidence, the suspect soon confessed. In this case, it was really unusual in practice that fingernail debris extracted from the suspect was used to accuse the suspect himself. This case demonstrates the usefulness of the modified DNA pretreatment method and the possibility of getting DNA profiles from fingernail clippings with 2 days' lapse between the incident and recovery of the evidential material.

  15. 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.

  16. Mixing in polymeric microfluidic devices.

    SciTech Connect

    Schunk, Peter Randall; Sun, Amy Cha-Tien; Davis, Robert H.; Brotherton, Christopher M. (University of Colorado at Boulder, Boulder, CO)

    2006-04-01

    This SAND report describes progress made during a Sandia National Laboratories sponsored graduate fellowship. The fellowship was funded through an LDRD proposal. The goal of this project is development and characterization of mixing strategies for polymeric microfluidic devices. The mixing strategies under investigation include electroosmotic flow focusing, hydrodynamic focusing, physical constrictions and porous polymer monoliths. For electroosmotic flow focusing, simulations were performed to determine the effect of electroosmotic flow in a microchannel with heterogeneous surface potential. The heterogeneous surface potential caused recirculations to form within the microchannel. These recirculations could then be used to restrict two mixing streams and reduce the characteristic diffusion length. Maximum mixing occurred when the ratio of the mixing region surface potential to the average channel surface potential was made large in magnitude and negative in sign, and when the ratio of the characteristic convection time to the characteristic diffusion time was minimized. Based on these results, experiments were performed to evaluate the manipulation of surface potential using living-radical photopolymerization. The material chosen to manipulate typically exhibits a negative surface potential. Using living-radical surface grafting, a positive surface potential was produced using 2-(Dimethylamino)ethyl methacrylate and a neutral surface was produced using a poly(ethylene glycol) surface graft. Simulations investigating hydrodynamic focusing were also performed. For this technique, mixing is enhanced by using a tertiary fluid stream to constrict the two mixing streams and reduce the characteristic diffusion length. Maximum mixing occurred when the ratio of the tertiary flow stream flow-rate to the mixing streams flow-rate was maximized. Also, like the electroosmotic focusing mixer, mixing was also maximized when the ratio of the characteristic convection time to the

  17. Anomalous Sediment Mixing by Bioturbation

    NASA Astrophysics Data System (ADS)

    Roche, K. R.; Aubeneau, A. F.; Xie, M.; Packman, A. I.

    2013-12-01

    Bioturbation, the reworking of sediments by animals and plants, is the dominant mode of sediment mixing in low-energy environments, and plays an important role in sedimentary biogeochemical processes. Mixing resulting from bioturbation has historically been modeled as a diffusive process. However, diffusion models often do not provide a sufficient description of sediment mixing due to bioturbation. Stochastic models, such as the continuous time random walk (CTRW) model, provide more general descriptions of mixing behavior that are applicable even when regular diffusion assumptions are not met. Here we present results from an experimental investigation of anomalous sediment mixing by bioturbation in freshwater sediments. Clean and heavy-metal-contaminated sediments were collected from Lake DePue, a backwater lake of the Illinois River. The burrowing worm species Lumbriculus variegatus was introduced to homogenized Lake DePue sediments in aerated aquaria. We then introduced inert fine fluorescent particles to the sediment-water interface. Using time-lapse photography, we observed the mixing of the fluorescent particles into the sediment bed over a two-week period. We developed image analysis software to characterize the concentration distribution of the fluorescent particles as a function of sediment depth, and applied this to the time-series of images to evaluate sediment mixing. We fit a one-dimensional CTRW model to the depth profiles to evaluate the underlying statistical properties of the mixing behavior. This analysis suggests that the sediment mixing caused by L. variegatus burrowing is subdiffusive in time and superdiffusive in space. We also found that heavy metal contamination significantly reduces L. variegatus burrowing, causing increasingly anomalous sediment mixing. This result implies that there can be important feedbacks between sediment chemistry, organism behavior, and sediment mixing that are not considered in current environmental models.

  18. Toward Contactless Biology: Acoustophoretic DNA Transfection

    PubMed Central

    Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

    2016-01-01

    Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors. PMID:26828312

  19. Familial searching on DNA mixtures with dropout.

    PubMed

    Slooten, K

    2016-05-01

    Familial searching, the act of searching a database for a relative of an unknown individual whose DNA profile has been obtained, is usually restricted to cases where the DNA profile of that person has been unambiguously determined. Therefore, it is normally applied only with a good quality single source profile as starting point. In this article we investigate the performance of the method if applied to mixtures with and without allelic dropout, when likelihood ratios are computed with a semi-continuous (binary) model. We show that mixtures with dropout do not necessarily perform worse than mixtures without, especially if some separation between the donors is possible due to their different dropout probabilities. The familial searching true and false positive rates of mixed profiles on 15 loci are in some cases better than those of single source profiles on 10 loci. Thus, the information loss due to the fact that the person of interest's DNA has been mixed with that of other, and is affected by dropout, can be less than the loss of information corresponding to having 5 fewer loci available for a single source trace. Profiles typed on 10 autosomal loci are often involved in familial searching casework since many databases, including the Dutch one, in part consist of such profiles. Therefore, from this point of view, there seems to be no objection to extend familial searching to mixed or degraded profiles.

  20. Toward Contactless Biology: Acoustophoretic DNA Transfection

    NASA Astrophysics Data System (ADS)

    Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

    2016-02-01

    Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors.

  1. 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

  2. Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker

    PubMed Central

    Schneider, Kevin L.; Marrero, Glorimar; Alvarez, Anne M.; Presting, Gernot G.

    2011-01-01

    A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained

  3. Characterization of IS6110 insertions in the dnaA-dnaN intergenic region of Mycobacterium tuberculosis clinical isolates.

    PubMed

    Turcios, L; Casart, Y; Florez, I; de Waard, J; Salazar, L

    2009-02-01

    Mycobacterium tuberculosis isolates with identical IS6110 restriction fragment length polymorphism (RFLP) patterns are considered to be clonally related. The presence of IS6110 in the dnaA-dnaN intergenic region, one preferential locus for the integration of IS6110, was evaluated in 125 M. tuberculosis isolates. Five isolates had IS6110 inserted in this region, and two consisted of a mix of isogenic strains that putatively have evolved during a single infection. Strains from the same isolate had identical spoligo and mycobacterial interspersed repetitive unit-variable-number tandem repeat profiles, but had slight variations in IS6110 RFLP patterns, due to the presence of IS6110 in the dnaA-dnaN intergenic region. Duplication of the dnaA-dnaN intergenic region was found in one isogenic strain.

  4. Microfluidic mixing using contactless dielectrophoresis.

    PubMed

    Salmanzadeh, Alireza; Shafiee, Hadi; Davalos, Rafael V; Stremler, Mark A

    2011-09-01

    The first experimental evidence of mixing enhancement in a microfluidic system using contactless dielectrophoresis (cDEP) is presented in this work. Pressure-driven flow of deionized water containing 0.5 μm beads was mixed in various chamber geometries by imposing a dielectrophoresis (DEP) force on the beads. In cDEP the electrodes are not in direct contact with the fluid sample but are instead capacitively coupled to the mixing chamber through thin dielectric barriers, which eliminates many of the problems encountered with standard DEP. Four system designs with rectangular and circular mixing chambers were fabricated in PDMS. Mixing tests were conducted for flow rates from 0.005 to 1 mL/h subject to an alternating current signal range of 0-300 V at 100-600 kHz. When the time scales of the bulk fluid motion and the DEP motion were commensurate, rapid mixing was observed. The rectangular mixing chambers were found to be more efficient than the circular chambers. This approach shows potential for mixing low diffusivity biological samples, which is a very challenging problem in laminar flows at small scales.

  5. Mixed-Methods Research Methodologies

    ERIC Educational Resources Information Center

    Terrell, Steven R.

    2012-01-01

    Mixed-Method studies have emerged from the paradigm wars between qualitative and quantitative research approaches to become a widely used mode of inquiry. Depending on choices made across four dimensions, mixed-methods can provide an investigator with many design choices which involve a range of sequential and concurrent strategies. Defining…

  6. Mixed Waste Working Group report

    SciTech Connect

    Not Available

    1993-11-09

    The treatment of mixed waste remains one of this country`s most vexing environmental problems. Mixed waste is the combination of radioactive waste and hazardous waste, as defined by the Resource Conservation and Recovery Act (RCRA). The Department of Energy (DOE), as the country`s largest mixed waste generator, responsible for 95 percent of the Nation`s mixed waste volume, is now required to address a strict set of milestones under the Federal Facility Compliance Act of 1992. DOE`s earlier failure to adequately address the storage and treatment issues associated with mixed waste has led to a significant backlog of temporarily stored waste, significant quantities of buried waste, limited permanent disposal options, and inadequate treatment solutions. Between May and November of 1993, the Mixed Waste Working Group brought together stakeholders from around the Nation. Scientists, citizens, entrepreneurs, and bureaucrats convened in a series of forums to chart a course for accelerated testing of innovative mixed waste technologies. For the first time, a wide range of stakeholders were asked to examine new technologies that, if given the chance to be tested and evaluated, offer the prospect for better, safer, cheaper, and faster solutions to the mixed waste problem. In a matter of months, the Working Group has managed to bridge a gap between science and perception, engineer and citizen, and has developed a shared program for testing new technologies.

  7. Fern spore extracts can damage DNA

    PubMed Central

    Simán, S E; Povey, A C; Ward, T H; Margison, G P; Sheffield, E

    2000-01-01

    The carcinogenicity of the vegetative tissues of bracken fern (Pteridium) has long been established. More recently, the carcinogenic effects of the spores of bracken have also been recognized. Both vegetative tissues and spores of bracken can induce adducts in DNA in animal tissues, but the possible genotoxic or carcinogenic effects of spores from fern species other than bracken are unknown. The single-cell gel electrophoresis (‘comet’) assay was used to investigate whether fern spores can cause DNA damage in vitro. Extracts of spores from six fern species were administered to cultured human premyeloid leukaemia (K562) cells. Spore extracts of five fern species: Anemia phyllitidis, Dicksonia antarctica, Pteridium aquilinum, Pteris vittata and Sadleria pallida, induced significantly more DNA strand breaks than those in the control groups. Only in one species, Osmunda regalis, was the effect no different from that in the control groups. Using extracts from A. phyllitidis and P. vittata, the extent of DNA damage was increased by increasing the original dose 10 times, whereas an experiment in which exposure times were varied suggested that the highest levels of strand breaks appear after 2 h exposure. Simultaneous incubation with human S9 liver enzyme mix ablated the damaging effect of the extracts. Our data show that fern spore extracts can cause DNA damage in human cells in vitro. Considering the strong correlation between DNA damage and carcinogenic events, the observations made in this report may well have some implications for human health. © 2000 Cancer Research Campaign PMID:10883670

  8. Mixed connective tissue disease.

    PubMed

    Gunnarsson, Ragnar; Hetlevik, Siri Opsahl; Lilleby, Vibke; Molberg, Øyvind

    2016-02-01

    The concept of mixed connective tissue disease (MCTD) as a separate connective tissue disease (CTD) has persisted for more than four decades. High titers of antibodies targeting the U1 small nuclear ribonucleoprotein particle (U1 snRNP) in peripheral blood are a sine qua non for the diagnosis of MCTD, in addition to distinct clinical features including Raynaud's phenomenon (RP), "puffy hands," arthritis, myositis, pleuritis, pericarditis, interstitial lung disease (ILD), and pulmonary hypertension (PH). Recently, population-based epidemiology data from Norway estimated the point prevalence of adult-onset MCTD to be 3.8 per 100,000 and the mean annual incidence to be 2.1 per million per year, supporting the notion that MCTD is the least common CTD. Little is known about the etiology of MCTD, but recent genetic studies have confirmed that MCTD is a strongly HLA (​human leukocyte antigen)-linked disease, as the HLA profiles of MCTD differ distinctly from the corresponding profiles of ethnically matched healthy controls and other CTDs. In the first section of this review, we provide an update on the clinical, immunological, and genetic features of MCTD and discuss the relationship between MCTD and the other CTDs. Then we proceed to discuss the recent advances in therapy and our current understanding of prognosis and prognostic factors, especially those that are associated with the more serious pulmonary and cardiovascular complications of the disease. In the final section, we discuss some of the key, unresolved questions related to anti-RNP-associated diseases and indicate how these questions may be approached in future studies.

  9. Biomass conversion to mixed alcohols

    SciTech Connect

    Holtzapple, M.T.; Loescher, M.; Ross, M.

    1996-10-01

    This paper discusses the MixAlco Process which converts a wide variety of biomass materials (e.g. municipal solid waste, sewage sludge, agricultural residues) to mixed alcohols. First, the biomass is treated with lime to enhance its digestibility. Then, a mixed culture of acid-forming microorganisms converts the lime-treated biomass to volatile fatty acids (VFA) such as acetic, propionic, and butyric acids. To maintain fermentor pH, a neutralizing agent (e.g. calcium carbonate or lime) is added, so the fermentation actually produces VFA salts such as calcium acetate, propionate, and butyrate. The VFA salts are recovered and thermally converted to ketones (e.g. acetone, methylethyl ketone, diethyl ketone) which are subsequently hydrogenated to mixed alcohols (e.g. isopropanol, isobutanol, isopentanol). Processing costs are estimated at $0.72/gallon of mixed alcohols making it potentially attractive for transportation fuels.

  10. 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.

  11. Mixing in confined stratified aquifers

    NASA Astrophysics Data System (ADS)

    Bolster, Diogo; Valdés-Parada, Francisco J.; LeBorgne, Tanguy; Dentz, Marco; Carrera, Jesus

    2011-03-01

    Spatial variability in a flow field leads to spreading of a tracer plume. The effect of microdispersion is to smooth concentration gradients that exist in the system. The combined effect of these two phenomena leads to an 'effective' enhanced mixing that can be asymptotically quantified by an effective dispersion coefficient (i.e. Taylor dispersion). Mixing plays a fundamental role in driving chemical reactions. However, at pre-asymptotic times it is considerably more difficult to accurately quantify these effects by an effective dispersion coefficient as spreading and mixing are not the same (but intricately related). In this work we use a volume averaging approach to calculate the concentration distribution of an inert solute release at pre-asymptotic times in a stratified formation. Mixing here is characterized by the scalar dissipation rate, which measures the destruction of concentration variance. As such it is an indicator for the degree of mixing of a system. We study pre-asymptotic solute mixing in terms of explicit analytical expressions for the scalar dissipation rate and numerical random walk simulations. In particular, we divide the concentration field into a mean and deviation component and use dominant balance arguments to write approximate governing equations for each, which we then solve analytically. This allows us to explicitly evaluate the separate contributions to mixing from the mean and the deviation behavior. We find an approximate, but accurate expression (when compared to numerical simulations) to evaluate mixing. Our results shed some new light on the mechanisms that lead to large scale mixing and allow for a distinction between solute spreading, represented by the mean concentration, and mixing, which comes from both the mean and deviation concentrations, at pre-asymptotic times.

  12. Baroclinic mixing in HE fireballs

    SciTech Connect

    Kuhl, A.L.; Ferguson, R.E.; Priolo, F.; Chien, K.Y.; Collins, J.P.

    1993-08-01

    Numerical simulations of the turbulent mixing in the fireball of an HE blast wave were performed with a second-order Godunov code. Adaptive mesh refinement was used to capture the convective mixing processes on the computational grid. The calculations revealed that the interface between the shock-compressed air and the dense detonation products was unstable. Vorticity was generated in that region by baroclinic effects. This caused the interface to roll-up into a turbulent mixing layer. Four phases of mixing were identified: a strong blast wave phase, where the mixing region was swept outward by the shockinduced flow; an implosion phase, that stretched the inner boundary of the mixing region back toward the origin; a re-shocking phase, where the imploding shock expands back outward from the origin and re-energizes the mixing later by RichtmyerMeshkov effects; and an asymptotic mixing phase, where line-scale structures are continually recreated by folding effects but the overall vorticity decays through a cascade process. The flowfield was azimuthally averaged to evaluate the mean-flow profiles and r.m.s. fluctuation profiles across the mixing layer. The mean kinetic energy rapidly approached zero as the blast wave decayed, but the fluctuating kinetic energy asymptotically approached a small constant value. This represents the rotational kinetic energy driven by the vorticity field, that continued to mix the fluid at late times. It was shown that the vorticity field corresponds to a function that fluctuates between plus and minus values-with a volume-averaged mean of zero.

  13. 32P-postlabelling analysis of DNA adducts in the skin of mice treated with petrol and diesel engine lubricating oils and exhaust condensates.

    PubMed

    Schoket, B; Hewer, A; Grover, P L; Phillips, D H

    1989-08-01

    Samples of unused or used petrol and diesel engine lubricating oils were applied to the shaved dorsal skin of 4- to 6-week-old male Parkes mice, either as a single treatment (50 microliters/mouse) or as four consecutive daily treatments (50 microliters/application). DNA isolated from the skin 24 h after the final treatment was digested to 3'-mononucleotides and analysed by 32P-postlabelling for the presence of aromatic adducts. Enhancement of sensitivity using butanol extraction or nuclease P1 digestion of the DNA hydrolysates led to the detection of up to eight adduct spots on polyethyleneimine-cellulose thin-layer chromatograms with samples of DNA from skin treated with used engine oils, at levels of 40-150 amol total adducts/micrograms DNA. Multiple treatments with the used oils gave rise to similar patterns of adducts in lung DNA. A single treatment of mouse skin with petrol engine exhaust condensate (50 microliters), or diesel engine exhaust condensate (50 microliters), containing 20 and 46 micrograms benzo[a]pyrene (BaP)/g respectively, gave rise to approximately 75 amol total adducts/micrograms DNA in skin. A significant proportion, 31 and 48% respectively, of the adducts formed by the petrol and diesel engine exhaust condensates co-chromatographed with the major BaP-DNA adduct, but with the used engine oils, only petrol engine oil, and not diesel engine oil, produced significant amounts of an adduct (22% of total) that corresponded to the BaP-DNA adduct.

  14. 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)

  15. 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.

  16. 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.

  17. 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)

  18. Compressibility effects on turbulent mixing

    NASA Astrophysics Data System (ADS)

    Panickacheril John, John; Donzis, Diego

    2016-11-01

    We investigate the effect of compressibility on passive scalar mixing in isotropic turbulence with a focus on the fundamental mechanisms that are responsible for such effects using a large Direct Numerical Simulation (DNS) database. The database includes simulations with Taylor Reynolds number (Rλ) up to 100, turbulent Mach number (Mt) between 0.1 and 0.6 and Schmidt number (Sc) from 0.5 to 1.0. We present several measures of mixing efficiency on different canonical flows to robustly identify compressibility effects. We found that, like shear layers, mixing is reduced as Mach number increases. However, data also reveal a non-monotonic trend with Mt. To assess directly the effect of dilatational motions we also present results with both dilatational and soleniodal forcing. Analysis suggests that a small fraction of dilatational forcing decreases mixing time at higher Mt. Scalar spectra collapse when normalized by Batchelor variables which suggests that a compressive mechanism similar to Batchelor mixing in incompressible flows might be responsible for better mixing at high Mt and with dilatational forcing compared to pure solenoidal mixing. We also present results on scalar budgets, in particular on production and dissipation. Support from NSF is gratefully acknowledged.

  19. Mixed features in bipolar disorder.

    PubMed

    Solé, Eva; Garriga, Marina; Valentí, Marc; Vieta, Eduard

    2016-12-29

    Mixed affective states, defined as the coexistence of depressive and manic symptoms, are complex presentations of manic-depressive illness that represent a challenge for clinicians at the levels of diagnosis, classification, and pharmacological treatment. The evidence shows that patients with bipolar disorder who have manic/hypomanic or depressive episodes with mixed features tend to have a more severe form of bipolar disorder along with a worse course of illness and higher rates of comorbid conditions than those with non-mixed presentations. In the updated Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5), the definition of "mixed episode" has been removed, and subthreshold nonoverlapping symptoms of the opposite pole are captured using a "with mixed features" specifier applied to manic, hypomanic, and major depressive episodes. However, the list of symptoms proposed in the DSM-5 specifier has been widely criticized, because it includes typical manic symptoms (such as elevated mood and grandiosity) that are rare among patients with mixed depression, while excluding symptoms (such as irritability, psychomotor agitation, and distractibility) that are frequently reported in these patients. With the new classification, mixed depressive episodes are three times more common in bipolar II compared with unipolar depression, which partly contributes to the increased risk of suicide observed in bipolar depression compared to unipolar depression. Therefore, a specific diagnostic category would imply an increased diagnostic sensitivity, would help to foster early identification of symptoms and ensure specific treatment, as well as play a role in suicide prevention in this population.

  20. Mapping the Mixed Methods–Mixed Research Synthesis Terrain

    PubMed Central

    Sandelowski, Margarete; Voils, Corrine I.; Leeman, Jennifer; Crandell, Jamie L.

    2012-01-01

    Mixed methods–mixed research synthesis is a form of systematic review in which the findings of qualitative and quantitative studies are integrated via qualitative and/or quantitative methods. Although methodological advances have been made, efforts to differentiate research synthesis methods have been too focused on methods and not focused enough on the defining logics of research synthesis—each of which may be operationalized in different ways—or on the research findings themselves that are targeted for synthesis. The conduct of mixed methods–mixed research synthesis studies may more usefully be understood in terms of the logics of aggregation and configuration. Neither logic is preferable to the other nor tied exclusively to any one method or to any one side of the qualitative/quantitative binary. PMID:23066379

  1. Computational design of co-assembling protein-DNA nanowires

    NASA Astrophysics Data System (ADS)

    Mou, Yun; Yu, Jiun-Yann; Wannier, Timothy M.; Guo, Chin-Lin; Mayo, Stephen L.

    2015-09-01

    Biomolecular self-assemblies are of great interest to nanotechnologists because of their functional versatility and their biocompatibility. Over the past decade, sophisticated single-component nanostructures composed exclusively of nucleic acids, peptides and proteins have been reported, and these nanostructures have been used in a wide range of applications, from drug delivery to molecular computing. Despite these successes, the development of hybrid co-assemblies of nucleic acids and proteins has remained elusive. Here we use computational protein design to create a protein-DNA co-assembling nanomaterial whose assembly is driven via non-covalent interactions. To achieve this, a homodimerization interface is engineered onto the Drosophila Engrailed homeodomain (ENH), allowing the dimerized protein complex to bind to two double-stranded DNA (dsDNA) molecules. By varying the arrangement of protein-binding sites on the dsDNA, an irregular bulk nanoparticle or a nanowire with single-molecule width can be spontaneously formed by mixing the protein and dsDNA building blocks. We characterize the protein-DNA nanowire using fluorescence microscopy, atomic force microscopy and X-ray crystallography, confirming that the nanowire is formed via the proposed mechanism. This work lays the foundation for the development of new classes of protein-DNA hybrid materials. Further applications can be explored by incorporating DNA origami, DNA aptamers and/or peptide epitopes into the protein-DNA framework presented here.

  2. Mixed deterministic and probabilistic networks.

    PubMed

    Mateescu, Robert; Dechter, Rina

    2008-11-01

    The paper introduces mixed networks, a new graphical model framework for expressing and reasoning with probabilistic and deterministic information. The motivation to develop mixed networks stems from the desire to fully exploit the deterministic information (constraints) that is often present in graphical models. Several concepts and algorithms specific to belief networks and constraint networks are combined, achieving computational efficiency, semantic coherence and user-interface convenience. We define the semantics and graphical representation of mixed networks, and discuss the two main types of algorithms for processing them: inference-based and search-based. A preliminary experimental evaluation shows the benefits of the new model.

  3. Mixed deterministic and probabilistic networks

    PubMed Central

    Dechter, Rina

    2010-01-01

    The paper introduces mixed networks, a new graphical model framework for expressing and reasoning with probabilistic and deterministic information. The motivation to develop mixed networks stems from the desire to fully exploit the deterministic information (constraints) that is often present in graphical models. Several concepts and algorithms specific to belief networks and constraint networks are combined, achieving computational efficiency, semantic coherence and user-interface convenience. We define the semantics and graphical representation of mixed networks, and discuss the two main types of algorithms for processing them: inference-based and search-based. A preliminary experimental evaluation shows the benefits of the new model. PMID:20981243

  4. [Marketing mix in health service].

    PubMed

    Ameri, Cinzia; Fiorini, Fulvio

    2015-01-01

    The marketing mix is the combination of the marketing variables that a firm employs with the purpose to achieve the expected volume of business within its market. In the sale of goods, four variables compose the marketing mix (4 Ps): Product, Price, Point of sale and Promotion. In the case of providing services, three further elements play a role: Personnel, Physical Evidence and Processes (7 Ps). The marketing mix must be addressed to the consumers as well as to the employees of the providing firm. Furthermore, it must be interpreted as employees ability to satisfy customers (interactive marketing).

  5. Waveguide Four-Wave Mixing

    DTIC Science & Technology

    1991-10-01

    PL-TR--91-1045 /’--"PL-TR-- AD-A243 555 91-1045 WAVEGUIDE FOUR -WAVE MIXING Thomas B. Simpson Jia-ming Liu JAYCOR San Diego, CA 92186-5154 October...Final Report; May 88 - Mar 91 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS WAVEGUIDE FOUR -WAVE MIXING C: F29601-88-C-0023 PE: 62601F PR: 3326 6. AUTHOR(S...for public release; distribution unlimited. 13. ABSTRACT (Maximum 200 words) This program has investigated four -wave mixing (4-win) in non- linear

  6. 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.

  7. Biodegradation of mixed pesticides by mixed pesticide enriched cultures.

    PubMed

    Krishna, K Rama; Philip, Ligy

    2009-01-01

    This paper discusses the degradation kinetics of mixed (lindane, methyl parathion and carbofuran) pesticides by mixed pesticide enriched cultures (MEC) under various environmental conditions. The bacterial strains isolated from the mixed microbial consortium were identified as Pseudomonas aeruginosa (MTCC 9236), Bacillus sp. (MTCC 9235) and Chryseobacterium joostei (MTCC 9237). Batch studies were conducted to estimate the biokinetic parameters like the maximum specific growth rate (mu(max)), Yield Coefficient (Y(T)), half saturation concentration (K(s)) and inhibition concentration (Ki) for individual and mixed pesticide enriched cultures. The cultures enriched in a particular pollutant always showed high growth rate and low inhibition in that particular pollutant compared to MEC. After seven weeks of incubation, mixed pesticide enriched cultures were able to degrade 72% lindane, 95% carbofuran and 100% of methyl parathion in facultative co-metabolic conditions. In aerobic systems, degradation efficiencies of lindane methyl parathion and carbofuran were increased by the addition of 2g L(- 1) of dextrose. Though many metabolic compounds of mixed pesticides were observed at different time intervals, none of the metabolites were persistent. Based on the observed metabolites, a degradation pathway was postulated for different pesticides under various environmental conditions.

  8. 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.

  9. Thermodynamic studies on PNA and PNA/DNA dendrimer formation.

    PubMed

    Moccia, Maria; Musumeci, Domenica; Valente, Margherita; Roviello, Giovanni N; Sapio, Roberto; Pedone, Carlo; Bucci, Enrico M

    2007-01-01

    In this work we report a kinetic and thermodynamic study relative to the formation of gel systems based on PNA and PNA/DNA dendrimers, useful for drug delivery or diagnostic applications. We realized two kinds of systems: a PNA-based monomolecular system formed by an autoassembling PNA tridendron (A) and a PNA/DNA bimolecular system based on a PNA tridendron with a mixed sequence and a DNA crosslinker (B). Both systems have the ability to form a three-dimensional network by means of specific W-C base pairing.

  10. Modeling Mix in ICF Implosions

    NASA Astrophysics Data System (ADS)

    Weber, C. R.; Clark, D. S.; Chang, B.; Eder, D. C.; Haan, S. W.; Jones, O. S.; Marinak, M. M.; Peterson, J. L.; Robey, H. F.

    2014-10-01

    The observation of ablator material mixing into the hot spot of ICF implosions correlates with reduced yield in National Ignition Campaign (NIC) experiments. Higher Z ablator material radiatively cools the central hot spot, inhibiting thermonuclear burn. This talk focuses on modeling a ``high-mix'' implosion from the NIC, where greater than 1000 ng of ablator material was inferred to have mixed into the hot spot. Standard post-shot modeling of this implosion does not predict the large amounts of ablator mix necessary to explain the data. Other issues are explored in this talk and sensitivity to the method of radiation transport is found. Compared with radiation diffusion, Sn transport can increase ablation front growth and alter the blow-off dynamics of capsule dust. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  11. Is the tribimaximal mixing accidental?

    SciTech Connect

    Abbas, Mohammed; Smirnov, A. Yu.

    2010-07-01

    The tribimaximal (TBM) mixing is not accidental if structures of the corresponding leptonic mass matrices follow immediately from certain (residual or broken) flavor symmetry. We develop a simple formalism which allows one to analyze effects of deviations of the lepton mixing from TBM on the structure of the neutrino mass matrix and on the underlying flavor symmetry. We show that possible deviations from the TBM mixing can lead to strong modifications of the mass matrix and strong violation of the TBM-mass relations. As a result, the mass matrix may have an 'anarchical' structure with random values of elements or it may have some symmetry that differs from the TBM symmetry. Interesting examples include matrices with texture zeros, matrices with certain 'flavor alignment' as well as hierarchical matrices with a two-component structure, where the dominant and subdominant contributions have different symmetries. This opens up new approaches to understanding the lepton mixing.

  12. Cutaneous mixed infections in AIDS.

    PubMed

    Piérard, G E; Piérard-Franchimont, C; Estrada, J A; Rurangirwa, A; Dosal, F L

    1990-02-01

    We report a new case of mixed infection occurring at the same site of the skin in a human immune deficiency virus-positive patient. Hyperkeratotic and crusted erosions contained fusospirochetal organisms, Cryptococcus neoformans, and another unidentified fungus.

  13. Mixed-mu superconducting bearings

    DOEpatents

    Hull, John R.; Mulcahy, Thomas M.

    1998-01-01

    A mixed-mu superconducting bearing including a ferrite structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet structure. The ferrite structure is levitated by said stationary permanent magnet structure.

  14. Mixed-mu superconducting bearings

    DOEpatents

    Hull, J.R.; Mulcahy, T.M.

    1998-03-03

    A mixed-mu superconducting bearing is disclosed including a ferrite structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet structure. The ferrite structure is levitated by said stationary permanent magnet structure. 9 figs.

  15. 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)

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Mixed jamming method for SAR

    NASA Astrophysics Data System (ADS)

    Zhao, Hong-feng; Zhang, Peng; Wang, Yong-sheng

    2007-11-01

    The mixed jamming method of synthetic aperture radar is analyzed and discussed. The methods of active noise and deception jamming and the signal model of transmitting is described. The raw echo signal of SAR and the model of jammed echo signal are expatiated, the characteristic of SAR and the evaluating method of jamming effect are established. Finally, the mixed jamming imaging of SAR is simulated.

  1. 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.

  2. 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.

  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. Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections ▿

    PubMed Central

    O'Donnell, Kerry; Sutton, Deanna A.; Rinaldi, Michael G.; Sarver, Brice A. J.; Balajee, S. Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C.; Robert, Vincent A. R. G.; Crous, Pedro W.; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M.

    2010-01-01

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the

  5. Spermine Condenses DNA, but Not RNA Duplexes

    SciTech Connect

    Katz, Andrea M.; Tolokh, Igor S.; Pabit, Suzette A.; Baker, Nathan; Onufriev, Alexey V.; Pollack, Lois

    2017-01-01

    Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA, and some RNAs such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA, but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA and compare our findings with predictions of molecular dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence, containing a mixture of 14 GC pairs and 11 AU pairs, resists condensation relative to DNA of an equivalent sequence or to 25 base pair poly(rA):poly(rU) RNA. Comparison of wide-angle x-ray scattering profiles with simulation suggests that spermine is sequestered deep within the major groove of mixed sequence RNA, preventing condensation by limiting opportunities to bridge to other molecules as well as stabilizing the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds external to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble, and available for interaction with other molecules in the cell, despite the presence of spermine at concentrations high enough to precipitate DNA.

  6. The unusual and dynamic character of PX-DNA

    PubMed Central

    Niu, Dong; Jiang, Hualin; Sha, Ruojie; Canary, James W.; Seeman, Nadrian C.

    2015-01-01

    PX-DNA is a four-stranded DNA structure that has been implicated in the recognition of homology, either continuously, or in an every-other-half-turn fashion. Some of the structural features of the molecule have been noted previously, but the structure requires further characterization. Here, we report atomic force microscopic characterization of PX molecules that contain periodically placed biotin groups, enabling the molecule to be labeled by streptavidin molecules at these sites. In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure. Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure. Circular dichroism spectroscopy indicates unusual features in the PX molecule that are absent in both the molecules to which it is compared. PMID:26184876

  7. The unusual and dynamic character of PX-DNA

    DOE PAGES

    Niu, Dong; Jiang, Hualin; Sha, Ruojie; ...

    2015-07-15

    PX-DNA is a four-stranded DNA structure that has been implicated in the recognition of homology, either continuously, or in an every-other-half-turn fashion. Some of the structural features of the molecule have been noted previously, but the structure requires further characterization. Here, we report atomic force microscopic characterization of PX molecules that contain periodically placed biotin groups, enabling the molecule to be labeled by streptavidin molecules at these sites. In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure. Moreover, the spacing between the nucleotide pairs alongmore » the helix axis is shorter, suggesting a mixed B/A structure. Circular dichroism spectroscopy indicates unusual features in the PX molecule that are absent in both the molecules to which it is compared.« less

  8. The unusual and dynamic character of PX-DNA

    SciTech Connect

    Niu, Dong; Jiang, Hualin; Sha, Ruojie; Canary, James W.; Seeman, Nadrian C.

    2015-07-15

    PX-DNA is a four-stranded DNA structure that has been implicated in the recognition of homology, either continuously, or in an every-other-half-turn fashion. Some of the structural features of the molecule have been noted previously, but the structure requires further characterization. Here, we report atomic force microscopic characterization of PX molecules that contain periodically placed biotin groups, enabling the molecule to be labeled by streptavidin molecules at these sites. In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure. Moreover, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure. Circular dichroism spectroscopy indicates unusual features in the PX molecule that are absent in both the molecules to which it is compared.

  9. Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer

    PubMed Central

    AL-ATTAS*, ASMAA; ASSIDI*, MOURAD; AL-MAGHRABI, JAUDAH; DALLOL, ASHRAF; SCHULTEN, HANS-JUERGEN; ABU-ELMAGD, MUHAMMAD; CHAUDHARY, ADEEL; ABUZENADAH, ADEL; BUDOWLE, BRUCE; BUHMEIDA, ABDELBASET; AL-QAHTANI, MOHAMMED

    2016-01-01

    Background/Aim: To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses. Materials and Methods: FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide’s image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed. Results: High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed. Conclusion: This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists’ knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine. *These Authors contributed equally to this manuscript. PMID:27566658

  10. DNA barcoding as a tool for Great Lakes biological assessment

    EPA Science Inventory

    Enumerating organisms found in water samples in support of biodiversity and biological condition assessment is a mainstay of aquatic ecology, yet can require considerable resources and expertise. DNA-based identification of mixed-organism samples offers the potential to greatly ...

  11. Dysphoric mania, mixed states, and mania with mixed features specifier: are we mixing things up?

    PubMed

    McElroy, Susan L; Keck, Paul E

    2016-11-21

    Various terms have been used to describe mania when it is accompanied by depressive symptoms. In this article, we attempt to define and discuss 3 of these terms: dysphoric mania, mixed state, and mania with mixed features specifier. We conclude that whatever term is used, it is important to be aware that mania is more often unpleasant than pleasant, and that the unpleasantness is not limited to depression.

  12. 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.

  13. 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

  14. DNA methylation profiles at birth and child ADHD symptoms.

    PubMed

    van Mil, Nina H; Steegers-Theunissen, Régine P M; Bouwland-Both, Marieke I; Verbiest, Michael M P J; Rijlaarsdam, Jolien; Hofman, Albert; Steegers, Eric A P; Heijmans, Bastiaan T; Jaddoe, Vincent W V; Verhulst, Frank C; Stolk, Lisette; Eilers, Paul H C; Uitterlinden, André G; Tiemeier, Henning

    2014-02-01

    Attention deficit/hyperactivity disorder (ADHD) is a common and highly heritable psychiatric disorder. In addition, early life environmental factors contribute to the occurrence of ADHD. Recently, DNA methylation has emerged as a mechanism potentially mediating genetic and environmental effects. Here, we investigated whether newborn DNA methylation patterns of selected candidate genes involved in psychiatric disorders or fetal growth are associated with ADHD symptoms in childhood. Participants were 426 children from a large population based cohort of Dutch national origin. Behavioral data were obtained at age 6 years with the Child Behavior Checklist. For the current study, 11 regions at 7 different genes were selected. DNA methylation levels of cord blood DNA were measured for the 11 regions combined and for each region separately. We examined the association between DNA methylation levels at different regions and ADHD symptoms with linear mixed models. DNA methylation levels were negatively associated with ADHD symptom score in the overall analysis of all 11 regions. This association was largely explained by associations of DRD4 and 5-HTT regions. Other candidate genes showed no association between DNA methylation levels and ADHD symptom score. Associations between DNA methylation levels and ADHD symptom score were attenuated by co-occurring Oppositional defiant disorder and total symptoms. Lower DNA methylation levels of the 7 genes assessed at birth, were associated with more ADHD symptoms of the child at 6 years of age. Further studies are needed to confirm our results and to investigate the possible underlying mechanism.

  15. 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. Here we tried to solve this problem through developing a new method, superorigami, to construct finite sized DNA structure with much larger dimension, which can be as large as 500nm. The second problem will be explored the ability of DNA structure to assemble inorganic nanomaterials for novel photonic or electronic properties. Here we tried to utilize DNA Origami method to assemble AuNPs with controlled 3D spacial position for possible chiral photonic complex. We also tried to assemble SWNT with discrete length for possible field effect transistor device. In addition, we tried to mimic in vivo compartment with DNA structure to study internalized enzyme behavior. From our results, constructed DNA cage origami can protect encapsulated enzyme from degradation, and internalized enzyme activity can be boosted for up to 10 folds. In summary, DNA structure can serve as an ideal template for construction of functional nanomaterials with lots of possibilities to be explored.

  16. Potential for DNA-based identification of Great Lakes fauna: Match and mismatch between taxa inventories and DNA barcode libraries

    EPA Science Inventory

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However, the abi...

  17. GHEP-ISFG collaborative exercise on mixture profiles of autosomal STRs (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03): results and evaluation.

    PubMed

    Crespillo, M; Barrio, P A; Luque, J A; Alves, C; Aler, M; Alessandrini, F; Andrade, L; Barretto, R M; Bofarull, A; Costa, S; García, M A; García, O; Gaviria, A; Gladys, A; Gorostiza, A; Hernández, A; Herrera, M; Hombreiro, L; Ibarra, A A; Jiménez, M J; Luque, G M; Madero, P; Martínez-Jarreta, B; Masciovecchio, M V; Modesti, N M; Moreno, F; Pagano, S; Pedrosa, S; Plaza, G; Prat, E; Puente, J; Rendo, F; Ribeiro, T; Sala, A; Santamaría, E; Saragoni, V G; Whittle, M R

    2014-05-01

    One of the main objectives of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the area of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise on analysis and interpretation of autosomal short tandem repeat (STR) mixture profiles. Until now, three exercises have been organized (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03), with 32, 24 and 17 participant laboratories respectively. The exercise aims to give a general vision by addressing, through the proposal of mock cases, aspects related to the edition of mixture profiles and the statistical treatment. The main conclusions obtained from these exercises may be summarized as follows. Firstly, the data show an increased tendency of the laboratories toward validation of DNA mixture profiles analysis following international recommendations (ISO/IEC 17025:2005). Secondly, the majority of discrepancies are mainly encountered in stutters positions (53.4%, 96.0% and 74.9%, respectively for the three editions). On the other hand, the results submitted reveal the importance of performing duplicate analysis by using different kits in order to reduce errors as much as possible. Regarding the statistical aspect (GHEP-MIX02 and 03), all participants employed the likelihood ratio (LR) parameter to evaluate the statistical compatibility and the formulas employed were quite similar. When the hypotheses to evaluate the LR value were locked by the coordinators (GHEP-MIX02) the results revealed a minor number of discrepancies that were mainly due to clerical reasons. However, the GHEP-MIX03 exercise allowed the participants to freely come up with their own hypotheses to

  18. Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals

    PubMed Central

    Sveegaard, Signe; Wahlberg, Magnus; Kielgast, Jos; Kyhn, Line A.; Salling, Andreas B.; Galatius, Anders; Orlando, Ludovic; Gilbert, M. Thomas P.

    2012-01-01

    The exploitation of non-invasive samples has been widely used in genetic monitoring of terrestrial species. In aquatic ecosystems, non-invasive samples such as feces, shed hair or skin, are less accessible. However, the use of environmental DNA (eDNA) has recently been shown to be an effective tool for genetic monitoring of species presence in freshwater ecosystems. Detecting species in the marine environment using eDNA potentially offers a greater challenge due to the greater dilution, amount of mixing and salinity compared with most freshwater ecosystems. To determine the potential use of eDNA for genetic monitoring we used specific primers that amplify short mitochondrial DNA sequences to detect the presence of a marine mammal, the harbor porpoise, Phocoena phocoena, in a controlled environment and in natural marine locations. The reliability of the genetic detections was investigated by comparing with detections of harbor porpoise echolocation clicks by static acoustic monitoring devices. While we were able to consistently genetically detect the target species under controlled conditions, the results from natural locations were less consistent and detection by eDNA was less successful than acoustic detections. However, at one site we detected long-finned pilot whale, Globicephala melas, a species rarely sighted in the Baltic. Therefore, with optimization aimed towards processing larger volumes of seawater this method has the potential to compliment current visual and acoustic methods of species detection of marine mammals. PMID:22952587

  19. DNA nanotech: Expanding the repertoire of DNA for the assembly of nanoscale objects and electrical devices

    NASA Astrophysics Data System (ADS)

    Fahlman, Richard Peter

    Much recent interest has focused on DNA as a material for the construction of objects and the templating of other materials on the nanometer to micrometer scale. Such constructions have made use of the recognition of "complementary" nucleotide sequence by single-stranded stretches of DNA in the formation of double helices. The ability of DNA double helices to act as a semi-conductor for electron transfer has opened more opportunities for using DNA in nanoscale devices. This work describes several advancements involving structural and functional aspect of DNA based nanotechnologies. We have developed a new approach to assemble DNA nanostructures in a cation dependent manner. Association is via the formation of guanine quartets from two G-G mismatch domains within a duplex DNA framework. Association can be regulated by the addition or removal of cation species that promote guanine quartet formation (i.e. K+ or Sr2+). We have also demonstrated that these domains can be 'programmed' to be self-specific in mixed solutions by patterning the G·G mismatches into distinct domains. We have evaluated the process of charge transfer through immobile DNA junctions. This work compares anthraquinone- and rhodium-based methods to induce charge transfer through DNA and identifies some pitfalls in one of the prominently used systems. We have also demonstrated that the conformational transitions of folded DNA structures, more complex than simple double helical DNA, can be utilized in regulating charge transfer. We have successfully constructed 'electrical on/off switches' composed of DNA, which are modulated by the presence or absence of particular compounds in solution. Switches that are modulated by the small molecule adenosine and as well as ones modulated by short oligonucleotides have been assembled. The construction and demonstration of their operation now opens a new window of opportunity for the development of DNA detector systems, which could be directly coupled to

  20. Mixed ligand complexes of Cu(II)/Zn(II) ions containing (m-)/(p-) carboxylato phenyl azo pentane 2,4-dione and 2,2‧-bipyridine/1,10 phenanthroline: Synthesis, characterization, DNA binding, nuclease and topoisomerase I inhibitory activity

    NASA Astrophysics Data System (ADS)

    Hasan, Md. Amin; Kumari, Niraj; Singh, Kanhaiya; Singh, Kiran; Mishra, Lallan

    2016-01-01

    Metal complexes of type [Cu(L1H)2(bpy)] (1), [Zn(L1H)2(bpy)] (2), [Cu(L2H)2(bpy)] (3) and [Cu(L2H)2(Phen)] (4) (L1H2 = 3-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, L2H2 = 4-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, bpy = 2,2‧-bipyridine, Phen = 1,10 phenanthroline) are synthesized and characterized using spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, electronic absorption and emission) and elemental analysis data. The assembly of the complexes involving intramolecular H-bonding is displayed using corresponding crystal structure. Binding of the complexes separately with Calf Thymus DNA is monitored using UV-vis spectral titrations. The displacement of ethidium bromide (EB) bound to DNA by the complexes, in phosphate buffer solution (pH ∼ 7.2) is monitored using fluorescence spectral titrations. Nuclease activity of the complexes follow the order 4 > 3 > 1 > 2. The gel electrophoretic mobility assay measurement in presence of minor groove binder 4‧,6-diamidino-2-phenylindole (DAPI), suggests that complexes preferably bind with the minor groove of DNA. Topoisomerase I inhibitory activity of the complexes 3 and 4 inhibit topoisomerase I activity with IC50 values of 112 and 87 μM respectively.

  1. The DNA-polymerase-X family: controllers of DNA quality?

    PubMed

    Ramadan, Kristijan; Shevelev, Igor; Hübscher, Ulrich

    2004-12-01

    Synthesis of the genetic material of the cell is achieved by a large number of DNA polymerases. Besides replicating the genome, they are involved in DNA-repair processes. Recent studies have indicated that certain DNA-polymerase-X-family members can synthesize unusual DNA structures, and we propose that these DNA structures might serve as 'flag wavers' for the induction of DNA-repair and/or DNA-damage-checkpoint pathways.

  2. DNA supercoiling during transcription

    PubMed Central

    Ma, Jie; Wang, Michelle D.

    2017-01-01

    The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and recently new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field. We highlight the significant impact of DNA supercoiling in transcription, but also more broadly in all processes operating on DNA.

  3. Rifampin and vaccinia DNA.

    PubMed Central

    Esteban, M

    1977-01-01

    The effect of rifampin on the replication of vaccinia DNA was studied in mouse L cells by a cytochemical techinque and by alkaline sucrose sedimentation analysis of newly synthesized viral DNA molecules. By the use of a fluorescent DNA-binding compound (Hoechst 33258), the sequential appearance, size, and location of the viral "factories" in rifampin-treated, virus-infected cells were found to be indistinguishable from those observed in untreated, infected cells. Sedimentation analysis in alkaline scurose gradients of the viral DNA molecules labeled in pulse-chase experiments showed that formation of small fragments, elongation into "intermediate"-sized molecules, and maturation into full-length viral DNA and, finally, into cross-linked viral DNA molecules occurred in the absence or presence of rifampin. The results support the view that the primary effect of the drug is related to assembly or morphogenesis. Images PMID:833950

  4. Electrocatalysis in DNA Sensors

    PubMed Central

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

    2014-01-01

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

  5. DNA profiles from fingermarks.

    PubMed

    Templeton, Jennifer E L; Linacre, Adrian

    2014-11-01

    Criminal investigations would be considerably improved if DNA profiles could be routinely generated from single fingermarks. Here we report a direct DNA profiling method that was able to generate interpretable profiles from 71% of 170 fingermarks. The data are based on fingermarks from all 5 digits of 34 individuals. DNA was obtained from the fingermarks using a swab moistened with Triton-X, and the fibers were added directly to one of two commercial DNA profiling kits. All profiles were obtained without increasing the number of amplification cycles; therefore, our method is ideally suited for adoption by the forensic science community. We indicate the use of the technique in a criminal case in which a DNA profile was generated from a fingermark on tape that was wrapped around a drug seizure. Our direct DNA profiling approach is rapid and able to generate profiles from touched items when current forensic practices have little chance of success.

  6. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  7. Formation of DNA adducts in the skin of psoriasis patients, in human skin in organ culture, and in mouse skin and lung following topical application of coal-tar and juniper tar.

    PubMed

    Schoket, B; Horkay, I; Kósa, A; Páldeák, L; Hewer, A; Grover, P L; Phillips, D H

    1990-02-01

    Preparations of coal-tar and juniper tar (cade oil) that are used in the treatment of psoriasis are known to contain numerous potentially carcinogenic polycyclic aromatic hydrocarbons (PAH). Evidence of covalent binding to DNA by components of these mixtures was sought in a) human skin biopsy samples from 12 psoriasis patients receiving therapy with these agents, b) human skin explants maintained in organ culture and treated topically with the tars, and c) the skin and lungs of mice treated with repeated doses of the formulations following the regimen used in the clinic. DNA was isolated from the human and mouse tissues and digested enzymically to mononucleotides. 32P-Post-labeling analysis revealed the presence of aromatic DNA adducts in the biopsy samples at levels of up to 0.4 fmol total adducts/microgram DNA. Treatment of human skin in organ culture produced similar levels of adducts, while treatment with dithranol, a non-mutagenic therapeutic agent, resulted in chromatograms indistinguishable from those from untreated controls. In mouse skin, coal-tar ointment and juniper tar gave similar DNA adduct levels, with a similar time-course of removal: maximum levels (0.5 fmol/microgram DNA) at 24 h after the final treatment declined rapidly to 0.05 fmol/microgram at 7 d, thereafter declining slowly over the succeeding 25 d. However, while coal-tar ointment produced only very low levels of adducts in mouse lung (less than 0.03 fmol/microgram DNA), juniper tar produced adducts at a high level (0.7 fmol/microgram DNA) that were persistent in this tissue. These results provide direct evidence for the formation of potentially carcinogenic DNA damage in human and mouse tissue by components of these therapeutic tar preparations.

  8. Turbulent mix experiments and simulations

    SciTech Connect

    Dimonte, G.; Schneider, M.; Frerking, C.E.

    1995-08-01

    Hydrodynamic instabilities produce material mixing that can significantly degrade weapons performance. We investigate the Richtmyer-Meshkov (RM) and Rayleigh-Taylor (RT) instabilities in the turbulent regime in two experimental venues. RM experiments are conducted on the Nova laser with strong radiatively driven shocks (Mach > 20) in planar, two fluid targets. Interfacial perturbations are imposed with single sinusoidal modes to test linear theory and with three dimensional (3D) random modes to produce turbulent mix. RT experiments are conducted on a new facility, the Linear Electric Motor (LEM), in which macroscopic fluids are accelerated with arbitrary temporal profiles. This allows detailed diagnosis of the turbulence over a wide range of conditions. The Nova experiments study the high compression regime whereas the LEM experiments are incompressible. The results are compared to hydrodynamic simulations with the arbitrary Lagrangian-Eulerian code (CALE). The goal is to develop and test engineering models of mix.

  9. Ion mixing of semiconductor superlattices

    NASA Astrophysics Data System (ADS)

    Xia, W.; Hsu, S. N.; Han, C. C.; Pappert, S. A.; Zhu, B.; Cozzolino, C.; Yu, P. K. L.; Lau, S. S.; Poker, D. B.; White, C. W.; Schwarz, S. A.

    1991-07-01

    Compositional disordering of III-V compound superlattice structures has received considerable attention recently due to its potential application for photonic devices. The conventional method to induce compositional disorder is to implant a moderate dose of impurity ions (˜ 10 15 cm -2) into the structure at room temperature, followed by a high-temperature annealing step (this process is referred to as IA here). Ion irradiation at room temperature alone does not cause any significant intermixing of layers. The subsequent high-temperature annealing step tends to restrict device processing flexibility. Ion mixing (IM) is capable of enhancing compositional disordering of layers at a rate which increases exponentially with the ion irradiation temperature. As a processing technique to planarize devices, ion mixing appears to be an attractive technology. In this work, we investigate compositional disordering in the AlGaAs/GaAs and the InGaAs/InP systems using ion mixing. We found that the ion mixing behavior of these two systems shows a thermally activated regime as well as an athermal regime, similar to that observed for metal-metal and metal-semiconductor systems. Ion mixing is observed to induce compositional disordering at significantly lower temperatures than that for the IA process. We have compared the two processes in terms of four parameters (1) irradiation temperature, (2) dose dependence, (3) annealing, and (4) electrically active ions. We found that the IM process is more efficient in utilizing the defects generated by ion irradiation to cause disordering. Both the physical mechanism of ion mixing and possible device implications will be discussed.

  10. Ion mixing of semiconductor superlattices

    NASA Astrophysics Data System (ADS)

    Xia, W.; Hsu, S. N.; Han, C. C.; Pappert, S. A.; Zhu, B.; Cozzolino, C.; Yu, P. K. L.; Lau, S. S.; Poker, D. B.; White, C. W.

    Compositional disordering of III-V compound superlattice structures has received considerable attention recently due to its potential application for photonic devices. The conventional method in induce compositional disorder is to implant a moderate dose of impurity ions (approx. 10 (exp 15)/sq cm) into the structure at room temperature, followed by a high temperature annealing step (this process is referred to as IA here). Ion irradiation at room temperature alone does not cause any significant intermixing of layers. The subsequent high temperature annealing step tends to restrict device processing flexibility. Ion mixing (IM) is capable of enhancing compositional disordering of layers at a rate which increases exponentially with the ion irradiation temperature. As a processing technique to planarize devices, ion mixing appears to be an attractive technology. Compositional disordering was studied disordering in the AlGaAs/GaAs and the InGaAs/InP systems using ion mixing. It was found that the ion mixing behavior of these two systems shows a thermally activated regime as well as an athermal regime, similar to that observed for metal-metal and metal-semiconductor systems. Ion mixing is observed to induce compositional disordering at significantly lower temperatures than that for the IA process. The two processes were compared in terms of five parameters (1) irradiation temperature, (2) dose dependence (3) annealing, and (4) electrically active ions. It was found that the IM process is more efficient in utilizing the defects generated by ion irradiation to cause disordering. Both the physical mechanism of ion mixing and possible device implications will be discussed.

  11. Further evidence for mixed emotions.

    PubMed

    Larsen, Jeff T; McGraw, A Peter

    2011-06-01

    Emotion theorists have long debated whether valence, which ranges from pleasant to unpleasant states, is an irreducible aspect of the experience of emotion or whether positivity and negativity are separable in experience. If valence is irreducible, it follows that people cannot feel happy and sad at the same time. Conversely, if positivity and negativity are separable, people may be able to experience such mixed emotions. The authors tested several alternative interpretations for prior evidence that happiness and sadness can co-occur in bittersweet situations (i.e., those containing both pleasant and unpleasant aspects). One possibility is that subjects who reported mixed emotions merely vacillated between happiness and sadness. The authors tested this hypothesis in Studies 1-3 by asking subjects to complete online continuous measures of happiness and sadness. Subjects reported more simultaneously mixed emotions during a bittersweet film clip than during a control clip. Another possibility is that subjects in earlier studies reported mixed emotions only because they were explicitly asked whether they felt happy and sad. The authors tested this hypothesis in Studies 4-6 with open-ended measures of emotion. Subjects were more likely to report mixed emotions after the bittersweet clip than the control clip. Both patterns occurred even when subjects were told that they were not expected to report mixed emotions (Studies 2 and 5) and among subjects who did not previously believe that people could simultaneously feel happy and sad (Studies 3 and 6). These results provide further evidence that positivity and negativity are separable in experience.

  12. Mixing in Magnetized Turbulent Media

    NASA Astrophysics Data System (ADS)

    Sur, Sharanya; Pan, Liubin; Scannapieco, Evan

    2014-04-01

    Turbulent motions are essential to the mixing of entrained fluids and are also capable of amplifying weak initial magnetic fields by small-scale dynamo action. Here we perform a systematic study of turbulent mixing in magnetized media, using three-dimensional magnetohydrodynamic simulations that include a scalar concentration field. We focus on how mixing depends on the magnetic Prandtl number, Pm, from 1 to 4 and the Mach number, { {M}}, from 0.3 to 2.4. For all subsonic flows, we find that the velocity power spectrum has a k -5/3 slope in the early kinematic phase, but steepens due to magnetic back reactions as the field saturates. The scalar power spectrum, on the other hand, flattens compared to k -5/3 at late times, consistent with the Obukohov-Corrsin picture of mixing as a cascade process. At higher Mach numbers, the velocity power spectrum also steepens due to the presence of shocks, and the scalar power spectrum again flattens accordingly. Scalar structures are more intermittent than velocity structures in subsonic turbulence, whereas for supersonic turbulence, velocity structures appear more intermittent than the scalars only in the kinematic phase. Independent of the Mach number of the flow, scalar structures are arranged in sheets in both the kinematic and saturated phases of the magnetic field evolution. For subsonic turbulence, scalar dissipation is hindered in the strong magnetic field regions, probably due to Lorentz forces suppressing the buildup of scalar gradients, whereas for supersonic turbulence, scalar dissipation increases monotonically with increasing magnetic field strength. At all Mach numbers, mixing is significantly slowed by the presence of dynamically important small-scale magnetic fields, implying that mixing in the interstellar medium and in galaxy clusters is less efficient than modeled in hydrodynamic simulations.

  13. Nonideal Rayleigh-Taylor mixing

    SciTech Connect

    Sharp, David Howland; Lin, Hyun K; Iwerks, Justin G; Gliman, James G

    2009-01-01

    Rayleigh-Taylor mixing is a classical hydrodynamic Instability, which occurs when a light fluid pushes against a heavy fluid. The two main sources of nonideal behavior in Rayleigh-Taylor (RT) mixing are regularizations (physical and numerical) which produce deviations from a pure Euler equation, scale Invariant formulation, and non Ideal (i.e. experimental) initial conditions. The Kolmogorov theory of turbulence predicts stirring at all length scales for the Euler fluid equations without regularization. We Interpret mathematical theories of existence and non-uniqueness in this context, and we provide numerical evidence for dependence of the RT mixing rate on nonideal regularizations, in other words indeterminacy when modeled by Euler equations. Operationally, indeterminacy shows up as non unique solutions for RT mixing, parametrized by Schmidt and Prandtl numbers, In the large Reynolds number (Euler equation) limit. Verification and validation evidence is presented for the large eddy simulation algorithm used here. Mesh convergence depends on breaking the nonuniqueness with explicit use of the laminar Schmidt and PrandtJ numbers and their turbulent counterparts, defined in terms of subgrid scale models. The dependence of the mixing rate on the Schmidt and Prandtl numbers and other physical parameters will be illustrated. We demonstrate numerically the influence of initial conditions on the mixing rate. Both the dominant short wavelength Initial conditions and long wavelength perturbations are observed to playa role. By examination of two classes of experiments, we observe the absence of a single universal explanation, with long and short wavelength initial conditions, and the various physical and numerical regularizations contributing In different proportions In these two different contexts.

  14. Mixe de Tlahuitoltepec, Oaxaca (Mixe of Tlahuitoltepec, Oaxaca).

    ERIC Educational Resources Information Center

    Mexico Coll. (Mexico City)

    This document is one of 17 volumes on indigenous Mexican languages and is the result of a project undertaken by the Archivo de Lenguas Indigenas de Mexico. This volume contains information on Mixe, an indigenous language of Mexico spoken in Tlahuitoltepec, in the state of Oaxaca. The objective of collecting such a representative sampling of the…

  15. Use and abuse of mixing models (MixSIAR)

    EPA Science Inventory

    Background/Question/MethodsCharacterizing trophic links in food webs is a fundamental ecological question. In our efforts to quantify energy flow through food webs, ecologists have increasingly used mixing models to analyze biological tracer data, often from stable isotopes. Whil...

  16. Disentangling DNA molecules.

    PubMed

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  17. 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.

  18. Multiprotein DNA Looping

    NASA Astrophysics Data System (ADS)

    Vilar, Jose M. G.; Saiz, Leonor

    2006-06-01

    DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

  19. Forensic DNA testing.

    PubMed

    Butler, John M

    2011-12-01

    Forensic DNA testing has a number of applications, including parentage testing, identifying human remains from natural or man-made disasters or terrorist attacks, and solving crimes. This article provides background information followed by an overview of the process of forensic DNA testing, including sample collection, DNA extraction, PCR amplification, short tandem repeat (STR) allele separation and sizing, typing and profile interpretation, statistical analysis, and quality assurance. The article concludes with discussions of possible problems with the data and other forensic DNA testing techniques.

  20. Disentangling DNA molecules

    NASA Astrophysics Data System (ADS)

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  1. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

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

  2. Mixed ternary heterojunction solar cell

    DOEpatents

    Chen, Wen S.; Stewart, John M.

    1992-08-25

    A thin film heterojunction solar cell and a method of making it has a p-type layer of mixed ternary I-III-VI.sub.2 semiconductor material in contact with an n-type layer of mixed binary II-VI semiconductor material. The p-type semiconductor material includes a low resistivity copper-rich region adjacent the back metal contact of the cell and a composition gradient providing a minority carrier mirror that improves the photovoltaic performance of the cell. The p-type semiconductor material preferably is CuInGaSe.sub.2 or CuIn(SSe).sub.2.

  3. Polarization mixing optical parametric oscillator.

    SciTech Connect

    Pearl, Shaul; Smith, Arlee Virgil; Arie, Ady; Blau, Pinhas; Kalmani, Gal

    2005-05-01

    We report the experimental realization of a new type of optical parametric oscillator in which oscillation is achieved by polarization rotation in a linear retarder, followed by nonlinear polarization mixing. The mixing is performed by a type II degenerate parametric downconversion in a periodically poled KTP crystal pumped by a 1064 nm pulsed Nd:YAG pump. A single, linearly polarized beam, precisely at the degenerate wavelength is generated. The output spectrum has a narrow linewidth (below the instrumentation bandwidth of 1 nm) and is highly stable with respect to variations in the crystal temperature.

  4. Bs Mixing at the Tevatron

    SciTech Connect

    Gomez-Ceballos, Guillelmo; /Cantabria Inst. of Phys.

    2006-04-01

    The Tevatron collider at Fermilab provides a very rich environment for the study of B{sub s} mesons. B{sub s} Mixing is the most important analysis within the B Physics program of both experiments. In this paper they summarize the most recent results on this topic from both D0 and CDF experiments. There were very important updates in both experiments after his last talk, hence the organizers warmly recommended me to include the latest available results on B{sub s} mixing, instead of what he presents there.

  5. Function of transcription factors at DNA lesions in DNA repair.

    PubMed

    Malewicz, Michal; Perlmann, Thomas

    2014-11-15

    Cellular systems for DNA repair ensure prompt removal of DNA lesions that threaten the genomic stability of the cell. Transcription factors (TFs) have long been known to facilitate DNA repair via transcriptional regulation of specific target genes encoding key DNA repair proteins. However, recent findings identified TFs as DNA repair components acting directly at the DNA lesions in a transcription-independent fashion. Together this recent progress is consistent with the hypothesis that TFs have acquired the ability to localize DNA lesions and function by facilitating chromatin remodeling at sites of damaged DNA. Here we review these recent findings and discuss how TFs may function in DNA repair.

  6. Direct DNA isolation from solid biological sources without pretreatments with proteinase-K and/or homogenization through automated DNA extraction.

    PubMed

    Ki, Jang-Seu; Chang, Ki Byum; Roh, Hee June; Lee, Bong Youb; Yoon, Joon Yong; Jang, Gi Young

    2007-03-01

    Genomic DNA from solid biomaterials was directly isolated with an automated DNA extractor, which was based on magnetic bead technology with a bore-mediated grinding (BMG) system. The movement of the bore broke down the solid biomaterials, mixed crude lysates thoroughly with reagents to isolate the DNA, and carried the beads to the next step. The BMG system was suitable for the mechanical homogenization of the solid biomaterials and valid as an automated system for purifying the DNA from the solid biomaterials without the need for pretreatment or disruption procedures prior to the application of the solid biomaterials.

  7. Accurate quantification of supercoiled DNA by digital PCR.

    PubMed

    Dong, Lianhua; Yoo, Hee-Bong; Wang, Jing; Park, Sang-Ryoul

    2016-04-11

    Digital PCR (dPCR) as an enumeration-based quantification method is capable of quantifying the DNA copy number without the help of standards. However, it can generate false results when the PCR conditions are not optimized. A recent international comparison (CCQM P154) showed that most laboratories significantly underestimated the concentration of supercoiled plasmid DNA by dPCR. Mostly, supercoiled DNAs are linearized before dPCR to avoid such underestimations. The present study was conducted to overcome this problem. In the bilateral comparison, the National Institute of Metrology, China (NIM) optimized and applied dPCR for supercoiled DNA determination, whereas Korea Research Institute of Standards and Science (KRISS) prepared the unknown samples and quantified them by flow cytometry. In this study, several factors like selection of the PCR master mix, the fluorescent label, and the position of the primers were evaluated for quantifying supercoiled DNA by dPCR. This work confirmed that a 16S PCR master mix avoided poor amplification of the supercoiled DNA, whereas HEX labels on dPCR probe resulted in robust amplification curves. Optimizing the dPCR assay based on these two observations resulted in accurate quantification of supercoiled DNA without preanalytical linearization. This result was validated in close agreement (101~113%) with the result from flow cytometry.

  8. Accurate quantification of supercoiled DNA by digital PCR

    PubMed Central

    Dong, Lianhua; Yoo, Hee-Bong; Wang, Jing; Park, Sang-Ryoul

    2016-01-01

    Digital PCR (dPCR) as an enumeration-based quantification method is capable of quantifying the DNA copy number without the help of standards. However, it can generate false results when the PCR conditions are not optimized. A recent international comparison (CCQM P154) showed that most laboratories significantly underestimated the concentration of supercoiled plasmid DNA by dPCR. Mostly, supercoiled DNAs are linearized before dPCR to avoid such underestimations. The present study was conducted to overcome this problem. In the bilateral comparison, the National Institute of Metrology, China (NIM) optimized and applied dPCR for supercoiled DNA determination, whereas Korea Research Institute of Standards and Science (KRISS) prepared the unknown samples and quantified them by flow cytometry. In this study, several factors like selection of the PCR master mix, the fluorescent label, and the position of the primers were evaluated for quantifying supercoiled DNA by dPCR. This work confirmed that a 16S PCR master mix avoided poor amplification of the supercoiled DNA, whereas HEX labels on dPCR probe resulted in robust amplification curves. Optimizing the dPCR assay based on these two observations resulted in accurate quantification of supercoiled DNA without preanalytical linearization. This result was validated in close agreement (101~113%) with the result from flow cytometry. PMID:27063649

  9. Oxidative DNA modifications.

    PubMed

    Poulsen, Henrik E

    2005-07-01

    Oxidative DNA modifications are frequent in mammalian DNA and have been suggested an important mechanism in carcinogenesis, diabetes and ageing. The foundations for this suggestion are: Evidence for the importance of oxidative DNA modifications in cancer development is: high levels of oxidative lesions in cancer tissue; highly conserved and specific DNA repair systems targeting oxidative lesions; high levels of oxidative DNA lesions in oxidative DNA repair knock-out animals; defective repair of oxidative lesions in cancer-prone progeria syndromes; reduced cancer incidence in populations with high dietary antioxidant intake; and increased oxidative stress to DNA in tobacco smokers. Conflicting evidence for a relation between oxidative stress to DNA and cancer is: disagreement about the true levels and occurrence of the oxidative lesions in vivo; failure to identify the localization of oxidative lesions in important genes, e.g. tumor suppressor and oncogenes; lack of evidence that the oxidative lesions induce mutations in vivo; no cancer development in animals knocked-out for specific DNA repair enzymes in spite of high tissue levels of oxidative lesions; and unchanged cancer rates after antioxidant interventions in large clinical controlled and randomized trials. The rate of DNA oxidation has been estimated from urinary excretion of repair products and it is evident that if these lesions were not repaired, a large part of DNA would be oxidized to a degree not compatible with living. The methodologies by which oxidative DNA modifications are measured cover a wide and different range, advantages and disadvantages will be presented. One particular problem is artificial oxidation, and methods to prevent such artifacts will be presented together with results from a large interlaboratory standardization program. The methodology by which the lesions can be measured is complicated and prone to artifacts during DNA isolation, digestion, derivatization and maybe even during

  10. On the quantification of mixing in microfluidics.

    PubMed

    Hashmi, Ali; Xu, Jie

    2014-10-01

    Methods for quantifying mixing in microfluidics have varied largely in the past, and various indices have been employed to represent the extent of mixing. Mixing between two or more colored liquids is usually quantified using simple mathematical functions operated over a sequence of images. The function, usually termed mixing indices, involves a measure of standard deviation. Here, we first review some mixing indices and then experimentally verify the index most representative of a mixing event. It is observed that the relative mixing index is not affected by the lighting conditions, unlike other known mixing indices. Based on this finding, the use of a relative mixing index is advocated for further use in the lab-on-a-chip community for quantifying mixing events.

  11. Many Ways to Loop DNA

    PubMed Central

    Griffith, Jack D.

    2013-01-01

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

  12. Colour Mixing Based on Daylight

    ERIC Educational Resources Information Center

    Meyn, Jan-Peter

    2008-01-01

    Colour science is based on the sensation of monochromatic light. In contrast to that, surface colours are caused by reflection of wide sections of the daylight spectrum. Non-spectral colours like magenta and purple appear homologous to colours with spectral hue, if the approach of mixing monochromatic light is abandoned. It is shown that a large…

  13. Advances in compressible turbulent mixing

    SciTech Connect

    Dannevik, W.P.; Buckingham, A.C.; Leith, C.E.

    1992-01-01

    This volume includes some recent additions to original material prepared for the Princeton International Workshop on the Physics of Compressible Turbulent Mixing, held in 1988. Workshop participants were asked to emphasize the physics of the compressible mixing process rather than measurement techniques or computational methods. Actual experimental results and their meaning were given precedence over discussions of new diagnostic developments. Theoretical interpretations and understanding were stressed rather than the exposition of new analytical model developments or advances in numerical procedures. By design, compressibility influences on turbulent mixing were discussed--almost exclusively--from the perspective of supersonic flow field studies. The papers are arranged in three topical categories: Foundations, Vortical Domination, and Strongly Coupled Compressibility. The Foundations category is a collection of seminal studies that connect current study in compressible turbulent mixing with compressible, high-speed turbulent flow research that almost vanished about two decades ago. A number of contributions are included on flow instability initiation, evolution, and transition between the states of unstable flow onset through those descriptive of fully developed turbulence. The Vortical Domination category includes theoretical and experimental studies of coherent structures, vortex pairing, vortex-dynamics-influenced pressure focusing. In the Strongly Coupled Compressibility category the organizers included the high-speed turbulent flow investigations in which the interaction of shock waves could be considered an important source for production of new turbulence or for the enhancement of pre-existing turbulence. Individual papers are processed separately.

  14. Mixing and transport. [Water pollution

    SciTech Connect

    Roberts, P.J.W.

    1982-06-01

    The mixing and transport of water pollution is the subject of this literature review with 110 references. The environmental transport of pollutants is examined in streams, rivers, reservoirs, ponds, estuaries, salt marshes and coastal waters. The dynamics of fluid flow, and the physical properties of jets, plumes, and stratified fluids are discussed. (KRM)

  15. Turbulent Mixing Chemistry in Disks

    NASA Astrophysics Data System (ADS)

    Semenov, D.; Wiebe, D.

    2006-11-01

    A gas-grain chemical model with surface reaction and 1D/2D turbulent mixing is available for protoplanetary disks and molecular clouds. Current version is based on the updated UMIST'95 database with gas-grain interactions (accretion, desorption, photoevaporation, etc.) and modified rate equation approach to surface chemistry (see also abstract for the static chemistry code).

  16. Racially Mixed People in America.

    ERIC Educational Resources Information Center

    Root, Maria P. P., Ed.

    This book offers a comprehensive look at the social and psychological adjustment of multiracial people, models for identity development, contemporary immigration and marriage patterns, and methodological issues involved in conducting research with mixed-race people, all in the context of America's multiracial past and present. The following 26…

  17. Bayesian stable isotope mixing models

    EPA Science Inventory

    In this paper we review recent advances in Stable Isotope Mixing Models (SIMMs) and place them into an over-arching Bayesian statistical framework which allows for several useful extensions. SIMMs are used to quantify the proportional contributions of various sources to a mixtur...

  18. Simple rheology of mixed proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mixing different proteins to form strong gel networks for food applications may create synergistic increases in viscoelasticity that cannot be achieved with a single protein. In this study, small amplitude oscillatory shear analyses were used to investigate the rheology of calcium caseinate (CC), e...

  19. Mixing It Up with Acrylics.

    ERIC Educational Resources Information Center

    Laird, Shirley

    1999-01-01

    Presents an art activity for fifth-grade students in which they learn about basic shapes and what happens when shapes overlap, draw seven overlapping geometric shapes, review the use of acrylic paint and mixing colors, and finally paint with primary colors. (CMK)

  20. Towards understanding turbulent scalar mixing

    NASA Technical Reports Server (NTRS)

    Girimaji, Sharath S.

    1992-01-01

    In an effort towards understanding turbulent scalar mixing, we study the effect of molecular mixing, first in isolation and then by accounting for the effects of the velocity field. The chief motivation for this approach stems from the strong resemblance of the scalar probability density function (PDF) obtained from the scalar field evolving from the heat conduction equation that arises in a turbulent velocity field. However, the evolution of the scalar dissipation is different for the two cases. We attempt to account for these differences, which are due to the velocity field, using a Lagrangian frame analysis. After establishing the usefulness of this approach, we use the heat-conduction simulations (HCS), in lieu of the more expensive direct numerical simulations (DNS), to study many of the less understood aspects of turbulent mixing. Comparison between the HCS data and available models are made whenever possible. It is established that the beta PDF characterizes the evolution of the scalar PDF during mixing from all types of non-premixed initial conditions.

  1. Reductant injection and mixing system

    SciTech Connect

    Reeves, Matt; Henry, Cary A.; Ruth, Michael J.

    2016-02-16

    A gaseous reductant injection and mixing system is described herein. The system includes an injector for injecting a gaseous reductant into an exhaust gas stream, and a mixer attached to a surface of the injector. The injector includes a plurality of apertures through which the gaseous reductant is injected into an exhaust gas stream. The mixer includes a plurality of fluid deflecting elements.

  2. Bilarge neutrino mixing and the Cabibbo angle

    NASA Astrophysics Data System (ADS)

    Boucenna, S. M.; Morisi, S.; Tórtola, M.; Valle, J. W. F.

    2012-09-01

    Recent measurements of the neutrino mixing angles cast doubt on the validity of the so-far popular tribimaximal mixing Ansatz. We propose a parametrization for the neutrino mixing matrix where the reactor angle seeds the large solar and atmospheric mixing angles, equal to each other in first approximation. We suggest such a bilarge mixing pattern as a model-building standard, realized when the leading order value of θ13 equals the Cabibbo angle λC.

  3. Curating DNA specimens

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  4. Human Mitochondrial DNA Replication

    PubMed Central

    Holt, Ian J.; Reyes, Aurelio

    2012-01-01

    Elucidation of the process of DNA replication in mitochondria is in its infancy. For many years, maintenance of the mitochondrial genome was regarded as greatly simplified compared to the nucleus. Mammalian mitochondria were reported to lack all DNA repair systems, to eschew DNA recombination, and to possess but a single DNA polymerase, polymerase γ. Polγ was said to replicate mitochondrial DNA exclusively via one mechanism, involving only two priming events and a handful of proteins. In this “strand-displacement model,” leading strand DNA synthesis begins at a specific site and advances approximately two-thirds of the way around the molecule before DNA synthesis is initiated on the “lagging” strand. Although the displaced strand was long-held to be coated with protein, RNA has more recently been proposed in its place. Furthermore, mitochondrial DNA molecules with all the features of products of conventional bidirectional replication have been documented, suggesting that the process and regulation of replication in mitochondria is complex, as befits a genome that is a core factor in human health and longevity. PMID:23143808

  5. Behavior of supercoiled DNA.

    PubMed Central

    Strick, T R; Allemand, J F; Bensimon, D; Croquette, V

    1998-01-01

    We study DNA supercoiling in a quantitative fashion by micromanipulating single linear DNA molecules with a magnetic field gradient. By anchoring one end of the DNA to multiple sites on a magnetic bead and the other end to multiple sites on a glass surface, we were able to exert torsional control on the DNA. A rotating magnetic field was used to induce rotation of the magnetic bead, and reversibly over- and underwind the molecule. The magnetic field was also used to increase or decrease the stretching force exerted by the magnetic bead on the DNA. The molecule's degree of supercoiling could therefore be quantitatively controlled and monitored, and tethered-particle motion analysis allowed us to measure the stretching force acting on the DNA. Experimental results indicate that this is a very powerful technique for measuring forces at the picoscale. We studied the effect of stretching forces ranging from 0.01 pN to 100 pN on supercoiled DNA (-0.1 < sigma < 0.2) in a variety of ionic conditions. Other effects, such as stretching-relaxing hysteresis and the braiding of two DNA molecules, are discussed. PMID:9545060

  6. 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.

  7. Routine DNA testing

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  8. DNA-cell conjugates

    DOEpatents

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

    2016-05-03

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

  9. Stool DNA Test

    MedlinePlus

    ... result. A test is considered negative if DNA markers common to colon cancer or precancerous polyps and signs of blood are ... result. A test is considered positive if DNA markers common to colon cancer or precancerous polyps or signs of blood are ...

  10. Modeling DNA Replication Intermediates

    SciTech Connect

    Broyde, S.; Roy, D.; Shapiro, R.

    1997-06-01

    While there is now available a great deal of information on double stranded DNA from X-ray crystallography, high resolution NMR and computer modeling, very little is known about structures that are representative of the DNA core of replication intermediates. DNA replication occurs at a single strand/double strand junction and bulged out intermediates near the junction can lead to frameshift mutations. The single stranded domains are particularly challenging. Our interest is focused on strategies for modeling the DNA of these types of replication intermediates. Modeling such structures presents special problems in addressing the multiple minimum problem and in treating the electrostatic component of the force field. We are testing a number of search strategies for locating low energy structures of these types and we are also investigating two different distance dependent dielectric functions in the coulombic term of the force field. We are studying both unmodified DNA and DNA damaged by aromatic amines, carcinogens present in the environment in tobacco smoke, barbecued meats and automobile exhaust. The nature of the structure adopted by the carcinogen modified DNA at the replication fork plays a key role in determining whether the carcinogen will cause a mutation during replication that can initiate the carcinogenic process. In the present work results are presented for unmodified DNA.

  11. Recombinant DNA for Teachers.

    ERIC Educational Resources Information Center

    Duvall, James G., III

    1992-01-01

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

  12. Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries.

    PubMed

    Trebitz, Anett S; Hoffman, Joel C; Grant, George W; Billehus, Tyler M; Pilgrim, Erik M

    2015-07-22

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections.

  13. Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries

    PubMed Central

    Trebitz, Anett S.; Hoffman, Joel C.; Grant, George W.; Billehus, Tyler M.; Pilgrim, Erik M.

    2015-01-01

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections. PMID:26199185

  14. Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries

    NASA Astrophysics Data System (ADS)

    Trebitz, Anett S.; Hoffman, Joel C.; Grant, George W.; Billehus, Tyler M.; Pilgrim, Erik M.

    2015-07-01

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections.

  15. A mixed relaxed clock model

    PubMed Central

    2016-01-01

    Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325829

  16. A mixed relaxed clock model.

    PubMed

    Lartillot, Nicolas; Phillips, Matthew J; Ronquist, Fredrik

    2016-07-19

    Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

  17. DNA replication in thermophiles.

    PubMed

    Majerník, A I; Jenkinson, E R; Chong, J P J

    2004-04-01

    DNA replication enzymes in the thermophilic Archaea have previously attracted attention due to their obvious use in methods such as PCR. The proofreading ability of the Pyrococcus furiosus DNA polymerase has resulted in a commercially successful product (Pfu polymerase). One of the many notable features of the Archaea is the fact that their DNA processing enzymes appear on the whole to be more like those found in eukaryotes than bacteria. These proteins also appear to be simpler versions of those found in eukaryotes. For these reasons, archaeal organisms make potentially interesting model systems to explore the molecular mechanisms of processes such as DNA replication, repair and recombination. Why archaeal DNA-manipulation systems were adopted over bacterial systems by eukaryotic cells remains a most interesting question that we suggest may be linked to thermophily.

  18. Analysis of G-5x Quadruplex DNA

    NASA Astrophysics Data System (ADS)

    Weglarz, Meredith; Vesenka, James; Fritzsche, Wolfgang; Yerkes, Sarah; Kmiec, Eric

    2008-10-01

    Pure guanine-rich oligonucleotide (GRO) DNA will self-assemble into quadruplex "G-wire" DNA in the absence of stabilizing monovalent cations. Atomic force microscopy of GRO G-wires bound to freshly cleaved mica and imaged in air reveal extensive networks of connected quadruplex DNA auto-oriented on the next nearest neighbor spacing of the mica substrate. Electrical measurements of GRO G-wires across micro-fabricated gold electrodes on silicon oxide indicate the GRO G-wire networks are electrical insulators. The suspected random nature of the GRO incorporation into quadruplex DNA suggested an alternative mechanism of incorporating metal ions into G-wires: through direct weak ionic binding to the extensive phosphate backbone exposure of both the quadruplex and partially assembled oligonucelotide sequences. High densities of GRO mixed with CuCl2 or AgNO3 produced dramatically wider wires that we believe are combinations of weakly interacting metal ions and GRO. After reduction by exposure to light the Ag+ doped structures appear to be electrically conductive. This process provides a simpler method for the creation of nanometer-scale conductive wires.

  19. Quantitative analysis of DNA methylation in the promoter region of the methylguanine-O(6) -DNA-methyltransferase gene by COBRA and subsequent native capillary gel electrophoresis.

    PubMed

    Goedecke, Simon; Mühlisch, Jörg; Hempel, Georg; Frühwald, Michael C; Wünsch, Bernhard

    2015-12-01

    Along with histone modifications, RNA interference and delayed replication timing, DNA methylation belongs to the key processes in epigenetic regulation of gene expression. Therefore, reliable information about the methylation level of particular DNA fragments is of major interest. Herein the methylation level at two positions of the promoter region of the gene methylguanine-O(6) -DNA-Methyltransferase (MGMT) was investigated. Previously, it was demonstrated that the epigenetic status of this DNA region correlates with response to alkylating anticancer agents. An automated CGE method with LIF detection was established to separate the six DNA fragments resulting from combined bisulfite restriction analysis of the methylated and non-methylated MGMT promoter. In COBRA, the DNA was treated with bisulfite converting cytosine into uracil. During PCR uracil pairs with adenine, which changes the original recognition site of the restriction enzyme Taql. Artificial probes generated by mixing appropriate amounts of DNA after bisulfite treatment and PCR amplification were used for validation of the method. The methylation levels of these samples could be determined with high accuracy and precision. DNA samples prepared by mixing the corresponding clones first and then performing PCR amplification led to non-linear correlation between the corrected peak areas and the methylation levels. This effect is explained by slightly different PCR amplification of DNA with different sequences present in the mixture. The superiority of CGE over PAGE was clearly demonstrated. Finally, the established method was used to analyze the methylation levels of human brain tumor tissue samples.

  20. mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.

    PubMed

    Weissensteiner, Hansi; Forer, Lukas; Fuchsberger, Christian; Schöpf, Bernd; Kloss-Brandstätter, Anita; Specht, Günther; Kronenberg, Florian; Schönherr, Sebastian

    2016-07-08

    Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at.

  1. mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud

    PubMed Central

    Weissensteiner, Hansi; Forer, Lukas; Fuchsberger, Christian; Schöpf, Bernd; Kloss-Brandstätter, Anita; Specht, Günther; Kronenberg, Florian; Schönherr, Sebastian

    2016-01-01

    Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at. PMID:27084948

  2. The Application of DNA-Biosensors and Differential Scanning Calorimetry to the Study of the DNA-Binding Agent Berenil.

    PubMed

    De Abreu, Fabiane C; De Paula, Francine S; Ferreira, Danielle C M; Nascimento, Valberes B; Lopes, Julio C D; Santos, Alexandre M C; Santoro, Marcelo M; Salas, Carlos E; Goulart, Marília O F

    2008-03-03

    The in situ DNA-damaging capacity of berenil (1) has been investigated usingan electrochemical approach employing double stranded (ds) DNA-modified glassy carbonelectrode biosensors. Electrochemical voltammetric sensing of damage caused by 1 todsDNA was monitored by the appearance of peaks diagnostic of the oxidation of guanineand adenine. When 1 was incorporated directly onto the biosensor surface, DNA damagecould be observed at concentrations of additive as low as 10 μM. In contrast, when thedsDNA-modified biosensor was exposed to 1, in acetate buffer solution, the method wasmuch less sensitive and DNA damage could be detected only in the presence of 100 μMberenil. When mixed solutions of 1 and single stranded (ss) DNA, polyguanylic acid orpolyadenylic acid were submitted to voltammetric study, the oxidation signals of therespective bases decreased in a concentration-dependent manner and the major variation ofthe adenine current peak indicated preferential binding of 1 to adenine. The electrochemical results were in close agreement with those deriving from a differentialscanning calorimetric study of the DNA-berenil complex.

  3. DNA supercoiling and its role in DNA decatenation and unknotting

    PubMed Central

    Witz, Guillaume; Stasiak, Andrzej

    2010-01-01

    Chromosomal and plasmid DNA molecules in bacterial cells are maintained under torsional tension and are therefore supercoiled. With the exception of extreme thermophiles, supercoiling has a negative sign, which means that the torsional tension diminishes the DNA helicity and facilitates strand separation. In consequence, negative supercoiling aids such processes as DNA replication or transcription that require global- or local-strand separation. In extreme thermophiles, DNA is positively supercoiled which protects it from thermal denaturation. While the role of DNA supercoiling connected to the control of DNA stability, is thoroughly researched and subject of many reviews, a less known role of DNA supercoiling emerges and consists of aiding DNA topoisomerases in DNA decatenation and unknotting. Although DNA catenanes are natural intermediates in the process of DNA replication of circular DNA molecules, it is necessary that they become very efficiently decatenated, as otherwise the segregation of freshly replicated DNA molecules would be blocked. DNA knots arise as by-products of topoisomerase-mediated intramolecular passages that are needed to facilitate general DNA metabolism, including DNA replication, transcription or recombination. The formed knots are, however, very harmful for cells if not removed efficiently. Here, we overview the role of DNA supercoiling in DNA unknotting and decatenation. PMID:20026582

  4. Simple & Safe Genomic DNA Isolation.

    ERIC Educational Resources Information Center

    Moss, Robert; Solomon, Sondra

    1991-01-01

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

  5. Studying DNA in the Classroom.

    ERIC Educational Resources Information Center

    Zarins, Silja

    1993-01-01

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

  6. Folding and Characterization of a Bio-responsive Robot from DNA Origami.

    PubMed

    Amir, Yaniv; Abu-Horowitz, Almogit; Bachelet, Ido

    2015-12-03

    The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both stimuli and cargo can be tailored according to specific needs. Here we describe the DNA nanorobot fabrication protocol, with the use of the DNA origami technique. The procedure initiates by mixing short single-strand DNA staples into a stock mixture which is then added to a long, circular, single-strand DNA scaffold in presence of a folding buffer. A standard thermo cycler is programmed to gradually lower the mixing reaction temperature to facilitate the staples-to-scaffold annealing, which is the guiding force behind the folding of the nanorobot. Once the 60 hr folding reaction is complete, excess staples are discarded using a centrifugal filter, followed by visualization via agarose-gel electrophoresis (AGE). Finally, successful fabrication of the nanorobot is verified by transmission electron microscopy (TEM), with the use of uranyl-formate as negative stain.

  7. Mixed methods research in mental health nursing.

    PubMed

    Kettles, A M; Creswell, J W; Zhang, W

    2011-08-01

    Mixed methods research is becoming more widely used in order to answer research questions and to investigate research problems in mental health and psychiatric nursing. However, two separate literature searches, one in Scotland and one in the USA, revealed that few mental health nursing studies identified mixed methods research in their titles. Many studies used the term 'embedded' but few studies identified in the literature were mixed methods embedded studies. The history, philosophical underpinnings, definition, types of mixed methods research and associated pragmatism are discussed, as well as the need for mixed methods research. Examples of mental health nursing mixed methods research are used to illustrate the different types of mixed methods: convergent parallel, embedded, explanatory and exploratory in their sequential and concurrent combinations. Implementing mixed methods research is also discussed briefly and the problem of identifying mixed methods research in mental and psychiatric nursing are discussed with some possible solutions to the problem proposed.

  8. Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites

    USGS Publications Warehouse

    Roon, David A.; Thomas, M.E.; Kendall, K.C.; Waits, L.P.

    2005-01-01

    The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error-checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.

  9. A security system for personal genome information at DNA level.

    PubMed

    Kawazoe, Yumi; Shiba, Toshikazu; Yamamoto, Masahito; Ohuchi, Azuma

    2002-01-01

    The personal information encoded in genomic DNA should not be made available to the public. With the increasing discoveries of new genes, it has become necessary to establish a security system for personal genome information. Although many security systems that are applied for electrical information in computers have been developed and established, there is no security system for information at DNA level. In this paper, we describe a new security system for information encoded within DNA. The original genomic DNA was mixed with many kinds of dummy DNAs (mixtures of natural and/or artificial DNAs) resulting in the masking of the original information. Using these dummy molecules, we succeeded to completely 'lock'the original genome information. If this information must be 'unlocked', it can be extracted and analyzed by a removal of dummy DNAs using molecular tagging techniques or by selective amplification using key primers.

  10. DNA Based Molecular Scale Nanofabrication

    DTIC Science & Technology

    2015-12-04

    water adsorption on DNA origami template and its impact on DNA-mediated chemical reactions. We also extended the concept of DNA-mediated reaction to...other nanoscale templates, (b) Studied the thermal and chemical stability of DNA origami template. The result shows that the DNA nanostructures can be...potentially used in very harsh chemical environments, (c) Studied the effect of DNA origami template on the growth of self-assembled monolayer (SAM

  11. Application of an improved cDNA competition technique to identify prostate cancer-associated gene.

    PubMed

    Rinaldy, A R; Steiner, M S

    1999-11-01

    A technique to improve cDNA library screening was developed by using mixed probes derived from two closely related cDNA populations of high-metastatic MAT-LyLu and low-metastatic AT-1 Dunning R3227 rat prostate cancer sublines. The technique required the generation of a cDNA library from each subline followed by polymerase chain reaction (PCR) amplification of the cDNA insert population. The PCR products derived from the first library were radiolabeled and mixed with an excess amount of PCR products from the second library. The mixture and an excess amount of both the lambda and pBluescript DNA were used as a probe to screen the first cDNA library. This mixed probe (designated the competition probe) differentially cross-hybridized with the plaque lift of the screened first cDNA library. Weak radioactive signals indicated the cross-hybridization of cDNA sequences common to the competition probe mixture and the first cDNA library, whereas strong signals implied unhybridized unique or abundant cDNA sequences in the first cDNA library. The reproducibility of this technique was confirmed by showing that the full-length cDNA clones were associated with the phenotype of the screened first cell line. The isolated clones were characterized as rat nucleolar protein, rat mitochondrial genes coding for 16S and 12S rRNAs, and rat tRNAs specific for valine and phenyl-alanine. This result is consistent with the fact that the first cell line, MAT-LyLu, is metabolically more active than are AT-1 cells because of higher gene dosage or amplification of nucleolar and mitochondrial RNA and its associated genes. Another clone which had a strong signal represented a novel gene associated with the MAT-LyLu cancer phenotype.

  12. DNA UVB dosimeters.

    PubMed

    Regan, J D; Yoshida, H

    1995-11-01

    DNA can be used to establish and monitor solar UVB dose. Since the principal molecular site of UVB damage in living organisms is DNA, it is logical to quantitate biologically effective solar UVB in DNA dosimeters. In addition to their particular sensitivity to UVB, DNA dosimeters have the advantage of a 2 pi geometry for collecting diffuse UVB radiation from all vectors, low cost, small size and portability, and no moving parts. Both molecular (cyclobutane pyrimidine dimers) and biological (bacteriophage plaques) dosimeters can be quantitated as endpoints to yield the total dose. DNA dosimeters integrate the absorbed energy of all UVB wavelengths (290-320 nm), are highly sensitive to the differential biological effectiveness of these wavelengths, and also integrate over time in hours, days or weeks of exposure. Our experiments have focused on the demonstration of DNA solar dosimeters in the ocean at various depths, the application of the dosimeters to the terrestrial monitoring of solar UVB under various conditions, and the development of a mini-dosimeter which uses nanograms of DNA and is assayed by polymerase chain reaction.

  13. DNA Import into Mitochondria.

    PubMed

    Konstantinov, Yu M; Dietrich, A; Weber-Lotfi, F; Ibrahim, N; Klimenko, E S; Tarasenko, V I; Bolotova, T A; Koulintchenko, M V

    2016-10-01

    In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria. In this review, we discuss current state of investigations in this area, particularly specificity of DNA import into mitochondria and its features in plants, animals, and yeasts; a tentative mechanism of DNA import across the mitochondrial outer and inner membranes; experimental data evidencing several existing, but not yet fully understood mechanisms of DNA transfer into mitochondria. Currently available data regarding transport of informational macromolecules (DNA, RNA, and proteins) into the mitochondria do not rule out that the mechanism of protein and tRNA import as well as tRNA and DNA import into the mitochondria may partially overlap.

  14. Quantitive DNA Fiber Mapping

    SciTech Connect

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

    2008-01-28

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

  15. DNA-PK assay

    DOEpatents

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  16. DNA Fingerprinting of Mycobacterium leprae Strains Using Variable Number Tandem Repeat (VNTR) - Fragment Length Analysis (FLA)

    PubMed Central

    Jensen, Ronald W.; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

    2011-01-01

    gel electrophoresis to verify the presence of the desired DNA segments, and then submitted for fluorescent fragment length analysis (FLA) using capillary electrophoresis. DNA from armadillo passaged bacteria with a known number of repeat copies for each locus is used as a positive control. The FLA chromatograms are then examined using Peak Scanner software and fragment length is converted to number of VNTR copies (allele). Finally, the VNTR haplotypes are analyzed for patterns, and when combined with patient clinical data can be used to track distribution of strain types. PMID:21775969

  17. DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA).

    PubMed

    Jensen, Ronald W; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

    2011-07-15

    presence of the desired DNA segments, and then submitted for fluorescent fragment length analysis (FLA) using capillary electrophoresis. DNA from armadillo passaged bacteria with a known number of repeat copies for each locus is used as a positive control. The FLA chromatograms are then examined using Peak Scanner software and fragment length is converted to number of VNTR copies (allele). Finally, the VNTR haplotypes are analyzed for patterns, and when combined with patient clinical data can be used to track distribution of strain types.

  18. HETEROGENEOUS REBURNING BY MIXED FUELS

    SciTech Connect

    Wei-Yin Chen; Benson B. Gathitu

    2005-01-14

    Recent studies of heterogeneous reburning, i.e., reburning involving a coal-derived char, have elucidated its variables, kinetics and mechanisms that are valuable to the development of a highly efficient reburning process. Young lignite chars contain catalysts that not only reduce NO, but they also reduce HCN that is an important intermediate that recycles to NO in the burnout zone. Gaseous CO scavenges the surface oxides that are formed during NO reduction, regenerating the active sites on the char surface. Based on this mechanistic information, cost-effective mixed fuels containing these multiple features has been designed and tested in a simulated reburning apparatus. Remarkably high reduction of NO and HCN has been observed and it is anticipated that mixed fuel will remove 85% of NO in a three-stage reburning process.

  19. Topological mixing with ghost rods

    NASA Astrophysics Data System (ADS)

    Gouillart, Emmanuelle; Thiffeault, Jean-Luc; Finn, Matthew D.

    2006-03-01

    Topological chaos relies on the periodic motion of obstacles in a two-dimensional flow in order to form nontrivial braids. This motion generates exponential stretching of material lines, and hence efficient mixing. Boyland, Aref, and Stremler [J. Fluid Mech. 403, 277 (2000)] have studied a specific periodic motion of rods that exhibits topological chaos in a viscous fluid. We show that it is possible to extend their work to cases where the motion of the stirring rods is topologically trivial by considering the dynamics of special periodic points that we call “ghost rods”, because they play a similar role to stirring rods. The ghost rods framework provides a new technique for quantifying chaos and gives insight into the mechanisms that produce chaos and mixing. Numerical simulations for Stokes flow support our results.

  20. Topological mixing with ghost rods.

    PubMed

    Gouillart, Emmanuelle; Thiffeault, Jean-Luc; Finn, Matthew D

    2006-03-01

    Topological chaos relies on the periodic motion of obstacles in a two-dimensional flow in order to form nontrivial braids. This motion generates exponential stretching of material lines, and hence efficient mixing. Boyland, Aref, and Stremler [J. Fluid Mech. 403, 277 (2000)] have studied a specific periodic motion of rods that exhibits topological chaos in a viscous fluid. We show that it is possible to extend their work to cases where the motion of the stirring rods is topologically trivial by considering the dynamics of special periodic points that we call "ghost rods", because they play a similar role to stirring rods. The ghost rods framework provides a new technique for quantifying chaos and gives insight into the mechanisms that produce chaos and mixing. Numerical simulations for Stokes flow support our results.

  1. Pediatric Mixed Connective Tissue Disease.

    PubMed

    Berard, Roberta A; Laxer, Ronald M

    2016-05-01

    Pediatric-onset mixed connective tissue disease is among the rare disease entities in pediatric rheumatology and includes features of arthritis, polymyositis/dermatomyositis, systemic lupus erythematosus, and systemic sclerosis. Accurate recognition and diagnosis of the disease is paramount to prevent long-term morbidity. Advances in the genetic and immunologic understanding of the factors involved in the etiopathogenesis provide an opportunity for improvements in prognostication and targeted therapy. The development of a multinational cohort of patients with mixed connective tissue disease would be invaluable to provide more updated data regarding the clinical presentation, to develop a standardized treatment approach, disease activity and outcome tools, and to provide data on long-term outcomes and comorbidities.

  2. Kinetic mixing at strong coupling

    NASA Astrophysics Data System (ADS)

    Del Zotto, Michele; Heckman, Jonathan J.; Kumar, Piyush; Malekian, Arada; Wecht, Brian

    2017-01-01

    A common feature of many string-motivated particle physics models is additional strongly coupled U (1 )'s. In such sectors, electric and magnetic states have comparable mass, and integrating out modes also charged under U (1 ) hypercharge generically yields C P preserving electric kinetic mixing and C P violating magnetic kinetic mixing terms. Even though these extra sectors are strongly coupled, we show that in the limit where the extra sector has approximate N =2 supersymmetry, we can use formal methods from Seiberg-Witten theory to compute these couplings. We also calculate various quantities of phenomenological interest such as the cross section for scattering between visible sector states and heavy extra sector states as well as the effects of supersymmetry breaking induced from coupling to the minimal supersymmetric Standard Model.

  3. Heterogeneous Reburning By Mixed Fuels

    SciTech Connect

    Anderson Hall

    2009-03-31

    Recent studies of heterogeneous reburning, i.e., reburning involving a coal-derived char, have elucidated its variables, kinetics and mechanisms that are valuable to the development of a highly efficient reburning process. Young lignite chars contain catalysts that not only reduce NO, but they also reduce HCN that is an important intermediate that recycles to NO in the burnout zone. Gaseous CO scavenges the surface oxides that are formed during NO reduction, regenerating the active sites on the char surface. Based on this mechanistic information, cost-effective mixed fuels containing these multiple features has been designed and tested in a simulated reburning apparatus. Remarkably high reduction of NO and HCN has been observed and it is anticipated that mixed fuel will remove 85% of NO in a three-stage reburning process.

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

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

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

  5. Lidar for Lateral Mixing (LATMIX)

    DTIC Science & Technology

    2013-09-30

    km, i.e., the “ submesoscale ”. We aim to understand the underlying mechanisms and forcing, as well as the temporal, spatial, and scale variability of...the overall objectives of the Lateral Mixing DRI to try to determine the extent to which submesoscale stirring is driven by a cascade of energy down...technical goal of our work is to develop the use of airborne LIDAR surveys of evolving dye experiments as a tool for studying submesoscale lateral dispersion

  6. MISO - Mixed Integer Surrogate Optimization

    SciTech Connect

    Mueller, Juliane

    2016-01-20

    MISO is an optimization framework for solving computationally expensive mixed-integer, black-box, global optimization problems. MISO uses surrogate models to approximate the computationally expensive objective function. Hence, derivative information, which is generally unavailable for black-box simulation objective functions, is not needed. MISO allows the user to choose the initial experimental design strategy, the type of surrogate model, and the sampling strategy.

  7. Mixed real/complex factorization

    SciTech Connect

    Lima, L.T.G. . Dept. of Electrical Engineering); Martines, N.; Pinto, H.J.C.P. . Centro de Pesquisas de Energia Electrica)

    1993-02-01

    This paper describes a mixed real/complex sparse matrix factorization and solution scheme applied to a large matrix problem. Large system eigenanalysis and frequency domain methods will directly benefit from the proposed scheme, which can reduce both memory and CPU time requirements when compared to conventional complex-only solutions. The application in hand is the small signal electromechanical stability analysis of large power systems. The savings obtained are significant considering the CPU intensive nature of these matrix problems.

  8. Mixing in the solar tachocline

    NASA Astrophysics Data System (ADS)

    Brun, Allan Sacha

    We conduct numerical simulations of updated solar models including a physical treatment of the tachocline (Spiegel & Zahn 1992), the rotational transition layer localized at the base of the solar convection zone. We first describe what is the current understanding of this thin shear layer. We then show that we improve substantially the agreement between the models and the observed Sun by taking into account the macroscopic mixing occurring within this region.

  9. Coastal and Near Surface Mixing

    DTIC Science & Technology

    2016-06-07

    The challenge is to measure the mixing directly without relying on models and assumptions about the nature of turbulence. Sound is backscattered...turbulence vary considerably. The towed vehicle (Fig. 1) carries high-resolution velocity and temperature sensors (shear probes and thermistors), current...meters, a vertical array of three pairs of salinity and temperature sensors, and motion sensors. These sensors provide a measure of the density

  10. Plasmid DNA manufacturing technology.

    PubMed

    Carnes, Aaron E; Williams, James A

    2007-01-01

    Today, plasmid DNA is becoming increasingly important as the next generation of biotechnology products (gene medicines and DNA vaccines) make their way into clinical trials, and eventually into the pharmaceutical marketplace. This review summarizes recent patents and patent applications relating to plasmid manufacturing, in the context of a comprehensive description of the plasmid manufacturing intellectual property landscape. Strategies for plasmid manufacturers to develop or in-license key plasmid manufacturing technologies are described with the endpoint of efficiently producing kg quantities of plasmid DNA of a quality that meets anticipated European and FDA quality specifications for commercial plasmid products.

  11. Biology of DNA restriction.

    PubMed Central

    Bickle, T A; Krüger, D H

    1993-01-01

    Our understanding of the evolution of DNA restriction and modification systems, the control of the expression of the structural genes for the enzymes, and the importance of DNA restriction in the cellular economy has advanced by leaps and bounds in recent years. This review documents these advances for the three major classes of classical restriction and modification systems, describes the discovery of a new class of restriction systems that specifically cut DNA carrying the modification signature of foreign cells, and deals with the mechanisms developed by phages to avoid the restriction systems of their hosts. PMID:8336674

  12. Focus: DNA probes

    SciTech Connect

    Not Available

    1986-11-01

    Progress in the development of DNA probes for the identification and quantitation of specific genetic sequences in biological samples is reviewed. Current research efforts in the development of DNA probes for the diagnosis of a wide variety of bacterial, viral, and other infectious diseases, such as herpes simplex and cytomegalovirus, and inherited genetic diseases such as cystic fibrosis and sickle cell anemia are discussed. Progress in development of DNA probe assays for cancer diagnosis, detection of Salmonella food poisoning, tissue typing (detection of histocompatibility antigens), mutagen screening, and animal diseases, among other applications is included.

  13. Mixed Alcohol Synthesis Catalyst Screening

    SciTech Connect

    Gerber, Mark A.; White, James F.; Stevens, Don J.

    2007-09-03

    National Renewable Energy Laboratory (NREL) and Pacific Northwest National Laboratory (PNNL) are conducting research to investigate the feasibility of producing mixed alcohols from biomass-derived synthesis gas (syngas). PNNL is tasked with obtaining commercially available or preparing promising mixed-alcohol catalysts and screening them in a laboratory-scale reactor system. Commercially available catalysts and the most promising experimental catalysts are provided to NREL for testing using a slipstream from a pilot-scale biomass gasifier. From the standpoint of producing C2+ alcohols as the major product, it appears that the rhodium catalyst is the best choice in terms of both selectivity and space-time yield (STY). However, unless the rhodium catalyst can be improved to provide minimally acceptable STYs for commercial operation, mixed alcohol synthesis will involve significant production of other liquid coproducts. The modified Fischer-Tropsch catalyst shows the most promise for providing both an acceptable selectivity to C2+ alcohols and total liquid STY. However, further optimization of the Fischer-Tropsch catalysts to improve selectivity to higher alcohols is highly desired. Selection of a preferred catalyst will likely entail a decision on the preferred coproduct slate. No other catalysts tested appear amenable to the significant improvements needed for acceptable STYs.

  14. Assessing mixed waste treatment technologies

    SciTech Connect

    Berry, J.B.; Bloom, G.A.; Hart, P.W.

    1994-06-01

    The US Department of Energy (DOE) is responsible for the management and treatment of its mixed low-level wastes (MLLW). As discussed earlier in this conference MLLW are regulated under both the Resource Conservation and Recovery Act and various DOE orders. During the next 5 years, DOE will manage over 1,200,000 m{sup 3} of MLLW and mixed transuranic (MTRU) waste at 50 sites in 22 states (see Table 1). The difference between MLLW and MTRU waste is in the concentration of elements that have a higher atomic weight than uranium. Nearly all of this waste will be located at 13 sites. More than 1400 individual mixed waste streams exist with different chemical and physical matrices containing a wide range of both hazardous and radioactive contaminants. Their containment and packaging vary widely (e.g., drums, bins, boxes, and buried waste). This heterogeneity in both packaging and waste stream constituents makes characterization difficult, which results in costly sampling and analytical procedures and increased risk to workers.

  15. Ion mixing and phase diagrams

    NASA Astrophysics Data System (ADS)

    Lau, S. S.; Liu, B. X.; Nicolet, M.-A.

    1983-05-01

    Interactions induced by ion irradiation are generally considered to be non-equilibrium processes, whereas phase diagrams are determined by phase equilibria. These two entities are seemingly unrelated. However, if one assumes that quasi-equilibrium conditions prevail after the prompt events, subsequent reactions are driven toward equilibrium by thermodynamical forces. Under this assumption, ion-induced reactions are related to equilibrium and therefore to phase diagrams. This relationship can be seen in the similarity that exists in thin films between reactions induced by ion irradiation and reactions induced by thermal annealing. In the latter case, phase diagrams have been used to predict the phase sequence of stable compound formation, notably so in cases of silicide formation. Ion-induced mixing not only can lead to stable compound formation, but also to metastable alloy formation. In some metal-metal systems, terminal solubilities can be greatly extended by ion mixing. In other cases, where the two constituents of the system have different crystal structures, extension of terminal solubility from both sides of the phase diagram eventually becomes structurally incompatible and a glassy (amorphous) mixture can form. The composition range where this bifurcation is likely to occur is in the two-phase regions of the phase diagram. These concepts are potentially useful guides in selecting metal pairs that from metallic glasses by ion mixing. In this report, phenomenological correlation between stable (and metastable) phase formation and phase diagram is discussed in terms of recent experimental data.

  16. Scalable Lateral Mixing and Coherent Turbulence (LatMix) DRI: Turbulence-Resolving Simulations of Upper-Ocean Lateral Mixing

    DTIC Science & Technology

    2013-09-30

    The interaction of finescale and submesoscale upper-ocean mixing at fronts. OBJECTIVES Physically-based parameterizations of vertical mixed layer...dimensions of the oblong domain geometry on realized submesoscale instabilities. Figure 1: Surface buoyancy b from LES of baroclinic mixed layer

  17. Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

    SciTech Connect

    Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; Konopka, Allan E.; Nelson, William C.; Arntzen, Evan V.; Chrisler, William B.; Chu, Rosalie K.; Danczak, Robert E.; Fansler, Sarah J.; Kennedy, David W.; Resch, Charles T.; Tfaily, Malak

    2016-04-07

    Environmental transition zones are associated with geochemical gradients that overcome energy limitations to microbial metabolism, resulting in biogeochemical hot spots and moments. Riverine systems where groundwater mixes with surface water (the hyporheic zone) are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. To investigate the coupling among groundwater-surface water mixing, microbial communities, and biogeochemistry we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Mixing of groundwater and surface water resulted in a shift from transport-driven stochastic dynamics to a deterministic microbial structure associated with elevated biogeochemical rates. While the dynamics of the hyporheic make predictive modeling a challenge, we provide new knowledge that can improve the tractability of such models.

  18. Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

    PubMed Central

    Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; Konopka, Allan E.; Nelson, William C.; Arntzen, Evan V.; Chrisler, William B.; Chu, Rosalie K.; Danczak, Robert E.; Fansler, Sarah J.; Kennedy, David W.; Resch, Charles T.; Tfaily, Malak

    2016-01-01

    Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds. PMID:27052662

  19. Groundwater-Surface Water Mixing Shifts Ecological Assembly Processes and Stimulates Organic Carbon Turnover

    NASA Astrophysics Data System (ADS)

    Stegen, J.; Fredrickson, J.; Wilkins, M.; Konopka, A.; Nelson, W.; Arntzen, E.; Chrisler, W.; Chu, R. K.; Danczak, B.; Fansler, S.; Kennedy, D.; Resch, T.; Tfaily, M. M.

    2015-12-01

    Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hot spots and moments. Riverine systems where groundwater mixes with surface water (the hyporheic zone) are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. To investigate the coupling among groundwater-surface water mixing, microbial communities, and biogeochemistry we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone simultaneously (i) stimulated heterotrophic respiration, (ii) altered organic carbon composition, (iii) caused ecological processes to shift from stochastic to deterministic, and (iv) selected for microbial taxa capable of degrading a broad suite of organic compounds.

  20. FBI's DNA analysis program

    NASA Astrophysics Data System (ADS)

    Brown, John R.

    1994-03-01

    Forensic DNA profiling technology is a significant law enforcement tool due to its superior discriminating power. Applying the principles of population genetics to the DNA profile obtained in violent crime investigations results in low frequency of occurrence estimates for the DNA profile. These estimates often range from a frequency of occurrence of 1 in 50 unrelated individuals to 1 in a million unrelated individuals or even smaller. It is this power to discriminate among individuals in the population that has propelled forensic DNA technology to the forefront of forensic testing in violent crime cases. Not only is the technology extremely powerful in including or excluding a criminal suspect as the perpetrator, but it also gives rise to the potential of identifying criminal suspects in cases where the investigators of unknown suspect cases have exhausted all other available leads.

  1. Close encounters with DNA

    PubMed Central

    Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

    2014-01-01

    Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena and we review the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

  2. DNA-templated nanofabrication.

    PubMed

    Becerril, Héctor A; Woolley, Adam T

    2009-02-01

    Nanofabrication, or the organizational control over matter at the nanometre scale, is an intriguing scientific challenge requiring multidisciplinary tools for its solution. DNA is a biomolecule that can be combined with other nanometre-scale entities through chemical self-assembly to form a broad variety of nanomaterials. In this tutorial review we present the principles that allow DNA to interact with other chemical species, and describe the challenges and potential applications of DNA as a template for making both biological and inorganic features with nanometre resolution. As such, this report should be of interest to chemists, surface and materials scientists, biologists, and nanotechnologists, as well as others who seek to use DNA in nanofabrication.

  3. Multiplex analysis of DNA

    DOEpatents

    Church, George M.; Kieffer-Higgins, Stephen

    1992-01-01

    This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

  4. Making DNA Fingerprints.

    ERIC Educational Resources Information Center

    Nunley, Kathie F.

    1996-01-01

    Presents an activity to simulate electrophoresis using everyday items. Uses adding machine paper to construct a set of DNA fingerprints that can be used to solve crime cases designed by students in any biology class. (JRH)

  5. Retroviral DNA Integration

    PubMed Central

    2016-01-01

    The integration of a DNA copy of the viral RNA genome into host chromatin is the defining step of retroviral replication. This enzymatic process is catalyzed by the virus-encoded integrase protein, which is conserved among retroviruses and LTR-retrotransposons. Retroviral integration proceeds via two integrase activities: 3′-processing of the viral DNA ends, followed by the strand transfer of the processed ends into host cell chromosomal DNA. Herein we review the molecular mechanism of retroviral DNA integration, with an emphasis on reaction chemistries and architectures of the nucleoprotein complexes involved. We additionally discuss the latest advances on anti-integrase drug development for the treatment of AIDS and the utility of integrating retroviral vectors in gene therapy applications. PMID:27198982

  6. DNA damage and carcinogenesis

    SciTech Connect

    Stelow, R B

    1980-01-01

    Although cancer may arise as a result of many different types of molecular changes, there is little reason to doubt that changes to DNA are one of the more important ones in cancer initiation. Although DNA repair mechanisms seem able to eliminate a very large fraction of deleterious changes to DNA, we not only have little insight into the molecular mechanisms involved in such repair, but have a negligible amount of information to permit us to estimate the shape of dose response relations at low doses. The case of skin cancer is a special one, in that the average population is exposed to sufficient solar uv so that the effects of small increments in uv dose may be estimated. An approximate 85% reduction in DNA repair increases skin cancer incidence 10/sup 4/ fold.

  7. DNA sequencing conference, 2

    SciTech Connect

    Cook-Deegan, R.M.; Venter, J.C.; Gilbert, W.; Mulligan, J.; Mansfield, B.K.

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  8. DNA Vaccination in Chickens.

    PubMed

    Gupta, Shishir Kumar; Dey, Sohini; Chellappa, Madhan Mohan

    2016-01-01

    Robust and sustainable development of poultry industry requires prevention of deadly infectious diseases. Vigorous vaccination of the birds is a routine practice; however, the live and inactivated vaccines that are used have inherent disadvantages. New-generation vaccines such as DNA vaccines offer several advantages over conventional vaccines. DNA vaccines, which encode an antigen of interest or multiple antigens in the target host, are stable, easy to produce and administer, do not require cold chain maintenance, and are not affected by the maternal antibodies. In addition, DNA vaccines can also be administered in ovo, and thus, mass vaccination and early induction of immune response can effectively be achieved. In this chapter, we focus on the development of DNA vaccines against important infectious viral as well as parasitic diseases of poultry.

  9. Interaction of DNA and DNA-anti-DNA complexes to fibronectin

    SciTech Connect

    Gupta, R.C.; Simpson, W.A.; Raghow, R.; Hasty, K.

    1986-03-01

    Fibronectin (Fn) is a large multidomain glycoprotein found in the basement membrane, on cell surface and in plasma. The interactions of Fn with DNA may be significant in glomerular deposition of DNA-anti-DNA complexes in patients with systemic lupus erythematosus (SLE). The authors examined the binding of DNA and DNA-anti-DNA complexes to Fn by a solid phase assay in which Fn was coated to microtiter plates and reacted with (/sup 3/H)DNA or DNA complexes with a monoclonal anti-DNA antibody. The optimal interaction of DNA with Fn occurs at <0.1M NaCl suggesting that the binding is charge dependent; the specificity of this binding was shown by competitive inhibition and locking experiments using anti-Fn. The binding was maximum at pH 6.5 and in the absence of Ca/sup 2 +/. The addition of Clq enhanced the binding of DNA and DNA-anti-DNA complexes to Fn, whereas heparan sulfate inhibited such binding. The monomeric or aggregated IgC did not bind Fn but aggregated IgG bound to Fn in the presence of Clq. Furthermore, DNA-anti-DNA complexes in sera from active SLE patients bound Fn which was enhanced in the presence of Clq; DNase abolished this binding indicating that the interaction of these complexes was mediated by DNA. These observations may partially explain the molecular mechanism(s) of the deposition of DNA-anti-DNA complexes in basement membrane.

  10. Testing Mixed Distributions when the Mixing Distribution Is Known

    NASA Astrophysics Data System (ADS)

    Pommeret, Denys

    In this paper we present smooth goodness of fit tests for testing the mixture distribution of a sequence of i.i.d. random variables. We consider mixture models when the mixing distribution is known. We adapt a Schwarz’s criteria initiated by Ledwina (J Am Stat Assoc 89:1000-1005, 1994) and inspired by the Neyman (Skandinavian Aktuarial 20:149-199, 1937) smooth test procedure. A Monte Carlo study is provided in order to assess the performance of the test.

  11. Patterning nanocrystals using DNA

    NASA Astrophysics Data System (ADS)

    Williams, Shara Carol

    One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made. Here, we have sought to assemble larger and more complex nanostructures. Cold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA "trimer." This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than 20 mum, and

  12. Patterning nanocrystals using DNA

    SciTech Connect

    Williams, Shara Carol

    2003-01-01

    One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than

  13. Das DNA-Puzzle

    NASA Astrophysics Data System (ADS)

    Kirchner, Stefan

    Im Jahre 1953 wurde von James Watson und Francis Crick erstmalig der strukturelle Aufbau der sogenannten DNA (Desoxyribonukleinsäure) beschrieben, welche das Erbgut jedes Lebewesens enthält. Der wesentliche Teil des Erbguts wird dabei durch eine sehr lange Folge der vier Basen Adenin (A), Cytosin (C), Guanin (G) und Thymin (T) codiert. Seit einigen Jahren ist es möglich, die Folge der vier Basen zu einer gegebenen DNA zu bestimmen. Biologen bezeichnen diesen Vorgang als Sequenzierung.

  14. Blowing DNA bubbles.

    PubMed

    Severin, N; Zhuang, W; Ecker, C; Kalachev, A A; Sokolov, I M; Rabe, J P

    2006-11-01

    We report here experimental observations which indicate that topologically or covalently formed polymer loops embedded in an ultrathin liquid film on a solid substrate can be "blown" into circular "bubbles" during scanning force microscopy (SFM) imaging. In particular, supercoiled vector DNA has been unraveled, moved, stretched, and overstretched to two times its B-form length and then torn apart. We attribute the blowing of the DNA bubbles to the interaction of the tapping SFM tip with the ultrathin liquid film.

  15. Programming DNA tube circumferences.

    PubMed

    Yin, Peng; Hariadi, Rizal F; Sahu, Sudheer; Choi, Harry M T; Park, Sung Ha; Labean, Thomas H; Reif, John H

    2008-08-08

    Synthesizing molecular tubes with monodisperse, programmable circumferences is an important goal shared by nanotechnology, materials science, and supermolecular chemistry. We program molecular tube circumferences by specifying the complementarity relationships between modular domains in a 42-base single-stranded DNA motif. Single-step annealing results in the self-assembly of long tubes displaying monodisperse circumferences of 4, 5, 6, 7, 8, 10, or 20 DNA helices.

  16. Model Verification of Mixed Dynamic Systems

    NASA Technical Reports Server (NTRS)

    Evensen, D. A.; Chrostowski, J. D.; Hasselman, T. K.

    1982-01-01

    MOVER uses experimental data to verify mathematical models of "mixed" dynamic systems. The term "mixed" refers to interactive mechanical, hydraulic, electrical, and other components. Program compares analytical transfer functions with experiment.

  17. A survey of mixed finite element methods

    NASA Technical Reports Server (NTRS)

    Brezzi, F.

    1987-01-01

    This paper is an introduction to and an overview of mixed finite element methods. It discusses the mixed formulation of certain basic problems in elasticity and hydrodynamics. It also discusses special techniques for solving the discrete problem.

  18. Mode of formation and structural features of DNA-cationic liposome complexes used for transfection.

    PubMed

    Gershon, H; Ghirlando, R; Guttman, S B; Minsky, A

    1993-07-20

    Complexes formed between cationic liposomes and nucleic acids represent a highly efficient vehicle for delivery of DNA and RNA molecules into a large variety of eukaryotic cells. By using fluorescence, gel electrophoresis, and metal-shadowing electron microscopy techniques, the factors that affect the, yet unclear, interactions between DNA and cationic liposomes as well as the structural features of the resulting complexes have been elucidated. A model is suggested according to which cationic liposomes bind initially to DNA molecules to form clusters of aggregated vesicles along the nucleic acids. At a critical liposome density, two processes occur, namely, DNA-induced membrane fusion, indicated by lipid mixing studies, and liposome-induced DNA collapse, pointed out by the marked cooperativity of the encapsulation processes, by their modulations by DNA-condensing agents, and also by their conspicuous independence upon DNA length. The DNA collapse leads to the formation of condensed structures which can be completely encapsulated within the fused lipid bilayers in a fast, highly cooperative process since their exposed surface is substantially smaller than that of extended DNA molecules. The formation of the transfecting DNA-liposome complexes in which the nucleic acids are fully encapsulated within a positively-charged lipid bilayer is proposed, consequently, to be dominated by mutual effects exerted by the DNA and the cationic liposomes, leading to interrelated lipid fusion and DNA collapse.

  19. Simulation of DNA in water/ethanol mixture

    NASA Astrophysics Data System (ADS)

    Wen, Jing; Shen, Hao; Zhai, Yan-Rong; Zhang, Feng-Shou

    2016-05-01

    The study of B-DNA in mixed solvent comprised of water and ethanol with different concentrations at 298 K has been conducted by molecular dynamics simulation. We find that the structure of DNA is easily affected by the aqueous environment. Property and structure changes of the solvent will influence the local structure of DNA helix, induce the conformation transition between different forms, and even cause the degeneration of DNA. The addition of ethanol can reduce the activity of water, changes the solvent structure around DNA. DNA in the solvent with low concentration of ethanol changes little, when the ethanol increases in the solvent, large structure changes occur at the ends of the helix first, then show the characters of A-form, the minor groove becomes wider and shallower, and the length is shortened when in the solvent with the concentration of 0.88 g/cm3. The mechanism behind is discussed, and we find the competition between the solvent molecules and counterions coupling to the free oxygen atoms of the phosphate groups, and the breaking of the spin of water both contribute to the structure changes of DNA in the simulation.

  20. Variations in brain DNA

    PubMed Central

    Avila, Jesús; Gómez-Ramos, Alberto; Soriano, Eduardo

    2014-01-01

    It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain. PMID:25505410

  1. Transcription of mitochondrial DNA.

    PubMed

    Tabak, H F; Grivell, L A; Borst, P

    1983-01-01

    While mitochondrial DNA (mtDNA) is the simplest DNA in nature, coding for rRNAs and tRNAs, results of DNA sequence, and transcript analysis have demonstrated that both the synthesis and processing of mitochondrial RNAs involve remarkably intricate events. At one extreme, genes in animal mtDNAs are tightly packed, both DNA strands are completely transcribed (symmetric transcription), and the appearance of specific mRNAs is entirely dependent on processing at sites signalled by the sequences of the tRNAs, which abut virtually every gene. At the other extreme, gene organization in yeast (Saccharomyces) is anything but compact, with long stretches of AT-rich DNA interspaced between coding sequences and no obvious logic to the order of genes. Transcription is asymmetric and several RNAs are initiated de novo. Nevertheless, extensive RNA processing occurs due largely to the presence of split genes. RNA splicing is complex, is controlled by both mitochondrial and nuclear genes, and in some cases is accompanied by the formation of RNAs that behave as covalently closed circles. The present article reviews current knowledge of mitochondrial transcription and RNA processing in relation to possible mechanisms for the regulation of mitochondrial gene expression.

  2. DNA methylation and differentiation.

    PubMed Central

    Michalowsky, L A; Jones, P A

    1989-01-01

    The methylation of specific cytosine residues in DNA has been implicated in regulating gene expression and facilitating functional specialization of cellular phenotypes. Generally, the demethylation of certain CpG sites correlates with transcriptional activation of genes. 5-Azacytidine is an inhibitor of DNA methylation and has been widely used as a potent activator of suppressed genetic information. Treatment of cells with 5-azacytidine results in profound phenotypic alterations. The drug-induced hypomethylation of DNA apparently perturbs DNA-protein interactions that may consequently alter transcriptional activity and cell determination. The inhibitory effect of cytosine methylation may be exerted via altered DNA-protein interactions specifically or may be transduced by a change in the conformation of chromatin. Recent studies have demonstrated that cytosine methylation also plays a central role in parental imprinting, which in turn determines the differential expression of maternal and paternal genomes during embryogenesis. In other words, methylation is the mechanism whereby the embryo retains memory of the gametic origin of each component of genetic information. A memory of this type would probably persist during DNA replication and cell division as methylation patterns are stable and heritable. PMID:2466640

  3. DNA biosensors that reason.

    PubMed

    Sainz de Murieta, Iñaki; Rodríguez-Patón, Alfonso

    2012-08-01

    Despite the many designs of devices operating with the DNA strand displacement, surprisingly none is explicitly devoted to the implementation of logical deductions. The present article introduces a new model of biosensor device that uses nucleic acid strands to encode simple rules such as "IF DNA_strand(1) is present THEN disease(A)" or "IF DNA_strand(1) AND DNA_strand(2) are present THEN disease(B)". Taking advantage of the strand displacement operation, our model makes these simple rules interact with input signals (either DNA or any type of RNA) to generate an output signal (in the form of nucleotide strands). This output signal represents a diagnosis, which either can be measured using FRET techniques, cascaded as the input of another logical deduction with different rules, or even be a drug that is administered in response to a set of symptoms. The encoding introduces an implicit error cancellation mechanism, which increases the system scalability enabling longer inference cascades with a bounded and controllable signal-noise relation. It also allows the same rule to be used in forward inference or backward inference, providing the option of validly outputting negated propositions (e.g. "diagnosis A excluded"). The models presented in this paper can be used to implement smart logical DNA devices that perform genetic diagnosis in vitro.

  4. Quantification of African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV-UG) in single and mixed infected Cassava (Manihot esculenta Crantz) using quantitative PCR.

    PubMed

    Naseem, Saadia; Winter, Stephan

    2016-01-01

    The quantity of genomic DNA-A and DNA-B of African cassava mosaic virus (ACMV) and East African cassava mosaic virus Uganda (Uganda variant, EACMV-UG) was analysed using quantitative PCR to assess virus concentrations in plants from susceptible and tolerant cultivars. The concentrations of genome components in absolute and relative quantification experiments in single and mixed viral infections were determined. Virus concentration was much higher in symptomatic leaf tissues compared to non-symptomatic leaves and corresponded with the severity of disease symptoms. In general, higher titres were recorded for EACMV-UG Ca055 compared to ACMV DRC6. The quantitative assessment also showed that the distribution of both viruses in the moderately resistant cassava cv. TMS 30572 was not different from the highly susceptible cv. TME 117. Natural mixed infections with both viruses gave severe disease symptoms. Relative quantification of virus genomes in mixed infections showed higher concentrations of EACMV-UG DNA-A compared to ACMV DNA-A, but a marked reduction of EACMV-UG DNA-B. The higher concentrations of EACMV-UG DNA-B compared to EACMV DNA-A accumulation in single infections were consistent. Since DNA-B is implicated in virus cell-to-cell spread and systemic movement, the abundance of the EACMV-UG DNA-B may be an important factor driving cassava mosaic disease epidemic.

  5. Mixed aggregate formation in gemini surfactant/1,2-dialkyl-sn-glycero-3-phosphoethanolamine systems.

    PubMed

    Akbar, Javed; Tavakoli, Naser; Marangoni, D Gerrard; Wettig, Shawn D

    2012-07-01

    An evaluation of the physical interactions between gemini surfactants, DNA, and 1,2-dialkyl-sn-glycero-3-phosphoethanolamine helper lipid is presented in this work. Complexation between gemini surfactants and DNA was first investigated using surface tensiometry where the surface tension profiles obtained were found to be consistent with those typically observed for mixed surfactant-polymer systems; that is, there is a synergistic lowering of the surface tension, followed by a first (CAC) and second (CMC) break point in the plot. The surfactant alkyl tail length was observed to exhibit a significant effect on the CAC, thus demonstrating the importance of hydrophobic interactions during complexation between gemini surfactants and DNA. The second study presented is an investigation of the mixing interactions between gemini surfactants and DOPE using Clint's, Rubingh's, and Motomura's theories for mixed micellar formation. The mixing interactions between the 16-3-16/16-7-16/16-12-16/16-7NH-16 gemini surfactants and DOPE were observed to be antagonistic, where the strength of antagonism was found to be dependent upon the gemini surfactant spacer group and the solution composition.

  6. A bleached-kraft mill effluent fraction causing induction of a fish mixed-function oxygenase enzyme

    SciTech Connect

    Burnison, B.K.; Hodson, P.V.; Nuttley, D.J.; Efler, S.

    1996-09-01

    Pulp mill effluents contain a myriad of chemicals that have the potential to cause deleterious effects on aquatic biota in receiving waters. Some of these chemicals evoke an acute lethal response of exposed biota while others evoke sublethal responses. One such sublethal response is the induction of mixed-function oxygenases (MFO) in fish, specifically the CYP1A1 enzyme ethoxy-resorufin-o-deethylase (EROD). Compounds causing MFO induction include congeners of polychlorinated biphenyls (PCBs), dioxins, furans, and polycyclic aromatic hydrocarbons (PAHs). The authors followed the partitioning of the inducing chemicals in pulp mill effluent fractions by Toxicity Identification Evaluation (TIE), or bioassay-driven chemical analysis. This procedure was eventually modified to a more direct technique involving centrifugation, filtration, cleanup procedures, and C{sub 18} solid-phase adsorption. The extracts from the fractionation of two pulp mill effluents after secondary treatment were tested for EROD-inducing activity in a 4-d rainbow trout bioassay. The methanol extracts of particulates/colloids showed significant inducing capacity in Mill A effluent but not in Mill B effluent. The C{sub 18} methanol extracts induced activity from both effluents, with extracts from Mill A causing the greatest response. The particulate/colloidal extract (Mill A) was used as the source material for chemicals which caused EROD induction. The fraction was purified by solid-phase extraction techniques and reverse-phase high-performance liquid chromatography. The majority of the EROD activity was found in the moderately nonpolar region of the chromatogram (K{sub ow} = 4.6 to 5.1).

  7. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a pu GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

  8. Bounding CKM Mixing with a Fourth Family

    SciTech Connect

    Chanowitz, Michael S.

    2009-04-22

    CKM mixing between third family quarks and a possible fourth family is constrained by global fits to the precision electroweak data. The dominant constraint is from nondecoupling oblique corrections rather than the vertex correction to Z {yields} {bar b}b used in previous analyses. The possibility of large mixing suggested by some recent analyses of FCNC processes is excluded, but 3-4 mixing of the same order as the Cabbibo mixing of the first two families is allowed.

  9. Mixed wasted integrated program: Logic diagram

    SciTech Connect

    Mayberry, J.; Stelle, S.; O`Brien, M.; Rudin, M.; Ferguson, J.; McFee, J.

    1994-11-30

    The Mixed Waste Integrated Program Logic Diagram was developed to provide technical alternative for mixed wastes projects for the Office of Technology Development`s Mixed Waste Integrated Program (MWIP). Technical solutions in the areas of characterization, treatment, and disposal were matched to a select number of US Department of Energy (DOE) treatability groups represented by waste streams found in the Mixed Waste Inventory Report (MWIR).

  10. Contact sensitization to Compositae mix in children.

    PubMed

    Belloni Fortina, Anna; Romano, Ilaria; Peserico, Andrea

    2005-11-01

    The prevalence of contact sensitization to Compositae mix was investigated in 641 consecutive children. Seventeen children (12 with atopic dermatitis) tested positive for Compositae mix. We suggest adding Compositae mix to a pediatric screening series when investigating airborne dermatitis in children with atopic dermatitis.

  11. 7 CFR 51.2112 - Mixed varieties.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Sheller Run, U.S. Standard Sheller Run, U.S. No. 1 Whole and Broken may be designated as: “U.S. No. 1 Mixed;” “U.S. Select Sheller Run Mixed;” “U.S. Standard Sheller Run Mixed;” “U.S. No. 1 Whole and...

  12. Foam-Mixing-And-Dispensing Machine

    NASA Technical Reports Server (NTRS)

    Chong, Keith Y.; Toombs, Gordon R.; Jackson, Richard J.

    1996-01-01

    Time-and-money-saving machine produces consistent, homogeneously mixed foam, enhancing production efficiency. Automatically mixes and dispenses polyurethane foam in quantities specified by weight. Consists of cart-mounted, air-driven proportioning unit; air-activated mechanical mixing gun; programmable timer/counter, and controller.

  13. Pragmatism, Evidence, and Mixed Methods Evaluation

    ERIC Educational Resources Information Center

    Hall, Jori N.

    2013-01-01

    Mixed methods evaluation has a long-standing history of enhancing the credibility of evaluation findings. However, using mixed methods in a utilitarian way implicitly emphasizes convenience over engaging with its philosophical underpinnings (Denscombe, 2008). Because of this, some mixed methods evaluators and social science researchers have been…

  14. Moments, Mixed Methods, and Paradigm Dialogs

    ERIC Educational Resources Information Center

    Denzin, Norman K.

    2010-01-01

    I reread the 50-year-old history of the qualitative inquiry that calls for triangulation and mixed methods. I briefly visit the disputes within the mixed methods community asking how did we get to where we are today, the period of mixed-multiple-methods advocacy, and Teddlie and Tashakkori's third methodological moment. (Contains 10 notes.)

  15. A Call for Conducting Multivariate Mixed Analyses

    ERIC Educational Resources Information Center

    Onwuegbuzie, Anthony J.

    2016-01-01

    Several authors have written methodological works that provide an introductory- and/or intermediate-level guide to conducting mixed analyses. Although these works have been useful for beginning and emergent mixed researchers, with very few exceptions, works are lacking that describe and illustrate advanced-level mixed analysis approaches. Thus,…

  16. Mixed pneumoconiosis: silicosis, asbestosis, talcosis, and berylliosis.

    PubMed

    Mark, G J; Monroe, C B; Kazemi, H

    1979-06-01

    Mixed pneumoconiosis is pulmonary disease due to two or more inhaled mineral irritants. Chronic disease due to beryllium has not been a component of any described mixed pneumoconiosis. A man with occupational exposure to a combination of dusts developed severe pulmonary disease. Silicosis, talcosis, asbestosis, and berylliosis were all documented by an open biopsy of the lung. The varieties of mixed pneumoconiosis are summarized.

  17. Entropy of Mixing of Distinguishable Particles

    ERIC Educational Resources Information Center

    Kozliak, Evguenii I.

    2014-01-01

    The molar entropy of mixing yields values that depend only on the number of mixing components rather than on their chemical nature. To explain this phenomenon using the logic of chemistry, this article considers mixing of distinguishable particles, thus complementing the well-known approach developed for nondistinguishable particles, for example,…

  18. Qualitative Approaches to Mixed Methods Practice

    ERIC Educational Resources Information Center

    Hesse-Biber, Sharlene

    2010-01-01

    This article discusses how methodological practices can shape and limit how mixed methods is practiced and makes visible the current methodological assumptions embedded in mixed methods practice that can shut down a range of social inquiry. The article argues that there is a "methodological orthodoxy" in how mixed methods is practiced…

  19. DNA Release from Lipoplexes by Anionic Lipids: Correlation with Lipid Mesomorphism, Interfacial Curvature, and Membrane Fusion

    PubMed Central

    Tarahovsky, Yury S.; Koynova, Rumiana; MacDonald, Robert C.

    2004-01-01

    DNA release from lipoplexes is an essential step during lipofection and is probably a result of charge neutralization by cellular anionic lipids. As a model system to test this possibility, fluorescence resonance energy transfer between DNA and lipid covalently labeled with Cy3 and BODIPY, respectively, was used to monitor the release of DNA from lipid surfaces induced by anionic liposomes. The separation of DNA from lipid measured this way was considerably slower and less complete than that estimated with noncovalently labeled DNA, and depends on the lipid composition of both lipoplexes and anionic liposomes. This result was confirmed by centrifugal separation of released DNA and lipid. X-ray diffraction revealed a clear correlation of the DNA release capacity of the anionic lipids with the interfacial curvature of the mesomorphic structures developed when the anionic and cationic liposomes were mixed. DNA release also correlated with the rate of fusion of anionic liposomes with lipoplexes. It is concluded that the tendency to fuse and the phase preference of the mixed lipid membranes are key factors for the rate and extent of DNA release. The approach presented emphasizes the importance of the lipid composition of both lipoplexes and target membranes and suggests optimal transfection may be obtained by tailoring lipoplex composition to the lipid composition of target cells. PMID:15298910

  20. Novel DNA nanoparticles and networks.

    PubMed

    Seela, Frank; Jawalekar, Anup M; Sirivolu, Venkata R; Rosemeyer, Helmut; He, Yang; Leonard, Peter

    2005-01-01

    Joining the thrombin-binding aptamer 5-d(GGTTGGTGTGGTTGG) and the minihairpin 5-d(GCGAAGC) leads to new DNA nanoparticles, which are different from rod-like helical double-stranded DNA. Covalent interstrand cross-links in DNA duplexes generated by bifunctional alkadiyne chains were used to build-up the DNA networks.

  1. DNA as an Optical Material

    DTIC Science & Technology

    2011-07-01

    of DNA, and a natural DNA source is more appropriate. Currently available sources of natural DNA include fish sperm (e.g., from salmon or herring...harvesting of the fish’s waste milt and roe sacs. (Unlike meat and eggs , these elements are not used for cuisine.) From these, DNA is extracted and

  2. Intentional mixed buccal cell reference sample in a paternity case.

    PubMed

    Martinez-Gonzalez, Luis J; Lorente, Jose A; Martinez-Espin, Esther; Alvarez, J Carlos; Lorente, Miguel; Villanueva, Enrique; Budowle, Bruce

    2007-03-01

    We report a case where an alleged father (AF) attempted to substitute someone else's saliva sample for his reference sample in a paternity analysis. Buccal cells were collected from the AF and the child, and DNA analysis was performed using an autosomal STR loci (Identifiler). The profile from the AF showed extra peaks in some loci, as well as a much higher "X" allele peak relative to the "Y" allele peak at the amelogenin locus. After conducting reanalysis by another technician with another set of positive and negative controls, it was concluded that the only source of the mixed profile was by intentional introduction by the AF, at the time of sampling, of some foreign human biological material, most likely saliva from a woman. Owing to the inconclusive results, when the AF was called back to the lab and the peculiar results were explained to him, he admitted that he had introduced into his mouth saliva from another person in an attempt to be excluded as the father of the child. Although tampering with DNA reference samples is not common, some individuals may attempt to contaminate or otherwise adulterate specimens before DNA tests. Personnel responsible for sampling should be aware of this possibility and should try to establish procedures to avoid the problem.

  3. Thin film mixed potential sensors

    DOEpatents

    Garzon, Fernando H.; Brosha, Eric L.; Mukundan, Rangachary

    2007-09-04

    A mixed potential sensor for oxidizable or reducible gases and a method of making. A substrate is provided and two electrodes are formed on a first surface of the substrate, each electrode being formed of a different catalytic material selected to produce a differential voltage between the electrodes from electrochemical reactions of the gases catalyzed by the electrode materials. An electrolytic layer of an electrolyte is formed over the electrodes to cover a first portion of the electrodes from direct exposure to the gases with a second portion of the electrodes uncovered for direct exposure to the gases.

  4. Shedding light on the relative DNA contribution of two persons handling the same object.

    PubMed

    Oldoni, F; Castella, V; Hall, D

    2016-09-01

    Traces collected on crime scene objects frequently result in challenging DNA mixtures from several contributors in different DNA proportions. Understanding how the relative proportion of DNA deposited by different persons who handled the same object evolves through time has important bearings. For instance, this information may help determine whether the major contributor in a mixed DNA profile is more likely to correspond to the object owner or to the person who may have stolen this object. In this perspective, a simulation-based protocol was designed where randomly paired participants were asked to act either as first (object owner) or second (last) users. The first user was asked to handle/wear 9 different plastic-, metal-, nitrile- and fabric-made objects, commonly found at burglary/robbery crime scenes, for a minimum of 20min during 8 or 10 consecutive days. The second user subsequently used them for 5, 30 or 120min in three distinct simulation sessions. The analysis of the relative DNA contribution on the resulting 234 mock DNA traces revealed a large variability in the contribution depending on the time, substrate and pairs of participants. Despite this, a progressive increase of the second user's DNA contribution, relative to the first user, was observed over time in 93% of the traces. The second user was shown to become the major contributor in approximately 15%, 33% and 55% of the traces recovered from objects used for 5, 30 and 120min, respectively. Single-source DNA profiles were shown to represent only 1% of the traces. In addition, the DNA profiles of 165 out of 234 (71%) simulated traces displayed extra alleles. Most of these occurred in the minor fraction of mixed DNA profiles and were interpreted as artefacts. Nevertheless, DNA profiles of known participants either involved or not in the simulations were observed in 9 cases (4%). This confirms that indirect DNA transfer should be taken into account when interpreting "touch" DNA evidence.

  5. From DNA to transistors

    NASA Astrophysics Data System (ADS)

    Braun, Erez; Keren, Kinneret

    2004-06-01

    The rapid advance in molecular biology and nanotechnology opens up the possibility to explore the interface between biology and electronics at the single-molecule level. We focus on the organization of molecular electronic circuits. Interconnecting an immense number of molecular devices into a functional circuit and constructing a framework for integrated molecular electronics requires new concepts. A promising avenue relies on bottom-up assembly where the information for the circuit connectivity and functionality is embedded in the molecular building blocks. Biology can provide concepts and mechanisms for advancing this approach, but there is no straightforward way to apply them to electronics since biological molecules are essentially electrically insulating. Bridging the chasm between biology and electronics therefore presents great challenges. Circuit organization on the molecular scale is considered and contrasted with the levels of organization presented by the living world. The discussion then focuses on our proposal to harness DNA and molecular biology to construct the scaffold for integrated molecular electronics. DNA metallization is used to convert the DNA scaffold into a conductive one. We present the framework of sequence-specific molecular lithography based on the biological mechanism of homologous genetic recombination and carried out by the bacterial protein RecA. Molecular lithography enables us to use the information encoded in the scaffold DNA molecules for directing the construction of an electronic circuit. We show that it can lead all the way from DNA molecules to working transistors in a test-tube. Carbon nanotubes are incorporated as the active electronic components in the DNA-templated transistors. Our approach can, in principle, be applied to the fabrication of larger-scale electronic circuits. The realization of complex DNA-based circuits will, however, require new concepts and additional biological machinery allowing, for example

  6. Forensic DNA Profiling and Database

    PubMed Central

    Panneerchelvam, S.; Norazmi, M.N.

    2003-01-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection. PMID:23386793

  7. A dynamic bead-based microarray for parallel DNA detection

    NASA Astrophysics Data System (ADS)

    Sochol, R. D.; Casavant, B. P.; Dueck, M. E.; Lee, L. P.; Lin, L.

    2011-05-01

    A microfluidic system has been designed and constructed by means of micromachining processes to integrate both microfluidic mixing of mobile microbeads and hydrodynamic microbead arraying capabilities on a single chip to simultaneously detect multiple bio-molecules. The prototype system has four parallel reaction chambers, which include microchannels of 18 × 50 µm2 cross-sectional area and a microfluidic mixing section of 22 cm length. Parallel detection of multiple DNA oligonucleotide sequences was achieved via molecular beacon probes immobilized on polystyrene microbeads of 16 µm diameter. Experimental results show quantitative detection of three distinct DNA oligonucleotide sequences from the Hepatitis C viral (HCV) genome with single base-pair mismatch specificity. Our dynamic bead-based microarray offers an effective microfluidic platform to increase parallelization of reactions and improve microbead handling for various biological applications, including bio-molecule detection, medical diagnostics and drug screening.

  8. Identification of tissue-specific cell death using methylation patterns of circulating DNA

    PubMed Central

    Lehmann-Werman, Roni; Neiman, Daniel; Zemmour, Hai; Moss, Joshua; Magenheim, Judith; Vaknin-Dembinsky, Adi; Rubertsson, Sten; Nellgård, Bengt; Blennow, Kaj; Zetterberg, Henrik; Spalding, Kirsty; Haller, Michael J.; Wasserfall, Clive H.; Schatz, Desmond A.; Greenbaum, Carla J.; Dorrell, Craig; Grompe, Markus; Zick, Aviad; Hubert, Ayala; Maoz, Myriam; Fendrich, Volker; Bartsch, Detlef K.; Golan, Talia; Ben Sasson, Shmuel A.; Zamir, Gideon; Razin, Aharon; Cedar, Howard; Shapiro, A. M. James; Glaser, Benjamin; Shemer, Ruth; Dor, Yuval

    2016-01-01

    Minimally invasive detection of cell death could prove an invaluable resource in many physiologic and pathologic situations. Cell-free circulating DNA (cfDNA) released from dying cells is emerging as a diagnostic tool for monitoring cancer dynamics and graft failure. However, existing methods rely on differences in DNA sequences in source tissues, so that cell death cannot be identified in tissues with a normal genome. We developed a method of detecting tissue-specific cell death in humans based on tissue-specific methylation patterns in cfDNA. We interrogated tissue-specific methylome databases to identify cell type-specific DNA methylation signatures and developed a method to detect these signatures in mixed DNA samples. We isolated cfDNA from plasma or serum of donors, treated the cfDNA with bisulfite, PCR-amplified the cfDNA, and sequenced it to quantify cfDNA carrying the methylation markers of the cell type of interest. Pancreatic β-cell DNA was identified in the circulation of patients with recently diagnosed type-1 diabetes and islet-graft recipients; oligodendrocyte DNA was identified in patients with relapsing multiple sclerosis; neuronal/glial DNA was identified in patients after traumatic brain injury or cardiac arrest; and exocrine pancreas DNA was identified in patients with pancreatic cancer or pancreatitis. This proof-of-concept study demonstrates that the tissue origins of cfDNA and thus the rate of death of specific cell types can be determined in humans. The approach can be adapted to identify cfDNA derived from any cell type in the body, offering a minimally invasive window for diagnosing and monitoring a broad spectrum of human pathologies as well as providing a better understanding of normal tissue dynamics. PMID:26976580

  9. Can whales mix the ocean?

    NASA Astrophysics Data System (ADS)

    Lavery, T. J.; Roudnew, B.; Seuront, L.; Mitchell, J. G.; Middleton, J.

    2012-07-01

    Ocean mixing influences global climate and enhances primary productivity by transporting nutrient rich water into the euphotic zone. The contribution of the swimming biosphere to diapycnal mixing in the ocean has been hypothesised to occur on scales similar to that of tides or winds, however, the extent to which this contributes to nutrient transport and stimulates primary productivity has not been explored. Here, we introduce a novel method to estimate the diapycnal diffusivity that occurs as a result of a sperm whale swimming through a pycnocline. Nutrient profiles from the Hawaiian Ocean are used to further estimate the amount of nitrogen transported into the euphotic zone and the primary productivity stimulated as a result. We estimate that the 80 sperm whales that travel through an area of 104 km2 surrounding Hawaii increase diapycnal diffusivity by 10-6 m2 s-1 which results in the flux of 105 kg of nitrogen into the euphotic zone each year. This nitrogen input subsequently stimulates 6 × 105 kg of carbon per year. The nutrient input of swimming sperm whales is modest compared to dominant modes of nutrient transport such as nitrogen fixation but occurs more consistently and thus may provide the nutrients necessary to enable phytoplankton growth and survival in the absence of other seasonal and daily nutrient inputs.

  10. Mixing in straight shear layers

    NASA Technical Reports Server (NTRS)

    Karasso, P. S.; Mungal, M. G.

    1992-01-01

    Planar laser-induced fluorescence measurements were performed in a liquid plane mixing layer to extract the probability density function (pdf) of the mixture fraction of a passive scalar across the layer. Three Reynolds number (Re) cases were studied, 10,000, 33,000 and 90,000, with Re based on velocity difference and visual thickness. The results show that a non-marching pdf (central hump invariant from edge to edge of the layer) exists for Re = 10,000 but that a marching type pdf characterizes the Re = 33,000 and Re = 90,000 cases. For all cases, a broad range of mixture fraction values is found at each location across the layer. Streamwise and spanwise ramps across the layer, and structure-to-structure variation were observed and are believed to be responsible for the above behavior of the composition field. Tripping the boundary layer on the high-speed side of the splitter plate for each of the above three cases resulted in increased three-dimensionality and a change in the composition field. Average and average mixed fluid compositions are reported for all cases.

  11. [Mixed states: evolution of classifications].

    PubMed

    Pringuey, D; Cherikh, F; Giordana, B; Fakra, E; Dassa, D; Cermolacce, M; Belzeaux, R; Maurel, M; Azorin, J-M

    2013-12-01

    The nosological position of mixed states has followed the course of classifying methods in psychiatry, the steps of the invention of the clinic, progress in the organization of care, including the discoveries of psychopharmacology. The clinical observation of a mixture of symptoms emerging from usually opposite clinical conditions is classical. In the 70s, a syndromic specification fixed the main symptom combinations but that incongruous assortment failed to stabilize the nosological concept. Then stricter criteriology was proposed. To be too restrictive, a consensus operates a dimensional opening that attempts to meet the pragmatic requirements of nosology validating the usefulness of the class system. This alternation between rigor of categorization and return to a more flexible criteriological option reflects the search for the right balance between nosology and diagnosis. The definition of mixed states is best determined by their clinical and prognostic severity, related to the risk of suicide, their lower therapeutic response, the importance of their psychiatric comorbidities, anxiety, emotional lability, alcohol abuse. Trying to compensate for the lack of categorical definitions and better reflecting the clinical field problems, new definitions complement criteriology with dimensional aspects, particularly taking into account temperaments.

  12. Nanoscale Mixing of Soft Solids

    SciTech Connect

    Choi, Soo-Hyung; Lee, Sangwoo; Soto, Haidy E.; Lodge, Timothy P.; Bates, Frank S.

    2013-03-07

    Assessing the state of mixing on the molecular scale in soft solids is challenging. Concentrated solutions of micelles formed by self-assembly of polystyrene-block-poly(ethylene-alt-propylene) (PS-PEP) diblock copolymers in squalane (C{sub 30}H{sub 62}) adopt a body-centered cubic (bcc) lattice, with glassy PS cores. Utilizing small-angle neutron scattering (SANS) and isotopic labeling ({sup 1}H and {sup 2}H (D) polystyrene blocks) in a contrast-matching solvent (a mixture of squalane and perdeuterated squalane), we demonstrate quantitatively the remarkable fact that a commercial mixer can create completely random mixtures of micelles with either normal, PS(H), or deuterium-labeled, PS(D), cores on a well-defined bcc lattice. The resulting SANS intensity is quantitatively modeled by the form factor of a single spherical core. These results demonstrate both the possibility of achieving complete nanoscale mixing in a soft solid and the use of SANS to quantify the randomness.

  13. Tracer mixing at fracture intersections

    SciTech Connect

    Li, Guomin

    2001-02-10

    Discrete network models are one of the approaches used to simulate a dissolved contaminant, which is usually represented as a tracer in modeling studies, in fractured rocks. The discrete models include large numbers of individual fractures within the network structure, with flow and transport described on the scale of an individual fracture. Numerical simulations for the mixing characteristics and transfer probabilities of a tracer through a fracture intersection are performed for this study. A random-walk, particle-tracking model is applied to simulate tracer transport in fracture intersections by moving particles through space using individual advective and diffusive steps. The simulation results are compared with existing numerical and analytical solutions for a continuous intersection over a wide range of Peclet numbers. This study attempts to characterize the relative concentration at the outflow branches for a continuous intersection with different flow fields. The simulation results demonstrate that the mixing characteristics at the fracture intersections are a function not only of the Peclet number but also of the flow field pattern.

  14. Mixed Strategies in cyclic competition

    NASA Astrophysics Data System (ADS)

    Intoy, Ben; Pleimling, Michel

    2015-03-01

    Physicists have been using evolutionary game theory to model and simulate cyclically competing species, with applications to lizard mating strategies and competing bacterial strains. However these models assume that each agent plays the same strategy, which is called a pure strategy in game theory, until they are beaten by a better strategy which they immediately adopt. We relax this constraint of an agent playing a single strategy by instead letting the agent pick its strategy randomly from a probability distribution, which is called a mixed strategy in game theory. This scheme is very similar to multiple occupancy models seen in the literature, the major difference being that interactions happen between sites rather than within them. Choosing strategies out of a distribution also has applications to economic/social systems such as the public goods game. We simulate a model of mixed strategy and cylic competition on a one-dimensional lattice with three and four strategies and find interesting spatial and stability properties depending on how discretized the choice of strategy is for the agents. This work is supported by the US National Science Foundation through Grant DMR-1205309.

  15. Mixed waste characterization reference document

    SciTech Connect

    1997-09-01

    Waste characterization and monitoring are major activities in the management of waste from generation through storage and treatment to disposal. Adequate waste characterization is necessary to ensure safe storage, selection of appropriate and effective treatment, and adherence to disposal standards. For some wastes characterization objectives can be difficult and costly to achieve. The purpose of this document is to evaluate costs of characterizing one such waste type, mixed (hazardous and radioactive) waste. For the purpose of this document, waste characterization includes treatment system monitoring, where monitoring is a supplement or substitute for waste characterization. This document establishes a cost baseline for mixed waste characterization and treatment system monitoring requirements from which to evaluate alternatives. The cost baseline established as part of this work includes costs for a thermal treatment technology (i.e., a rotary kiln incinerator), a nonthermal treatment process (i.e., waste sorting, macronencapsulation, and catalytic wet oxidation), and no treatment (i.e., disposal of waste at the Waste Isolation Pilot Plant (WIPP)). The analysis of improvement over the baseline includes assessment of promising areas for technology development in front-end waste characterization, process equipment, off gas controls, and monitoring. Based on this assessment, an ideal characterization and monitoring configuration is described that minimizes costs and optimizes resources required for waste characterization.

  16. Mixing stops at the LHC

    SciTech Connect

    Agrawal, Prateek; Frugiuele, Claudia

    2014-01-01

    We study the phenomenology of a light stop NLSP in the presence of large mixing with either the first or the second generation. R-symmetric models provide a prime setting for this scenario, but our discussion also applies to the MSSM when a significant amount of mixing can be accommodated. In our framework the dominant stop decay is through the flavor violating mode into a light jet and the LSP in an extended region of parameter space. There are currently no limits from ATLAS and CMS in this region. We emulate shape-based hadronic SUSY searches for this topology, and find that they have potential sensitivity. If the extension of these analyses to this region is robust, we find that these searches can set strong exclusion limits on light stops. If not, then the flavor violating decay mode is challenging and may represent a blind spot in stop searches even at 13 TeV. Thus, an experimental investigation of this scenario is well motivated.

  17. Mixing stops at the LHC

    DOE PAGES

    Agrawal, Prateek; Frugiuele, Claudia

    2014-01-01

    We study the phenomenology of a light stop NLSP in the presence of large mixing with either the first or the second generation. R-symmetric models provide a prime setting for this scenario, but our discussion also applies to the MSSM when a significant amount of mixing can be accommodated. In our framework the dominant stop decay is through the flavor violating mode into a light jet and the LSP in an extended region of parameter space. There are currently no limits from ATLAS and CMS in this region. We emulate shape-based hadronic SUSY searches for this topology, and find thatmore » they have potential sensitivity. If the extension of these analyses to this region is robust, we find that these searches can set strong exclusion limits on light stops. If not, then the flavor violating decay mode is challenging and may represent a blind spot in stop searches even at 13 TeV. Thus, an experimental investigation of this scenario is well motivated.« less

  18. Theory of electron transfer and molecular state in DNA

    NASA Astrophysics Data System (ADS)

    Endres, Robert Gunter

    2002-09-01

    In this thesis, a mechanism for long-range electron transfer in DNA and a systematic search for high conductance DNA are developed. DNA is well known for containing the genetic code of all living species. On the other hand, there are some experimental indications that DNA can mediate effectively long-range electron transfer leading to the concept of chemistry at a distance. This can be important for DNA damage and healing. In the first part of the thesis, a possible mechanism for long-range electron transfer is introduced. The weak distance dependent electron transfer was experimentally observed using transition metal intercalators for donor and acceptor. In our model calculations, the transfer is mediated by the molecular analogue of a Kondo bound state well known from solid state physics of mixed-valence rare-earth compounds. We believe this is quite realistic, since localized d orbitals of the transition metal ions could function as an Anderson impurity embedded in a reservoir of rather delocalized molecular orbitals of the intercalator ligands and DNA pi orbitals. The effective Anderson model is solved with a physically intuitive variational ansatz as well as with the essentially exact DMRG method. The electronic transition matrix element, which is important because it contains the donor-acceptor distance dependence, is obtained with the Mulliken-Hush algorithm as well as from Born-Oppenheimer potential energy surfaces. Our possible explanation of long-range electron transfer is put in context to other more conventional mechanisms which also could lead to similar behavior. Another important issue of DNA is its possible use for nano-technology. Although DNA's mechanical properties are excellent, the question whether it can be conducting and be used for nano-wires is highly controversial. Experimentally, DNA shows conducting, semi-conducting and insulating properties. Motivated by these wide ranging experimental results on the conductivity of DNA, we have

  19. Advancing taxonomy and bioinventories with DNA barcodes

    PubMed Central

    2016-01-01

    We use three examples—field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae—to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the ‘taxonomic impediment’, especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481791

  20. Microfabricated structures for integrated DNA analysis.

    PubMed Central

    Burns, M A; Mastrangelo, C H; Sammarco, T S; Man, F P; Webster, J R; Johnsons, B N; Foerster, B; Jones, D; Fields, Y; Kaiser, A R; Burke, D T

    1996-01-01

    Photolithographic micromachining of silicon is a candidate technology for the construction of high-throughput DNA analysis devices. However, the development of complex silicon microfabricated systems has been hindered in part by the lack of a simple, versatile pumping method for integrating individual components. Here we describe a surface-tension-based pump able to move discrete nanoliter drops through enclosed channels using only local heating. This thermocapillary pump can accurately mix, measure, and divide drops by simple electronic control. In addition, we have constructed thermal-cycling chambers, gel electrophoresis channels, and radiolabeled DNA detectors that are compatible with the fabrication of thermocapillary pump channels. Since all of the components are made by conventional photolithographic techniques, they can be assembled into more complex integrated systems. The combination of pump and components into self-contained miniaturized devices may provide significant improvements in DNA analysis speed, portability, and cost. The potential of microfabricated systems lies in the low unit cost of silicon-based construction and in the efficient sample handling afforded by component integration. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8643614