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Sample records for mixed dna chromatograms

  1. DNA Sequence Chromatogram Browsing Using JAVA and CORBA

    PubMed Central

    Parsons, Jeremy D.; Buehler, Eugen; Hillier, LaDeana

    1999-01-01

    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.] PMID:10077534

  2. SeqTrace: A Graphical Tool for Rapidly Processing DNA Sequencing Chromatograms

    PubMed Central

    Stucky, Brian J.

    2012-01-01

    Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate the entire workflow by facilitating easy batch processing of large numbers of trace files. SeqTrace can identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and end-trim finished sequences. The software features a graphical interface that includes a full-featured chromatogram viewer and sequence editor. SeqTrace runs on most popular operating systems and is freely available, along with supporting documentation, at http://seqtrace.googlecode.com/. PMID:22942788

  3. 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

  4. MS/MS Automated Selected Ion Chromatograms

    Energy Science and Technology Software Center (ESTSC)

    2005-12-12

    This program can be used to read a LC-MS/MS data file from either a Finnigan ion trap mass spectrometer (.Raw file) or an Agilent Ion Trap mass spectrometer (.MGF and .CDF files) and create a selected ion chromatogram (SIC) for each of the parent ion masses chosen for fragmentation. The largest peak in each SIC is also identified, with reported statistics including peak elution time, height, area, and signal to noise ratio. It creates severalmore » output files, including a base peak intensity (BPI) chromatogram for the survey scan, a BPI for the fragmentation scans, an XML file containing the SIC data for each parent ion, and a "flat file" (ready for import into a database) containing summaries of the SIC data statistics.« less

  5. DNA microarrays: design principles for maximizing ergodic, chaotic mixing.

    PubMed

    Hertzsch, Jan-Martin; Sturman, Rob; Wiggins, Stephen

    2007-02-01

    In this article we show that models of flows in DNA microarrays generated by pulsed source-sink pairs can be studied as linked twist maps. The significance of this is that it enables us to relate the flow to mathematically precise notions of chaotic mixing that can be realized through specific design criteria. We apply these techniques to three different mixing protocols, two of which have been previously described in the literature, and we are able to isolate the features of each mixer that lead to "good" or "bad" mixing. Based on this, we propose a new design to generate a "well-mixed" flow in a DNA microarray. PMID:17262763

  6. Evidence for plasmid DNA exchange after polyplex mixing.

    PubMed

    Pigeon, L; Gonçalves, C; Pichon, C; Midoux, P

    2016-08-17

    The self-assembly of a plasmid DNA (pDNA) with cationic polymers or cationic liposomes forms nanosized supramolecular structures called lipoplexes, polyplexes and lipopolyplexes. Here, we report that when two polyplex preparations made using the same polymer and the same pDNA but labelled with two different fluorophores are mixed together, pDNA molecules are exchanged. Indeed, when Flu-pDNA complexed with histidinylated lPEI (Flu-pDNA/His-lPEI) polyplexes are mixed with Cy5-pDNA complexed with histidinylated lPEI (Cy5-pDNA/His-lPEI) polyplexes, a high quantity of polyplexes emitting dual fluorescence is observed and FRET indicates that one single polyplex contains two kinds of fluorescent pDNA molecules. This phenomenon depends on the polymer-type and the strength of the pDNA/polymer interaction. No exchange is observed with polylysine polyplexes, caged His-lPEI polyplexes, lipoplexes, lipopolyplexes or when His-lPEI polyplexes are mixed with lipoplexes. Our results suggest that aggregation or collapse of polyplexes occurs after their interaction leading to their unpackaging followed by the formation of new polyplexes with the exchange of pDNA. PMID:27459887

  7. 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

  8. Robust algorithm for aligning two-dimensional chromatograms.

    PubMed

    Gros, Jonas; Nabi, Deedar; Dimitriou-Christidis, Petros; Rutler, Rebecca; Arey, J Samuel

    2012-11-01

    Comprehensive two-dimensional gas chromatography (GC × GC) chromatograms typically exhibit run-to-run retention time variability. Chromatogram alignment is often a desirable step prior to further analysis of the data, for example, in studies of environmental forensics or weathering of complex mixtures. We present a new algorithm for aligning whole GC × GC chromatograms. This technique is based on alignment points that have locations indicated by the user both in a target chromatogram and in a reference chromatogram. We applied the algorithm to two sets of samples. First, we aligned the chromatograms of twelve compositionally distinct oil spill samples, all analyzed using the same instrument parameters. Second, we applied the algorithm to two compositionally distinct wastewater extracts analyzed using two different instrument temperature programs, thus involving larger retention time shifts than the first sample set. For both sample sets, the new algorithm performed favorably compared to two other available alignment algorithms: that of Pierce, K. M.; Wood, Lianna F.; Wright, B. W.; Synovec, R. E. Anal. Chem.2005, 77, 7735-7743 and 2-D COW from Zhang, D.; Huang, X.; Regnier, F. E.; Zhang, M. Anal. Chem.2008, 80, 2664-2671. The new algorithm achieves the best matches of retention times for test analytes, avoids some artifacts which result from the other alignment algorithms, and incurs the least modification of quantitative signal information. PMID:23082816

  9. Insights of Mixing on the Assembly of DNA Nanoparticles

    NASA Astrophysics Data System (ADS)

    Williams, Manda S.

    Size is a crucial parameter in the delivery of nanoparticle therapeutics, affecting mechanisms such as tissue delivery, clearance, and cellular uptake. The morphology of nanoparticles is dependent both upon chemistry and the physical process of assembly. Polyplexes, a major class of non-viral gene delivery vectors, are conventionally prepared by vortex mixing, resulting in non-uniform nanoparticles and poor reproducibility. Better understanding and control of the physical process of assembly, and mixing in particular, will produce polyplexes of a more uniform and reliable size, optimizing their efficiency for laboratory and clinical use. "Mixing" is the reduction of length scale of a system to accelerate diffusion until a uniform concentration is achieved. Vortex mixing is poorly characterized and sensitive to protocols. Microfluidic systems are notable for predictable fluid behavior, and are ideal for analyzing and controlling the physical interaction of reagents on the microscale, realm where mixing occurs. Several microdevices for the preparation of DNA polyplexes are explored here. Firstly, the staggered herringbone mixer, a chaotic advection micromixer, is used to observe the effects of mixing time on nanoparticle size. Next, a novel device to surround the reagent flows with a sheath of buffer, preventing interaction with the walls and confining the complexation to a zone of lower, less variable shear and residence time, is used to demonstrate the role of shear in nanoparticle assembly. Lastly, uneven diffusion between ion pairs produces a small separation of charge at fluid interfaces; this short-lived electric field has a significant impact on the transport of DNA over the time scales of mixing and complexation. The effects of common buffers on the transport of DNA are examined for possible applications to mixing and complexation. These three investigations demonstrate the importance of the physical process in polyplex assembly, and indicate several

  10. Pairwise alignment of chromatograms using an extended Fisher-Rao metric.

    PubMed

    Wallace, W E; Srivastava, A; Telu, K H; Simón-Manso, Y

    2014-09-01

    A conceptually new approach for aligning chromatograms is introduced and applied to examples of metabolite identification in human blood plasma by liquid chromatography-mass spectrometry (LC-MS). A square-root representation of the chromatogram's derivative coupled with an extended Fisher-Rao metric enables the computation of relative differences between chromatograms. Minimization of these differences using a common dynamic programming algorithm brings the chromatograms into alignment. Application to a complex sample, National Institute of Standards and Technology (NIST) Standard Reference Material 1950, Metabolites in Human Plasma, analyzed by two different LC-MS methods having significantly different ranges of elution time is described. PMID:25109856

  11. Disentangling oil weathering using GC x GC. 1. chromatogram analysis.

    PubMed

    Arey, J Samuel; Nelson, Robert K; Reddy, Christopher M

    2007-08-15

    Historically, the thousands of compounds found in oils constituted an "unresolved complex mixture" that frustrated efforts to analyze oil weathering. Moreover, different weathering processes inflict rich and diverse signatures of compositional change in oil, and conventional methods do not effectively decode this elaborate record. Using comprehensive two-dimensional gas chromatography (GC x GC), we can separate thousands of hydrocarbon components and simultaneously estimate their chemical properties. We investigated 13 weathered field samples collected from the Bouchard 120 heavy fuel oil spill in Buzzards Bay, Massachusetts in 2003. We first mapped hydrocarbon vapor pressures and aqueous solubilities onto the compositional space explored by GC x GC chromatograms of weathered samples. Then we developed methods to quantitatively decouple mass loss patterns associated with evaporation and dissolution. The compositional complexity of oil, traditionally considered an obstacle, was now an advantage. We exploited the large inventory of chemical information encoded in oil to robustly differentiate signatures of mass transfer to air and water. With this new approach, we can evaluate mass transfer models (the Part 2 companion to this paper) and more properly account for evaporation, dissolution, and degradation of oil in the environment. PMID:17874781

  12. Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes.

    PubMed

    Anderson, Brooke A; Hrdlicka, Patrick J

    2016-04-15

    The development of molecular strategies that enable recognition of specific double-stranded DNA (dsDNA) regions has been a longstanding goal as evidenced by the emergence of triplex-forming oligonucleotides, peptide nucleic acids (PNAs), minor groove binding polyamides, and-more recently-engineered proteins such as CRISPR/Cas9. Despite this progress, an unmet need remains for simple hybridization-based probes that recognize specific mixed-sequence dsDNA regions under physiological conditions. Herein, we introduce pseudocomplementary Invader probes as a step in this direction. These double-stranded probes are chimeras between pseudocomplementary DNA (pcDNA) and Invader probes, which are activated for mixed-sequence dsDNA-recognition through the introduction of pseudocomplementary base pairs comprised of 2-thiothymine and 2,6-diaminopurine, and +1 interstrand zipper arrangements of intercalator-functionalized nucleotides, respectively. We demonstrate that certain pseudocomplementary Invader probe designs result in very efficient and specific recognition of model dsDNA targets in buffers of high ionic strength. These chimeric probes, therefore, present themselves as a promising strategy for mixed-sequence recognition of dsDNA targets for applications in molecular biology and nucleic acid diagnostics. PMID:26998918

  13. 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

  14. Direct determination of fluorescent whitening agents by absorption measurement in situ on thin layer chromatograms.

    PubMed

    Theidel, H

    1975-01-01

    The measuring technique for the chromatogram spectrophotometer (Zeiss) to determine the reflectance curves, the analysis according to the Kubelka-Munck function, and the basic outlines of the quantitative determination of stilbene fluorescent whitening agents (FWAs) are explained. PMID:1064527

  15. 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

  16. A new method for the authentication of plant samples by analyzing fingerprint chromatograms.

    PubMed

    Obradovic, Marko; Krajsek, Simona Strgulc; Dermastia, Marina; Kreft, Samo

    2007-01-01

    Chemical analysis by high-performance liquid chromatography or capillary electrophoresis of plant pulverized samples, juices or extracts is an excellent method for the authentication of medicinal plant species and their products, particularly when morphological authentication is not possible. In the conventional procedure, chromatograms are integrated and the heights or areas of several peaks are used in a supervised pattern recognition method to confirm the authenticity of the product. We propose a new section approach in analysing chromatograms, where chromatograms are split into sections, which are described by four variables (number of peaks in the section, average retention time of peaks in the section, total area of peaks in the section and average area of peaks in the section), and these variables are then used in statistical analysis. The method is especially useful when the peaks on the chromatogram are not well separated and it is not easy to link individual peaks on one chromatogram with corresponding peaks on other chromatograms. In comparison with the standard procedure, our approach in analyzing chromatographic data of willow-herb (Epilobium and Chamaenerion spp.) extracts was more objective, gave better results and was also easier to perform. PMID:17439013

  17. Slow Phase Separation in Mixed Columnar Phases of NanoDNA and Chromonic Dye

    NASA Astrophysics Data System (ADS)

    Smith, Gregory; Yi, Youngwoo; Walba, David; Clark, Noel

    2014-03-01

    The architecture of a DNA duplex with its externally exposed charged phosphate backbone and internally hidden aromatic bases, hydrophobically stacked at a spacing of 3.4 Å, is strikingly similar to aggregates of Liquid Crystal (LC) forming chromonic dyes such as Sunset Yellow (SSY). One might naturally question whether a DNA-like molecular column can be assembled from a subunit resembling a chromonic dye. Because little is known about direct mixtures of chromonics with DNA and how such a mixture might form mixed LC phases, we mixed blunt-end 12mer NanoDNA (GCGCTTAAGCGC) with SSY, both of these molecular species independently having well-described LC behavior. Observed mixtures are remarkably miscible, exhibiting a mixed chiral nematic phase with Grandjean texture that is distinct from SSY and DNA nematic forms. On transition to the columnar phase when the molecular species fractions are very close in proportion (about 1:1.3 DNA:SSY by weight) the columnar phase exhibits a slow but thermally reversible demixing to produce a striated texture whose assembly is guided by the columnar director structure. Grant support: NSF DRM 1207606 and NSF MRSEC DRM 0820579.

  18. Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes.

    PubMed

    Anderson, Brooke A; Karmakar, Saswata; Hrdlicka, Patrick J

    2015-01-01

    Development of probes that allow for sequence-unrestricted recognition of double-stranded DNA (dsDNA) continues to attract much attention due to the prospect for molecular tools that enable detection, regulation, and manipulation of genes. We have recently introduced so-called Invader probes as alternatives to more established approaches such as triplex-forming oligonucleotides, peptide nucleic acids and polyamides. These short DNA duplexes are activated for dsDNA recognition by installment of +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-N-(pyren-1-yl)methyl-2'-N-methyl-2'-aminouridine and 2'-O-(pyren-1-yl)methyluridine, which results in violation of the nearest neighbor exclusion principle and duplex destabilization. The individual probes strands have high affinity toward complementary DNA strands, which generates the driving force for recognition of mixed-sequence dsDNA regions. In the present article, we characterize Invader probes that are based on phosphorothioate backbones (PS-DNA Invaders). The change from the regular phosphodiester backbone furnishes Invader probes that are much more stable to nucleolytic degradation, while displaying acceptable dsDNA-recognition efficiency. PS-DNA Invader probes therefore present themselves as interesting probes for dsDNA-targeting applications in cellular environments and living organisms. PMID:26230684

  19. Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

    PubMed Central

    Gupta, Damini; Sheats, Julian; Muralidhar, Abhiram; Miller, Jeremy J.; Huang, Derek E.; Mahshid, Sara; Dorfman, Kevin D.; Reisner, Walter

    2014-01-01

    We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the “mixing” of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter. PMID:24908035

  20. 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

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

    PubMed Central

    HU, NA; CONG, BIN; GAO, TAO; CHEN, YU; SHEN, JUNYI; LI, SHUJIN; MA, CHUNLING

    2015-01-01

    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 (R2=−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

  2. Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide.

    PubMed

    Nocker, Andreas; Camper, Anne K

    2006-03-01

    The distinction between viable and dead bacterial cells poses a major challenge in microbial diagnostics. Due to the persistence of DNA in the environment after cells have lost viability, DNA-based quantification methods overestimate the number of viable cells in mixed populations or even lead to false-positive results in the absence of viable cells. On the other hand, RNA-based diagnostic methods, which circumvent this problem, are technically demanding and suffer from some drawbacks. A promising and easy-to-use alternative utilizing the DNA-intercalating dye ethidium monoazide bromide (EMA) was published recently. This chemical is known to penetrate only into "dead" cells with compromised cell membrane integrity. Subsequent photoinduced cross-linking was reported to inhibit PCR amplification of DNA from dead cells. We provide evidence here that in addition to inhibition of amplification, most of the DNA from dead cells is actually lost during the DNA extraction procedure, probably together with cell debris which goes into the pellet fraction. Exposure of bacteria to increasing stress and higher proportions of dead cells in defined populations led to increasing loss of genomic DNA. Experiments were performed using Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium as model pathogens and using real-time PCR for their quantification. Results showed that EMA treatment of mixed populations of these two species provides a valuable tool for selective removal of DNA of nonviable cells by using conventional extraction protocols. Furthermore, we provide evidence that prior to denaturing gradient gel electrophoresis, EMA treatment of a mature mixed-population drinking-water biofilm containing a substantial proportion of dead cells can result in community fingerprints dramatically different from those for an untreated biofilm. The interpretation of such fingerprints can have important implications in the field of microbial ecology. PMID:16517648

  3. Selective Removal of DNA from Dead Cells of Mixed Bacterial Communities by Use of Ethidium Monoazide

    PubMed Central

    Nocker, Andreas; Camper, Anne K.

    2006-01-01

    The distinction between viable and dead bacterial cells poses a major challenge in microbial diagnostics. Due to the persistence of DNA in the environment after cells have lost viability, DNA-based quantification methods overestimate the number of viable cells in mixed populations or even lead to false-positive results in the absence of viable cells. On the other hand, RNA-based diagnostic methods, which circumvent this problem, are technically demanding and suffer from some drawbacks. A promising and easy-to-use alternative utilizing the DNA-intercalating dye ethidium monoazide bromide (EMA) was published recently. This chemical is known to penetrate only into “dead” cells with compromised cell membrane integrity. Subsequent photoinduced cross-linking was reported to inhibit PCR amplification of DNA from dead cells. We provide evidence here that in addition to inhibition of amplification, most of the DNA from dead cells is actually lost during the DNA extraction procedure, probably together with cell debris which goes into the pellet fraction. Exposure of bacteria to increasing stress and higher proportions of dead cells in defined populations led to increasing loss of genomic DNA. Experiments were performed using Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium as model pathogens and using real-time PCR for their quantification. Results showed that EMA treatment of mixed populations of these two species provides a valuable tool for selective removal of DNA of nonviable cells by using conventional extraction protocols. Furthermore, we provide evidence that prior to denaturing gradient gel electrophoresis, EMA treatment of a mature mixed-population drinking-water biofilm containing a substantial proportion of dead cells can result in community fingerprints dramatically different from those for an untreated biofilm. The interpretation of such fingerprints can have important implications in the field of microbial ecology. PMID:16517648

  4. Decoding of complex isothermal chromatograms recovered from space missions : identification of molecular structure

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

    In the scientific payloads of current or future space probes, gas chromatography (GC) plays a predominant role to separate and identify the chemical species present in the complex environments investigated (Titan, comets, Mars). Specific requirements are imposed by flight conditions: the strongest constraint concerns energy saving imposing temperature and pressure limitations, so that isothermal GC separations are the only ones compatible with flight constrains. The low separation performance obtained under isothermal conditions results in an increase in signal involving and peak overlapping, usually present in separations of multicomponent mixtures as planetary atmospheres are. In this case, it is mandatory to use a mathematical approach to deconvolve incompletely resolved peaks and to interpret the chromatogram, in order to extract all the analytical information hidden in it, that is “ decoding ” the complex chromatogram. In this paper a chemometric approach based on the Fourier analysis is reported. It is based on the computation of Autocovariance Function (ACVF) on the experimental chromatogram. ACVF plot constitutes a fingerprint of the chromatogram since, in contrast with the original chromatogram very crowded of peaks, it retains in a simpler plot all the information on the nature and relative abundance of the compounds present in the mixture. From ACVF plot, information on the atmosphere complexity, as well as on the separation system, can be easily extracted: the number of components present in the sample can be estimated and the performance of the analytical separation can be evaluated. In order to identify the presence of an ordered retention pattern a time axis transformation is proposed, since isothermal GC chromatograms look inhomogeneous and disordered with peak density decreasing at higher retention times. The time axis is transformed into a new scale based on the retention times of n-alkanes. The order introduced into the chromatogram by

  5. Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis

    PubMed Central

    Lekang, Katrine; Langeland, Nina; Wiker, Harald G.

    2011-01-01

    The standard use of a single universal broad-range PCR in direct 16S rDNA sequencing from polybacterial samples leaves the minor constituents at risk of remaining undetected because all bacterial DNA will be competing for the same reagents. In this article we introduce a set of three broad-range group-specific 16S rDNA PCRs that together cover the clinically relevant bacteria and apply them in the investigation of 25 polybacterial clinical samples. Mixed DNA chromatograms from samples containing more than one species per primer group were analysed using RipSeq Mixed (iSentio, Norway), a web-based application for the interpretation of chromatograms containing up to three different species. The group-specific PCRs reduced complexity in the resulting DNA chromatograms and made the assay more sensitive in situations with unequal species concentrations. Together this allowed for identification of a significantly higher number of bacterial species than did standard direct sequencing with a single universal primer pair and RipSeq analysis (95 vs 51). The method could improve microbiological diagnostics for important groups of patients and can be established in any laboratory with experience in direct 16S rDNA sequencing. PMID:21436365

  6. [Identification of chromosomal aberration in esophageal cancer cells by mixed BAC DNA probes of chromosome arms and regions].

    PubMed

    Jiajie, Hao; Chunli, Wang; Wenyue, Gu; Xiaoyu, Cheng; Yu, Zhang; Xin, Xu; Yan, Cai; Mingrong, Wang

    2014-06-01

    Chromosomal aberration is an important genetic feature of malignant tumor cells. This study aimed to clarify whether BAC DNA could be used to identify chromosome region and arm alterations. For each chromosome region, five to ten 1 Mb BAC DNA clones were selected to construct mixed BAC DNA clones for the particular region. All of the mixed clones from regions which could cover the whole chromosome arm were then mixed to construct mixed BAC DNA clones for the arms. Mixed BAC DNA probes of arms and regions were labeled by degenerate oligonucleotide primed PCR (DOP-PCR) and Nick translation techniques, respectively. The specificities of these probes were validated by fluorescence in situ hybridization (FISH) on the metaphase chromosomes of normal human peripheral blood lymphocytes. FISH with arm-specific mixed BAC DNA probes showed that chromosomal rearrangements and involved chromosome arms were confirmed in several esophageal cancer cells. By using region-specific mixed probes, the breakpoint on 1q from the derivative chromosome t(1q;7q) was identified in 1q32-q41 in esophageal KYSE140 cells. In conclusion, we established an effective labeling method for 1 Mb BAC DNA mixed clone probes, and chromosome arm and region rearrangements could be identified in several esophageal cancer cells by using these probes. Our study provides a more precise method for identification of chromosomal aberration by M-FISH, and the established method may also be applied to the karyotype analysis of hematological malignancies and prenatal diagnosis. PMID:24929514

  7. 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

  8. 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

  9. Hybridization behavior of mixed DNA/alkylthiol monolayers on gold: characterization by surface plasmon resonance and 32P radiometric assay.

    PubMed

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

    2006-05-15

    Nucleic acid assay from a complex biological milieu is attractive but currently difficult and far from routine. In this study, DNA hybridization from serum dilutions into mixed DNA/mercaptoundecanol (MCU) adlayers on gold was monitored by surface plasmon resonance (SPR). Immobilized DNA probe and hybridized target densities on these surfaces were quantified using 32P-radiometric assays as a function of MCU diluent exposure. SPR surface capture results correlated with radiometric analysis for hybridization performance, demonstrating a maximum DNA hybridization on DNA/MCU mixed adlayers. The maximum target surface capture produced by MCU addition to the DNA probe layer correlates with structural and conformational data on identical mixed DNA/MCU adlayers on gold derived from XPS, NEXAFS, and fluorescence intensity measurements reported in a related study (Lee, C.-Y.; Gong, P.; Harbers, G. M.; Grainger, D. W.; Castner, D. G.; Gamble, L. J. Anal. Chem. 2006, 78, 3316-3325.). MCU addition into the DNA adlayer on gold also improved surface resistance to both nonspecific DNA and serum protein adsorption. Target DNA hybridization from serum dilutions was monitored with SPR on the optimally mixed DNA/MCU adlayers. Both hybridization kinetics and efficiency were strongly affected by nonspecific protein adsorption from a complex milieu even at a minimal serum concentration (e.g., 1%). No target hybridization was detected in SPR assays from serum concentrations above 30%, indicating nonspecific protein adsorption interference of DNA capture and hybridization from complex milieu. Removal of nonsignal proteins from nucleic acid targets prior to assay represents a significant issue for direct sample-to-assay nucleic acid diagnostics from food, blood, tissue, PCR mixtures, and many other biologically complex sample formats. PMID:16689533

  10. 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

  11. 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.

  12. Calculated and experimental chromatograms for distorted gradients and non-linear solvation strength retention models.

    PubMed

    Gritti, Fabrice; Guiochon, Georges

    2014-08-22

    Computer calculations of gradient chromatograms were performed by taking into account the adsorption behavior of the strong eluent in RPLC and the true Henry constant of the analytes. This improves the accuracy of classical gradient calculations, which all assume no affinity of the eluent modifier for the stationary phase and that the linear solvation strength model (LSSM) applies. The excess adsorption isotherm of acetonitrile with respect to water was measured by the minor disturbance method onto a Symmetry-C₁₈ RPLC adsorbent. The variations of the Henry constants of a nine compound mixture with the volume fraction of acetonitrile in the aqueous mobile phase were measured. The equilibrium dispersive model of chromatography combined with orthogonal collocation on finite elements was used to calculate chromatograms of the sample mixture for four gradient times decreasing from 25 to 1 min. The results predict a loss of resolution for the less retained analytes when the gradient times becomes smaller than 4 min. They also predict that this behavior can be eliminated when applying a quadratic gradient profile rather than a classical linear gradient. The predictions were validated by the agreement between the calculated and experimental chromatograms. PMID:24999065

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

    PubMed

    Lea, Amanda J; Tung, Jenny; Zhou, Xiang

    2015-11-01

    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

  14. 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

  15. 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

  16. Chemometric extraction of analyte-specific chromatograms in on-line gradient LC-infrared spectrometry.

    PubMed

    Kuligowski, Julia; Quintás, Guillermo; Garrigues, Salvador; de la Guardia, Miguel

    2009-12-01

    This work exploits the possibilities offered by the recently developed multivariate method named Science-Based Calibration (SBC), for the extraction of 'analyte-specific' chromatograms in on-line gradient reversed phase LC-infrared spectrometry (IR) in the presence of a high spectral and chromatographic overlapping between the analyte of interest, co-eluting sample matrix constituents and the mobile phase components. The SBC method uses an experimentally measured single response spectrum of the analyte of interest and representative noise to calculate an optimum regression vector (b(opt(1))). Then, the b(opt(1)) vector is used to predict the concentration of the analyte of interest in the spectra of the LC-IR sample chromatograms. To evaluate the advantages and pitfalls of the proposed approach, two different situations were analysed on real LC-IR data sets obtained from the injection of a series of standard solutions of four nitrophenols (p-nitrophenol, 3-methyl-4-nitrophenol, 2,4-dinitrophenol and 4-nitrophenol) in a reversed phase system under gradient conditions. In the first situation, the extraction of the 'analyte-specific' chromatogram was carried out without previous knowledge of the spectral features of other interferents present in the sample matrix. In a second situation evaluated, data obtained from the LC injection of a sample blank is available. Results show the potential applicability of this technique in a variety of situations and evidenced that the proposed chemometric approach improves the selectivity and sensitivity of the LC-IR hyphenation. PMID:19877149

  17. 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

  18. Resolution of mixed site DNA complexes with dimer-forming minor groove binders by using electrospray ionization mass spectrometry: Compound structure and DNA sequence effects

    PubMed Central

    Laughlin, Sarah; Wang, Siming; Kumar, Arvind; Farahat, Abdelbasset A.; Boykin, David W.; Wilson, W. David

    2015-01-01

    Small molecule targeting of the DNA minor groove is a promising approach to modulate genomic processes necessary for normal cellular function. For instance, dicationic diamindines, a well-known class of minor groove binding compounds, have been shown to inhibit interactions of transcription factors binding to genomic DNA. The applications of these compounds could be significantly expanded if we understand sequence-specific recognition of DNA better and could use the information to design more sequence-specific compounds. Aside from polyamides, minor groove binders typically recognize DNA at A-tract or alternating AT base pair sites. Targeting sites with GC base pairs, referred to here as mixed base pair sequences, is much more difficult than those rich in AT base pairs. Compound 1 is the first dicationic diamidine reported to recognize a mixed base pair site. It binds in the minor groove of ATGA sequences as a dimer with positive cooperativity. Due to the well-characterized behavior of 1 with ATGA and AT rich sequences, it provides a paradigm for understanding the elements that are key for recognition of mixed sequence sites. Electrospray ionization mass spectrometry (ESI-MS) is a powerful method to screen DNA complexes formed by analogs of 1 for specific recognition. We also report a novel approach to determine patterns of recognition by 1 for cognate ATGA and ATGA-mutant sequences. We found that functional group modifications and mutating the DNA target site significantly affect binding and stacking, respectively. Both compound conformation and DNA sequence directionality are crucial for recognition. PMID:25703690

  19. 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.

  20. Design and Synthesis of Heterocyclic Cations for Specific DNA Recognition: From AT-Rich to Mixed-Base-Pair DNA Sequences

    PubMed Central

    2015-01-01

    The compounds synthesized in this research were designed with the goal of establishing a new paradigm for mixed-base-pair DNA sequence-specific recognition. The design scheme starts with a cell-permeable heterocyclic cation that binds to AT base pair sites in the DNA minor groove. Modifications were introduced in the original compound to include an H-bond accepting group to specifically recognize the G-NH that projects into the minor groove. Therefore, a series of heterocyclic cations substituted with an azabenzimidazole ring has been designed and synthesized for mixed-base-pair DNA recognition. The most successful compound, 12a, had an azabenzimidazole to recognize G and additional modifications for general minor groove interactions. It binds to the DNA site −AAAGTTT– more strongly than the −AAATTT– site without GC and indicates the design success. Structural modifications of 12a generally weakened binding. The interactions of the new compound with a variety of DNA sequences with and without GC base pairs were evaluated by thermal melting analysis, circular dichroism, fluorescence emission spectroscopy, surface plasmon resonance, and molecular modeling. PMID:24422528

  1. Comparative evaluation of eight software programs for alignment of gas chromatography-mass spectrometry chromatograms in metabolomics experiments.

    PubMed

    Niu, Weihuan; Knight, Elisa; Xia, Qingyou; McGarvey, Brian D

    2014-12-29

    Since retention times of compounds in GC-MS chromatograms always vary slightly from chromatogram to chromatogram, it is necessary to align chromatograms before comparing them in metabolomics experiments. Several software programs have been developed to automate this process. Here we report a comparative evaluation of the performance of eight programs using prepared samples of mixtures of chemicals, and an extract of tomato vines spiked with three concentrations of a mixture of alkanes. The programs included in the comparison were SpectConnect, MetaboliteDetector 2.01a, MetAlign 041012, MZmine 2.0, TagFinder 04, XCMS Online 1.21.01, MeltDB and GAVIN. Samples were analyzed by GC-MS, chromatograms were aligned using the selected programs, and the resulting data matrices were preprocessed and submitted to principal components analysis. In the first trial, SpectConnect, MetAlign and MetaboliteDetector correctly identified ≥90% of the true positives. In the second trial, MetAlign and MetaboliteDetector correctly identified 87% and 81% of the true positives, respectively. In addition, in both trials >90% of the peaks identified by MetAlign and MetaboliteDetector were true positives. PMID:25435458

  2. 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. PMID:27038695

  3. Volume based vs. time based chromatograms: reproducibility of data for gradient separations under high and low pressure conditions.

    PubMed

    Stankovich, Joseph J; Gritti, Fabrice; Stevenson, Paul G; Vajda, Péter; Beaver, Lois Ann; Guiochon, Georges

    2014-05-23

    A critical aspect in fast gradient separations carried out under constant pressure, in the very high pressure liquid chromatography (VHPLC) mode is that time-based chromatograms may not yield highly reproducible separations. A proposed solution to improve the reproducibility of these separations involves plotting the chromatograms as functions of the volume eluted vs. UV absorbance instead of time vs. UV. To study the consequences of using the volume-based rather than the time-based chromatograms, separations were first performed under low pressures that do not generate significant amounts of heat and for which the variations of the eluent density along the columns are negligible. Secondly, they were performed under very high pressures that do generate heat and measurable variations of the local retention factor and eluent density along the column. Comparison of the results provides estimates of the improvements obtained when volume based chromatograms are used in gradient analyses. Using a column packed with fully porous particles, four different types of methods and several sets for each method were used to perform the gradient elution runs: two sets of constant flow rate operations, four sets of constant pressure operations, two sets of constant pressure operations with programmed flow rate, and one set using the constant heat loss approach. The differences between time-based and volume-based chromatograms are demonstrated by using eight replicates of early, middle, and last eluting peaks. The results show that volume-based chromatograms improve the retention time reproducibility of the four constant pressure methods by a factor of 3.7 on average. If the column is not thermally conditioned prior to performing a long series of separations, flow controlled methods (constant flow rate, programmed constant pressure, and constant wall heat approaches) are more precise. If one gradient run is used to bring the column to a relatively stable temperature, constant

  4. Evaluation of a blood-specific DNA methylated region and trial for allele-specific blood identification from mixed body fluid DNA.

    PubMed

    Watanabe, Ken; Akutsu, Tomoko; Takamura, Ayari; Sakurada, Koichi

    2016-09-01

    The identification of blood samples obtained from crime scenes has been an important step in forensic investigation. Recently, a novel approach using the blood-specific methylated CpG site cg06379435 has been reported. In this study, we developed a real-time polymerase-chain-reaction-based method that can simply and rapidly quantitate the methylation ratio of cg06379435 and its neighboring CpGs and set the threshold ratios for blood identification by analyzing various body fluid samples. Blood identification using the thresholds was successfully performed in the analysis of a small amount (1ng) of DNA from blood and various aged blood samples, including 29-year-old stains. We also demonstrated a test for allele-specific blood identification from a mixed DNA sample by bisulfite sequencing analysis of these CpG sites and their neighboring single nucleotide polymorphism, rs7359943 (A/G), which is of relevance in cases where mixed samples are obtained from crime scenes. The stability of DNA methylation in aged samples and the usefulness of neighboring genetic information shown in this study suggest that DNA-methylation-based body fluid identification will play a major role in future forensic investigations. PMID:27591539

  5. Structure and DNA Hybridization Properties of Mixed Nucleic Acid/Maleimide-Ethylene Glycol Monolayers

    SciTech Connect

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

    2007-01-01

    The surface structure and DNA hybridization performance of thiolated single-strand DNA (HS-ssDNA) covalently attached to a maleimide-ethylene glycol disulfide (MEG) monolayer on gold have been investigated. Monolayer immobilization chemistry and surface coverage of reactive ssDNA probes were studied by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry. Orientation of the ssDNA probes was determined by near-edge X-ray absorption fine structure (NEXAFS). Target DNA hybridization on the DNA-MEG probe surfaces was measured by surface plasmon resonance (SPR) to demonstrate the utility of these probe surfaces for detection of DNA targets from both purified target DNA samples and complex biological mixtures such as blood serum. Data from complementary techniques showed that immobilized ssDNA density is strongly dependent on the spotted bulk DNA concentration and buffer ionic strength. Variation of the immobilized ssDNA density had a profound influence on the DNA probe orientation at the surface and subsequent target hybridization efficiency. With increasing surface probe density, NEXAFS polarization dependence results (followed by monitoring the N 1s {yields} {pi}* transition) indicate that the immobilized ssDNA molecules reorient toward a more upright position on the MEG monolayer. SPR assays of DNA targets from buffer and serum showed that DNA hybridization efficiency increased with decreasing surface probe density. However, target detection in serum was better on the 'high-density' probe surface than on the 'high-efficiency' probe surface. The amounts of target detected for both ssDNA surfaces were several orders of magnitude poorer in serum than in purified DNA samples due to nonspecific serum protein adsorption onto the sensing surface.

  6. Mitochondrial DNA typing of laser-captured single sperm cells to differentiate individuals in a mixed semen stain.

    PubMed

    Zhang, Lu; Ding, Mei; Pang, Hao; Xing, Jiaxin; Xuan, Jinfeng; Wang, Chunhong; Lin, Ziqing; Han, Song; Liang, Kewei; Li, Chunmei; Yao, Jun; Wang, Baojie

    2016-08-01

    The identification of individuals in a mixture of two semen samples usually involves an analysis of autosomal and Y chromosomal short tandem repeats (STR) which can exclude unrelated individuals but cannot achieve the purpose of individual identification. In sperm cells, there are multiple copies of mitochondrial DNAs (mtDNA) which exhibit genetic polymorphisms in different matrilineal-related individuals. Single-cell capture technology can be applied to obtain some single sperm cells in a mixed semen sample, then polymerase chain reaction can be employed to amplify the mtDNA hypervariable region I (HVR I) from each cell. By pooling the cells with the same HVR I sequence, we can obtain the sufficient nuclear DNA for STR typing. PMID:27225075

  7. Absence of Y-specific DNA sequences in human 46,XX true hermaphrodites and in 45,X mixed gonadal dysgenesis.

    PubMed

    Waibel, F; Scherer, G; Fraccaro, M; Hustinx, T W; Weissenbach, J; Wieland, J; Mayerová, A; Back, E; Wolf, U

    1987-08-01

    A search for Y-specific DNA sequences has been performed in a sample of seven 46,XX true hermaphrodites and one 45,X mixed gonadal dysgenesis case and compared with a sample of 11 XX males. Using six Y-specific DNA probes no hybridization signal was obtained in the hermaphrodite group; in contrast, all XX males gave a positive signal with at least one probe. This difference is statistically highly significant. We conclude that the aetiology of true hermaphroditism is different from that of the XX male syndrome. As all cases of the hermaphrodite group are positive for the serological sex-specific antigen (Sxs) it is concluded that this antigen can be present even in the absence of Y-specific DNA. PMID:3038732

  8. Characterization of mixed monolayers of phosphatidylcholine and a dicationic gemini surfactant SS-1 with a langmuir balance: effects of DNA.

    PubMed Central

    Matti, V; Säily, J; Ryhänen, S J; Holopainen, J M; Borocci, S; Mancini, G; Kinnunen, P K

    2001-01-01

    Monolayers of a cationic gemini surfactant, 2,3-dimethoxy-1,4-bis(N-hexadecyl-N;N-dimethyl-ammonium)butane dibromide (abbreviated as SS-1) and its mixtures with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) were studied using a Langmuir balance. More specifically, we measured the force-area (pi-A) curves and determined the elastic area compressibility modulus (C) as a function of lateral packing pressure and the mole fraction of the cationic lipid (X(SS-1)), with and without DNA in the subphase. Both SS-1 and POPC exhibited smooth compression isotherms, indicating their monolayers to be in the liquid expanded state. Even low contents (X(SS-1) < 0.05) of SS-1 in a POPC monolayer condensed the film dramatically, up to 20% at 30 mN/m. This effect is suggested to reflect reorientation of the P(-)-N(+) dipole of the POPC headgroup. Accordingly, the magnitude of the condensing effect diminishes with X(SS-1) and is not observed for mixed films of dioleoylglycerol and SS-1. Reorientation of the P(-)-N(+) dipole is further supported by the pronounced increase in monolayer dipole potential psi due to SS-1. The presence of DNA in the subphase affected the mixed POPC/SS-1 monolayers differently depending on the constituent lipid stoichiometry as well as on the DNA/SS-1 charge ratio. At a DNA concentration of 0.63 microM (in base pairs) condensation of neat POPC monolayers was evident, and this effect remained up to X(SS-1) < 0.5, corresponding to DNA/SS-1 charge ratio of 1.25. An expansion due to DNA, evident as an increase in DeltaA/molecule, was observed at X(SS-1) > 0.5. At a higher concentration of DNA (1.88 microM base pairs) in the subphase corresponding to DNA/SS-1 charge ratio of 3.75 at X(SS-1) = 0.5, condensation was observed at all values of X(SS-1). PMID:11566784

  9. The discriminant pixel approach: a new tool for the rational interpretation of GCxGC-MS chromatograms.

    PubMed

    Vial, Jérôme; Pezous, Benoît; Thiébaut, Didier; Sassiat, Patrick; Teillet, Béatrice; Cahours, Xavier; Rivals, Isabelle

    2011-01-30

    GCxGC is now recognized as the most suited analytical technique for the characterization of complex mixtures of volatile compounds; it is implemented worldwide in academic and industrial laboratories. However, in the frame of comprehensive analysis of non-target analytes, going beyond the visual examination of the color plots remains challenging for most users. We propose a strategy that aims at classifying chromatograms according to the chemical composition of the samples while determining the origin of the discrimination between different classes of samples: the discriminant pixel approach. After data pre-processing and time-alignment, the discriminatory power of each chromatogram pixel for a given class was defined as its correlation with the membership to this class. Using a peak finding algorithm, the most discriminant pixels were then linked to chromatographic peaks. Finally, crosschecking with mass spectrometry data enabled to establish relationships with compounds that could consequently be considered as candidate class markers. This strategy was applied to a large experimental data set of 145 GCxGC-MS chromatograms of tobacco extracts corresponding to three distinct classes of tobacco. PMID:21215866

  10. 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. PMID:23818643

  11. 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

  12. 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

  13. 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. PMID:20593251

  14. 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. PMID:26961845

  15. 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

    2016-05-01

    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. PMID:27019159

  16. 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.

  17. Mixed-ligand copper(ii) Schiff base complexes: the role of the co-ligand in DNA binding, DNA cleavage, protein binding and cytotoxicity.

    PubMed

    Lian, Wen-Jing; Wang, Xin-Tian; Xie, Cheng-Zhi; Tian, He; Song, Xue-Qing; Pan, He-Ting; Qiao, Xin; Xu, Jing-Yuan

    2016-05-31

    Four novel mononuclear Schiff base copper(ii) complexes, namely, [Cu(L)(OAc)]·H2O (), [Cu(HL)(C2O4)(EtOH)]·EtOH (), [Cu(L)(Bza)] () and [Cu(L)(Sal)] () (HL = 1-(((2-((2-hydroxypropyl)amino)ethyl)imino)methyl)naphthalene-2-ol), Bza = benzoic acid, Sal = salicylic acid), were synthesized and characterized by X-ray crystallography, elemental analysis and infrared spectroscopy. Single-crystal diffraction analysis revealed that all the complexes were mononuclear molecules, in which the Schiff base ligand exhibited different coordination modes and conformations. The N-HO and O-HO inter- and intramolecular hydrogen bonding interactions linked these molecules into multidimensional networks. Their interactions with calf thymus DNA (CT-DNA) were investigated by UV-visible and fluorescence spectrometry, as well as by viscosity measurements. The magnitude of the Kapp values of the four complexes was 10(5), indicating a moderate intercalative binding mode between the complexes and DNA. Electrophoresis results showed that all these complexes induced double strand breaks of pUC19 plasmid DNA in the presence of H2O2 through an oxidative pathway. In addition, the fluorescence spectrum of human serum albumin (HSA) with the complexes suggested that the quenching mechanism of HSA by the complexes was a static process. Moreover, the antiproliferative activity of the four complexes against HeLa (human cervical carcinoma) and HepG-2 (human liver hepatocellular carcinoma) cells evaluated by colorimetric cell proliferation assay and clonogenic assay revealed that all four complexes had improved cytotoxicity against cancer cells. Inspiringly, complex , with salicylic acid as the auxiliary ligand, displayed a stronger anticancer activity, suggesting that a synergistic effect of the Schiff base complex and the nonsteroidal anti-inflammatory drug may be involved in the cell killing process. The biological features of mixed-ligand copper(ii) Schiff base complexes and how acetic auxiliary

  18. Limits of accuracy obtainable in the direct determination by fluorimetry of fluorescent whitening agents on thin layer chromatograms.

    PubMed

    Anders, G

    1975-01-01

    The quantitative direct determination of fluorescent whitening agents (FWAs) by thin layer chromatography involves limits of detection of 0.001 to 0.0005 mug. Visual assessment is about ten to a hundred times less sensitive than photometric measurement on thin layer chromatograms. The standard deviations in 10 measurements of two substances with different degrees of light sensitivity for a single measurement with a limit of detection of the order of 0.005 mug were about +/-13% to 44%. In the higher concentrations normally used (0.5 mug), the standard deviations were only +/-5% for both substances. PMID:1064526

  19. 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.

  20. Recognition of mixed-sequence DNA duplexes: Design guidelines for Invaders based on 2′-O-(pyren-1-yl)methyl-RNA monomers

    PubMed Central

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

    2013-01-01

    Development of agents that recognize mixed-sequence double-stranded DNA (dsDNA) is desirable due to their potential as tools for detection, regulation and modification of genes. Despite progress with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and other approaches, recognition of mixed-sequence dsDNA targets remains challenging. Our laboratory studies Invaders as an alternative approach toward this end. These double-stranded oligonucleotide probes are activated for recognition of mixed-sequence dsDNA through modification with +1 interstrand zippers of intercalator-functionalized nucleotides such as 2′-O-(pyren-1-yl)methyl-RNA monomers and have been recently shown to recognize linear dsDNA, DNA hairpins and chromosomal DNA. In the present work, we systematically study the role that the nucleobase moieties of the 2′-O-(pyren-1-yl)methyl-RNA monomers have on recognition efficiency of Invader duplexes. Results from thermal denaturation, binding energy, and recognition experiments using Invader duplexes with +1 interstrand zippers of the four canonical 2′-O-(pyren-1-yl)methyl-RNA A/C/G/U monomers, show that incorporation of these motifs is a general strategy for activation of probes for recognition of dsDNA. Probe duplexes with interstrand zippers comprised of C and/or U monomers result in the most efficient recognition of dsDNA. The insight gained from this study will drive the design of effective Invaders for applications in molecular biology, nucleic acid diagnostics and biotechnology. PMID:24195730

  1. 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

  2. Sandwich assay for mixed-sequence recognition of double-stranded DNA: Invader-based detection of targets specific to food pathogens†

    PubMed Central

    Denn, Benjamin; Karmakar, Saswata; Guenther, Dale C.; Hrdlicka, Patrick J.

    2014-01-01

    A 96-well plate sandwich assay based on Invader capture/signalling probes is used to recognize 28-mer mixed-sequence dsDNA targets specific to Salmonella, Campylobacter and Escherichia coli. Targets are detected at 20-55 pM concentration with excellent binding specificity. PMID:24036937

  3. 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

  4. In vitro cytotoxicity, DNA cleavage and SOD-mimic activity of copper(II) mixed-ligand quinolinonato complexes.

    PubMed

    Buchtík, Roman; Trávníček, Zdeněk; Vančo, Ján

    2012-11-01

    Six mixed-ligand copper(II) complexes with the composition [Cu(qui)(L)]BF(4)·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), were prepared, fully characterized and studied for their in vitro cytotoxicity on human osteosarcoma (HOS) and human breast adenocarcinoma (MCF7) cancer cell lines. The overall promising results of the cytotoxicity were found for all the complexes, while the best results were achieved for complex 6, with IC(50)=2.6 ± 0.8 μM (HOS), and 1.3 ± 0.5 μM (MCF7). The interactions of the Cu(II) complexes 1-6 with calf thymus DNA were investigated by the UV-visible spectral titration. An agarose-gel electrophoretic method of oxidative damage determination to circular plasmid pUC19 was used to assess the ability of the complexes to act as chemical nucleases. A high effectiveness of DNA cleavage was observed for 2, 4 and 5. In vitro antioxidative activity of the complexes was studied by the superoxide dismutase-mimic (SOD-mimic) method. The best result was afforded by complex 1 with IC(50)=4.7 ± 1.0 μM, which corresponds to 10.2% of the native Cu,Zn-SOD enzyme activity. The ability of the tested complexes to interact with sulfur-containing biomolecules (cysteine and reduced glutathione) at physiological levels was proved by electrospray-ionization mass spectrometry (ESI-MS). PMID:23022693

  5. 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)

  6. Effect of DNA interaction involving antioxidative 4-aminoantipyrine incorporating mixed ligand complexes having alpha-amino acid as co-ligand

    NASA Astrophysics Data System (ADS)

    Raman, Natarajan; Sakthivel, Arunagiri; Selvaganapathy, Muthusamy; Mitu, Liviu

    2014-02-01

    Few new mixed ligand transition metal complexes of the stoichiometry [ML(A)2], where M = Co(II), Ni(II), Cu(II) and Zn(II), L = FFAP (furfurylidene-4-aminoantipyrine) and A = amino acid (glycine/alanine/valine), have been designed, synthesized and characterized. The molar conductivity of the complexes in DMF at 10-3 M concentration shows that they are non-electrolytes. The interaction of these complexes with CT-DNA indicates that the valine mixed ligand complexes are having higher binding constant than alanine and glycine mixed ligand complexes. This analysis reveals that binding constant depends on the size of the alkyl group present in the amino acid. The binding constants of valine mixed ligand complexes are in the order of 104 to 105 M-1 revealing that the complexes interact with DNA through moderate intercalation mode. The metal complexes exhibit effective cleavage of pUC19 DNA but it is not preceded via radical cleavage and superoxide anion radical. They are good antimicrobial agents than the free ligand. On comparing the IC50 values, [Ni(L)(Gly)2] is considered as a potential drug to eliminate the hydroxyl radical.

  7. DNA barcoding to identify species of phlebotomine sand fly (Diptera: Psychodidae) in the mixed leishmaniasis focus of the Colombian Caribbean.

    PubMed

    Romero-Ricardo, Luis; Lastre-Meza, Natalia; Pérez-Doria, Alveiro; Bejarano, Eduar E

    2016-07-01

    Identification of the species of phlebotomine sand flies present in each focus of leishmaniasis is necessary to incriminate vectors and implement vector control strategies. Although the cytochrome oxidase I (COI) gene has been proposed as a barcode for the identification of animal species, less than 20% of New World phlebotomines have been characterized to date. In this study DNA barcoding was used to identify phlebotomine species of the mixed leishmaniasis focus in the Colombian Caribbean by means of three evolutionary models: Kimura's two parameter (K2P) nucleotide substitution model, that of (Tamura and Nei, 1993) (TN93) and proportional sequence divergence (p-distances). A 681bp sequence of the COI gene was obtained from 66 individuals belonging to 19 species of the genus Lutzomyia (Lu. abonnenci, Lu. atroclavata, Lu. bicolor, Lu. carpenteri, Lu. cayennensis cayennensis, Lu. dubitans, Lu. evansi, Lu. gomezi, Lu. gorbitzi, Lu. longipalpis, Lu. micropyga, Lu. migonei, Lu. panamensis, Lu. (Psathyromyia) sp., Lu. rangeliana, Lu. serrana, Lu. shannoni, Lu. trinidadensis and Lu. venezuelensis) and one of Brumptomyia (B. mesai). The genetic divergence values for TN93 among individuals of the same species fluctuated up to 3.2% (vs. 2.9% for K2P and 2.8% for p-distances), while the values between species ranged from 8.8-43.7% (vs. 6.8-19.6% for K2P and 6.6-17.4% for p-distances). A dendrogram constructed by means of the Neighbor-Joining method grouped phlebotomines into 20 clusters according to species, with bootstrap values of up to 100% in those with more than one individual. However, loss of the phylogenetic signal of the gene COI was observed at the supraspecific level as a consequence of substitutional saturation. In conclusion, irrespective of the evolutionary model selected, all phlebotomines were correctly assigned to species, showing 100% concordance with morphological identification. PMID:26992298

  8. Removal of a PCR inhibitor and resolution of DNA STR types in mixed human-canine stains from a five year old case.

    PubMed

    Shutler, G G; Gagnon, P; Verret, G; Kalyn, H; Korkosh, S; Johnston, E; Halverson, J

    1999-05-01

    The analysis of biological trace evidence from a reopened investigation into a 1991 murder from Vernon, B.C. revealed mixed human and dog bloodstains on blue jean pants that contained a PCR inhibitory substance. The presence of the inhibitory substance was detected by the inhibition caused from adding a small aliquot of the test DNA extract into a PCR reaction designed to produce a known standard product. The removal of the PCR inhibitory substance was accomplished by treating the extracted DNA with Thiopropyl Sepharose 6B beads. DNA profiles from two human contributors and a canine were obtained using species specific polymorphic STR markers. The two human DNA profiles obtained from blue jean pants were resolved, one matched the suspect and the other matched the victim. The DNA profile from the canine component matched that obtained from the known sample of the victim's dog who was also slain during the assault. This evidence along with other DNA typing evidence was critical in obtaining a resolution of the case. PMID:10408119

  9. 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)

  10. Chromodomain-helicase-DNA binding protein 5, 7 and pronecrotic mixed lineage kinase domain-like protein serve as potential prognostic biomarkers in patients with resected pancreatic adenocarcinomas

    PubMed Central

    Seldon, Crystal S; Colbert, Lauren E; Hall, William A; Fisher, Sarah B; Yu, David S; Landry, Jerome C

    2016-01-01

    Pancreatic cancer is one of the deadliest cancers with a very poor prognosis. Recently, there has been a significant increase in research directed towards identifying potential biomarkers that can be used to diagnose and provide prognostic information for pancreatic cancer. These markers can be used clinically to optimize and personalize therapy for individual patients. In this review, we focused on 3 biomarkers involved in the DNA damage response pathway and the necroptosis pathway: Chromodomain-helicase-DNA binding protein 5, chromodomain-helicase-DNA binding protein 7, and mixed lineage kinase domain-like protein. The aim of this article is to review present literature provided for these biomarkers and current studies in which their effectiveness as prognostic biomarkers are analyzed in order to determine their future use as biomarkers in clinical medicine. Based on the data presented, these biomarkers warrant further investigation, and should be validated in future studies. PMID:27096031

  11. MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments*

    PubMed Central

    Rardin, Matthew J.; Schilling, Birgit; Cheng, Lin-Yang; MacLean, Brendan X.; Sorensen, Dylan J.; Sahu, Alexandria K.; MacCoss, Michael J.; Vitek, Olga; Gibson, Bradford W.

    2015-01-01

    Quantitative analysis of discovery-based proteomic workflows now relies on high-throughput large-scale methods for identification and quantitation of proteins and post-translational modifications. Advancements in label-free quantitative techniques, using either data-dependent or data-independent mass spectrometric acquisitions, have coincided with improved instrumentation featuring greater precision, increased mass accuracy, and faster scan speeds. We recently reported on a new quantitative method called MS1 Filtering (Schilling et al. (2012) Mol. Cell. Proteomics 11, 202–214) for processing data-independent MS1 ion intensity chromatograms from peptide analytes using the Skyline software platform. In contrast, data-independent acquisitions from MS2 scans, or SWATH, can quantify all fragment ion intensities when reference spectra are available. As each SWATH acquisition cycle typically contains an MS1 scan, these two independent label-free quantitative approaches can be acquired in a single experiment. Here, we have expanded the capability of Skyline to extract both MS1 and MS2 ion intensity chromatograms from a single SWATH data-independent acquisition in an Integrated Dual Scan Analysis approach. The performance of both MS1 and MS2 data was examined in simple and complex samples using standard concentration curves. Cases of interferences in MS1 and MS2 ion intensity data were assessed, as were the differentiation and quantitation of phosphopeptide isomers in MS2 scan data. In addition, we demonstrated an approach for optimization of SWATH m/z window sizes to reduce interferences using MS1 scans as a guide. Finally, a correlation analysis was performed on both MS1 and MS2 ion intensity data obtained from SWATH acquisitions on a complex mixture using a linear model that automatically removes signals containing interferences. This work demonstrates the practical advantages of properly acquiring and processing MS1 precursor data in addition to MS2 fragment ion

  12. Mixed ligand copper(II) complexes of 2,9-dimethyl-1,10-phenanthroline: tridentate 3N primary ligands determine DNA binding and cleavage and cytotoxicity.

    PubMed

    Ganeshpandian, Mani; Ramakrishnan, Sethu; Palaniandavar, Mallayan; Suresh, Eringathodi; Riyasdeen, Anvarbatcha; Akbarsha, Mohammad Abdulkadher

    2014-11-01

    A series of mononuclear mixed ligand copper(II) complexes of the type [Cu(L)(2,9-dmp)](ClO4)21-4, where L is a tridentate 3N ligand such as diethylenetriamine (L1) (1) or N-methyl-N'-(pyrid-2-yl-methyl)ethylenediamine (L2) (2) or di(2-picolyl)amine (L3) (3) or bis(pyrid-2-ylmethyl)-N-methylamine (L4) (4) and 2,9-dmp is 2,9-dimethyl-1,10-phenanthroline, has been isolated and characterized. The complexes 1 and 3 possess square-based pyramidal coordination geometry. Absorption spectral studies reveal that the intrinsic DNA binding affinity varies as 1>2>3>4. The higher DNA binding affinity of 1 arises from L1, which offers lower steric hindrance toward intercalation of 2,9-dmp co-ligand into DNA base pairs and is involved in hydrogen bonding interaction with DNA. Interestingly, all the complexes cleave pUC19 supercoiled DNA in the absence of an activating agent. They also exhibit oxidative (H2O2) DNA cleavage ability, which varies as 1>2>3>4, the highest cleavage efficiency of 1 being due to the largest amount of ROS it generates. The tryptophan emission-quenching experiment reveals that the stronger binding of 3 and 4 with bovine serum albumin (BSA) in the hydrophobic region, which is in line with DNA viscosity measurements. The IC50 values of 1-4 for MCF-7 breast cancer cell line are lower than that of cisplatin. Flow cytometry analysis reveals that 1 mediates the arrest of S and G2/M phases in the cell cycle progression at 24h harvesting time, which progresses into apoptosis. Hoechst 33258 staining studies indicate the higher potency of 1 to induce apoptosis. PMID:25151036

  13. Identification and characterization of 2nd generation Invader Locked Nucleic Acids (LNAs) for mixed-sequence recognition of double-stranded DNA

    PubMed Central

    Sau, Sujay P.; Madsen, Andreas S.; Podbevsek, Peter; Andersen, Nicolai K.; Kumar, T. Santhosh; Andersen, Sanne; Rathje, Rie L.; Anderson, Brooke A.; Guenther, Dale C.; Karmakar, Saswata; Kumar, Pawan; Plavec, Janez; Wengel, Jesper

    2013-01-01

    Development of synthetic agents that recognize double-stranded DNA (dsDNA) is a long-standing goal that is inspired by the promise for tools that detect, regulate and modify genes. Progress has been made with triplex-forming oligonucleotides, PNAs, and polyamides, but substantial efforts are currently devoted to the development of alternative strategies that overcome limitations observed with the classic approaches. In 2005, we introduced Invader Locked Nucleic Acids (LNAs), i.e., double-stranded probes that are activated for mixed-sequence recognition of dsDNA through modification with ‘+1 interstrand zippers’ of 2’-N-(pyren-1-yl)methyl-2’-amino-α-L-LNA monomers. Despite promising preliminary results, progress has been slow due to the synthetic complexity of the building blocks. Here, we describe a study that led to the identification of two simpler classes of Invader monomers. We compare thermal denaturation characteristics of double-stranded probes featuring different interstrand zippers of pyrene-functionalized monomers based on 2’-amino-α-L-LNA, 2’-N-methyl-2’-amino-DNA, and RNA scaffolds. Insights from fluorescence spectroscopy, molecular modeling and NMR spectroscopy are used to elucidate the structural factors that govern probe activation. We demonstrate that probes with +1 zippers of 2’-O-(pyren-1-yl)methyl-RNA or 2’-N-methyl-2’-N-(pyren-1-yl)methyl-2’-amino-DNA monomers recognize DNA hairpins with similar efficiency as original Invader LNAs. Access to synthetically simple monomers will accelerate the use of Invader-mediated dsDNA-recognition for applications in molecular biology and nucleic acid diagnostics. PMID:24032477

  14. 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. PMID:26042527

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

    PubMed Central

    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. PMID:26042527

  16. Optimization of novel combi-molecules: identification of balanced and mixed bcr-abl/DNA targeting properties.

    PubMed

    Rachid, Zakaria; Katsoulas, Athanasia; Williams, Christopher; Larroque, Anne-Laure; McNamee, James; Jean-Claude, Bertrand J

    2007-08-01

    Steps toward the identification of combi-molecules with strong abl tyrosine kinase (TK) inhibitory property and significant DNA damaging potential are described. The optimized combi-molecule 13a was shown to induce approximately twofold stronger abl TK inhibitory activity than Gleevec and high levels of DNA damage in chronic myelogenous leukemic cells. PMID:17572088

  17. 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.

  18. Efficient DNA cleavage mediated by mononuclear mixed ligand copper(II) phenolate complexes: the role of co-ligand planarity on DNA binding and cleavage and anticancer activity.

    PubMed

    Jaividhya, Paramasivam; Dhivya, Rajkumar; Akbarsha, Mohamad Abdulkadhar; Palaniandavar, Mallayan

    2012-09-01

    The new mononuclear copper(II) complexes [Cu(L)(H(2)O)(2)](+)1 and [Cu(L)(diimine)](+)2-6, where LH=2-[(2-dimethylaminoethylimino)methyl]phenol and diimine=2,2'-bipyridine (bpy) (2), or 1,10-phenanthroline (phen) (3), or dipyrido[3,2-f:2',3'-h]quinoxaline (dpq) (4) or dipyrido[3,2-a:2',3'-c]phenazine (dppz) (5) or 11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine (dmdppz) (6), have been isolated and characterized. The X-ray crystal structures of 2 contains the monomeric complex molecule with a trigonal bipyramidal distorted square pyramidal (TBPDSP) coordination geometry, while 4 and 6 with square pyramidal distorted trigonal bipyramidal (SPDTBP) coordination geometry. The amine nitrogen of -NMe(2) group of the tridentate primary ligand is located at one of the corners of the square plane in 2 and 6 but in the axial position in 4. The interaction of the complexes with calf thymus DNA has been investigated using UV-visible and fluorescence spectroscopy, and viscosity measurements to understand the effect of diimine co-ligands on the mode and extent of DNA binding. The complexes 4 and 5 interact with calf thymus DNA more strongly than the other complexes through partial intercalation of the extended planar ring of the dpq (4) and dppz (5) co-ligands with the DNA base stack. All the complexes, except 1, effect the double strand DNA cleavage of plasmid DNA and 5 cleaves plasmid DNA in the absence of a reductant at a concentration (40 μM) lower than 4. It is remarkable that all the complexes display cytotoxicity against human breast cancer cell lines (MCF-7) and human cervical epidermoid carcinoma cell lines (ME 180) with potency higher than the currently used chemotherapeutic agent cisplatin and that 5 exhibits cytotoxicity higher than the other complexes. PMID:22841366

  19. Gene therapy for nucleus pulposus regeneration by heme oxygenase-1 plasmid DNA carried by mixed polyplex micelles with thermo-responsive heterogeneous coronas.

    PubMed

    Feng, Ganjun; Chen, Hongying; Li, Junjie; Huang, Qiang; Gupte, Melanie J; Liu, Hao; Song, Yueming; Ge, Zhishen

    2015-06-01

    Safe and high-efficiency gene therapy for nucleus pulposus (NP) regeneration was urgently desired to treat disc degeneration-associated diseases. In this work, an efficient nonviral cationic block copolymer gene delivery system was used to deliver therapeutic plasmid DNA (pDNA), which was prepared via complexation between the mixed cationic block copolymers, poly(ethylene glycol)-block-poly{N-[N-(2-aminoethyl)-2-aminoehtyl]aspartamide} [PEG-b-PAsp(DET)] and poly(N-isopropylacrylamide)-block-PAsp(DET) [PNIPAM-b-PAsp(DET)], and pDNA at 25 °C. The mixed polyplex micelles (MPMs) containing heterogeneous coronas with hydrophobic and hydrophilic microdomains coexisting could be obtained upon heating from 25 to 37 °C, which showed high tolerability against nuclease and strong resistance towards protein adsorption. The gene transfection efficiency of MPMs in NP cells was significantly higher than that of regular polyplex micelles prepared from sole block copolymer of PEG-b-PAsp(DET) (SPMs) in in vitro and in vivo evaluation due to the synergistic effect of improved colloidal stability and low cytotoxicity. High expression of heme oxygenase-1 (HO-1) in NP cells transfected by MPMs loading HO-1 pDNA significantly decreased the expression activity of matrix metalloproteinases 3 (MMP-3) and cyclo-oxygenase-2 (COX-2) induced by interleukin-1β (IL-1β), and simultaneously increased the NP phenotype-associated genes such as aggrecan, type II collagen, and SOX-9. Moreover, the therapeutic effects of MPMs loading pDNA were tested to treat disc degeneration induced by stab injury. The results demonstrated that administration of HO-1 pDNA carried by MPMs in rat tail discs apparently reduced inflammatory responses induced by need stab and increased glycosaminoglycan (GAG) content, finally achieving better therapeutic efficacy as compared with SPMs. Consequently, MPMs loading HO-1 pDNA were demonstrated to be potential as a safe and high-efficiency nonviral gene delivery system

  20. 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.

  1. Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution

    PubMed Central

    Friedrich, Sarah M.; Liu, Kelvin J.; Wang, Tza-Huei

    2016-01-01

    Limited tools exist that are capable of monitoring nucleic acid conformations, fluctuations, and distributions in free solution environments. Single molecule free solution hydrodynamic separation enables the unique ability to quantitatively analyze nucleic acid biophysics in free solution. Single molecule fluorescent burst data and separation chromatograms can give layered insight into global DNA conformation, binding interactions, and molecular distributions. First, we show that global conformation of individual DNA molecules can be directly visualized by examining single molecule fluorescent burst shapes and that DNA exists in a dynamic equilibrium of fluctuating conformations as it is driven by Poiseuille flow through micron-sized channels. We then show that this dynamic equilibrium of DNA conformations is reflected as shifts in hydrodynamic mobility that can be perturbed using salt and ionic strength to affect packing density. Next, we demonstrate that these shifts in hydrodynamic mobility can be used to investigate hybridization thermodynamics and binding interactions. We distinguish and classify multiple interactions within a single sample, and demonstrate quantification amidst large concentration differences for the detection of rare species. Finally, we demonstrate that these differences can resolve perfect complement, 2bp mismatched, and 3bp mismatched sequences. Such a system can be used to garner diverse information about DNA conformation and structure, and potentially be extended to other molecules and mixed-species interactions, such as between nucleic acids and proteins or synthetic polymers. PMID:26684193

  2. Mixed ligand ruthenium(III) complexes of benzaldehyde 4-methyl-3-thiosemicarbazones with triphenylphosphine/triphenylarsine co-ligands: Synthesis, DNA binding, DNA cleavage, antioxidative and cytotoxic activity

    NASA Astrophysics Data System (ADS)

    Sampath, K.; Sathiyaraj, S.; Raja, G.; Jayabalakrishnan, C.

    2013-08-01

    The new ruthenium(III) complexes with 4-methyl-3-thiosemicarbazone ligands, (E)-2-(2-chlorobenzylidene)-N-methylhydrazinecarbothioamide (HL1) and (E)-2-(2-nitrobenzylidene)-N-methylhydrazinecarbothioamide (HL2), were prepared and characterized by various physico-chemical and spectroscopic methods. The title compounds act as bidentate, monobasic chelating ligands with S and N as the donor sites and are preferably found in the thiol form in all the complexes studied. The molecular structure of HL1 and HL2 were determined by single crystal X-ray diffraction method. DNA binding of the ligands and complexes were investigated by absorption spectroscopy and IR spectroscopy. It reveals that the compounds bind to nitrogenous bases of DNA via intercalation. The oxidative cleavage of the complexes with CT-DNA inferred that the effects of cleavage are dose dependent. Antioxidant study of the ligands and complexes showed the significant antioxidant activity against DPPH radical. In addition, the in vitro cytotoxicity of the ligands and complexes against MCF-7 cell line was assayed which showed higher cytotoxic activity with the lower IC50 values indicating their efficiency in killing the cancer cells even at low concentrations.

  3. Synthesis, characterization, and binding properties towards CT-DNA and lipoxygenase of mixed-ligand silver(I) complexes with 2-mercaptothiazole and its derivatives and triphenylphosphine.

    PubMed

    Kyros, L; Banti, C N; Kourkoumelis, N; Kubicki, M; Sainis, I; Hadjikakou, S K

    2014-03-01

    Mixed-ligand silver(I) complexes of formulae [AgCl(TPP)2(MTZD)] (1), {[AgCl(TPP)2(MBZT)]·(MBZT)·2(toluene)} (2), and [AgCl(TPP)2(CMBZT)] (3) were obtained by refluxing toluene solutions of silver(I) chloride with triphenylphosphine (TPP) and the appropriate heterocyclic thioamides 2-mercaptothiazolidine (MTZD), 2-mercaptobenzothiazole (MBZT), and 5-chloro-2-mercaptobenzothiazole (CMBZT). The complexes were characterized by the melting point, vibrational spectroscopy (Fourier transform mid-IR), (1)H-NMR spectroscopy, UV-vis spectroscopy, and X-ray crystallography. DNA binding tests indicate the ability of complexes 1-3 to modify the activity of cells. The binding constants of 1-3 towards calf-thymus DNA (CT-DNA) [(3.5 ± 8.5) × 10(4) M(-1) for 1, (10.0 ± 0.0) × 10(4) M(-1) for 2, and (46.4 ± 7.0) × 10(4) M(-1) for 3] indicate strong interaction of 3. Changes in the fluorescence of ethidium bromide in the presence of DNA suggest intercalation into or electrostatic interactions with DNA. The corresponding apparent binding constants (K app) towards CT-DNA calculated through fluorescence spectra are (3.5 ± 0.7) × 10(4) M(-1) for 1, (10.0 ± 0.0) × 10(4) M(-1) for 2, and (46.4 ± 7.0) × 10(4) M(-1) for 3. Docking studies on DNA complexes confirm the binding of 1 and 2 in the major groove of CT-DNA and of 3 in the minor groove. Moreover, the influence of 1-3 on the catalytic peroxidation of linoleic acid to hydroperoxylinoleic acid by the enzyme lipoxygenase was studied kinetically and theoretically. The antibacterial effect of 1-3 against the bacterial species Pseudomonas aeruginosa and Escherichia coli was evaluated. Complex 1 exhibits the strongest activity. PMID:24445998

  4. Mixing of M segment DNA vaccines to Hantaan virus and Puumala virus reduces their immunogenicity in hamsters.

    PubMed

    Spik, Kristin W; Badger, Catherine; Mathiessen, Iacob; Tjelle, Torunn; Hooper, Jay W; Schmaljohn, Connie

    2008-09-19

    To determine if DNA vaccines for two hantaviruses causing hemorrhagic fever with renal syndrome, Hantaan virus and Puumala virus, are immunogenic when given in combination, we delivered them to hamsters separately or as mixtures by gene gun or by electroporation. Both vaccines elicited neutralizing antibodies when given alone but when they were delivered as a mixture, antibodies to only one of the two hantaviruses could be detected. In contrast, if the DNAs were given as separate vaccinations to a single animal, responses to both were observed. These studies suggest that the two DNA vaccines will need to be given as separate administrations. PMID:18482782

  5. Synthesis and Structure of a Ternary Copper(II) Complex with Mixed Ligands of Diethylenetriamine and Picrate: DNA/Protein-Binding Property and In Vitro Anticancer Activity Studies.

    PubMed

    Shi, Ya-Ning; Zheng, Kang; Zhu, Ling; Li, Yan-Tuan; Wu, Zhi-Yong; Yan, Cui-Wei

    2015-05-01

    Based on the importance of the design and synthesis of transition metal complexes with noncovalent DNA/protein-binding abilities in the field of metallo pharmaceuticals, a new mononuclear ternary copper(II) complex with mixed ligands of diethylenetriamine (dien) and picrate anion (pic), identified as [Cu(dien)(pic)](pic), was synthesized and characterized by elemental analysis, molar conductivity measurement, infrared spectrum, electronic spectral studies, and single-crystal X-ray diffractometry. The structure analysis reveals that the copper(II) complex crystallizes in the monoclinic space group P21 /c, and the copper(II) ion has a distorted square pyramidal coordination geometry. A two-dimensional supramolecular structure is formed through hydrogen bonds. The DNA/bovine serum albumin (BSA)-binding properties of the complex are explored, indicating that the complex can interact with herring sperm DNA via intercalation mode and bind to BSA responsible for quenching of tryptophan fluorescence by static quenching mechanism. The in vitro anticancer activity shows that the copper(II) complex is active against the selected tumor cell lines. PMID:25652782

  6. Isolation of a rat liver Golgi mannosidase II clone by mixed oligonucleotide-primed amplification of cDNA.

    PubMed Central

    Moremen, K W

    1989-01-01

    A clone encoding Golgi mannosidase II (MII; GlcNAc-transferase I-dependent alpha 1,3(alpha 1,6) mannosidase), an enzyme involved in asparagine-linked oligosaccharide processing, was isolated from a rat liver lambda gt11 cDNA library by a method that employs a modification of the polymerase chain reaction. Specific oligonucleotide primers were designed from two regions of protein sequence and were combined in an amplification reaction with a single-stranded cDNA preparation derived from rat liver poly(A)+ RNA. Based upon mapping of the protein sequences 42 kDa apart on the MII polypeptide, the procedure was expected to generate an approximately 1150-base-pair amplification product representing a segment of the MII gene between the two primer regions. The size of the amplified product (1170 base pairs) was in close agreement with this predicted fragment size. The authenticity of the amplified fragment was confirmed by the agreement of the DNA sequence with additional protein sequence data. A 1474-base-pair clone was isolated from a cDNA library by plaque hybridization using the amplification fragment as a radiolabeled probe. The nucleotide sequence of this clone predicts a single continuous open reading frame and, based upon a polypeptide molecular mass of 117 kDa for the enzyme subunit, is consistent with the clone representing approximately 50% of the coding sequence of MII. Both the clone and the amplification product hybridized to a rat liver mRNA of approximately 8 kilobases, a message size approximately 4.7 kilobases larger than the size of the predicted open reading frame. This extensive non-coding information on the MII message is a feature common to two other Golgi processing enzymes, both of which contain most of the non-coding information on the 3' end of their messages. The function of these disproportionately large untranslated regions is not clear. Images PMID:2748583

  7. 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. PMID:26900058

  8. 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.

  9. Ion trace detection algorithm to extract pure ion chromatograms to improve untargeted peak detection quality for liquid chromatography/time-of-flight mass spectrometry-based metabolomics data.

    PubMed

    Wang, San-Yuan; Kuo, Ching-Hua; Tseng, Yufeng J

    2015-03-01

    Able to detect known and unknown metabolites, untargeted metabolomics has shown great potential in identifying novel biomarkers. However, elucidating all possible liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS) ion signals in a complex biological sample remains challenging since many ions are not the products of metabolites. Methods of reducing ions not related to metabolites or simply directly detecting metabolite related (pure) ions are important. In this work, we describe PITracer, a novel algorithm that accurately detects the pure ions of a LC/TOF-MS profile to extract pure ion chromatograms and detect chromatographic peaks. PITracer estimates the relative mass difference tolerance of ions and calibrates the mass over charge (m/z) values for peak detection algorithms with an additional option to further mass correction with respect to a user-specified metabolite. PITracer was evaluated using two data sets containing 373 human metabolite standards, including 5 saturated standards considered to be split peaks resultant from huge m/z fluctuation, and 12 urine samples spiked with 50 forensic drugs of varying concentrations. Analysis of these data sets show that PITracer correctly outperformed existing state-of-art algorithm and extracted the pure ion chromatograms of the 5 saturated standards without generating split peaks and detected the forensic drugs with high recall, precision, and F-score and small mass error. PMID:25622715

  10. Separation of botulinum-positive and -negative fish samples by means of a pattern recognition method applied to headspace gas chromatograms.

    PubMed Central

    Snygg, B G; Andersson, J E; Krall, C A; Stöllman, U M; Akesson, C A

    1979-01-01

    A gas chromatographic headspace technique was used to analyze the gas produced during putrefaction of pond-raised, degutted trout, incubated in evacuated plastic pouches. The following samples were analyzed; 10 samples which, due to natural contamination with Clostridium botulinum, were toxic when injected into mice, 10 samples which were nontoxic when injected, and 9 samples inoculated with one strain of C. botulinum type E. The gas chromatograms showed the presence of 118 compounds in most samples. Quantitative differences among most chromatograms could be observed, but no compound was unique to any of the three groups. By means of a specific pattern recognition method, all negative samples were shown to fall into one group and were distinctly separated from the toxic samples. No differences could be observed between the two groups of inoculated and naturally contaminated trout samples. The results suggest that headspace analysis combined with pattern recognition analysis might prove to be a valuable method for screening studies of foods containing living cells of C. botulinum. PMID:393168

  11. 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

  12. 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. PMID:22727555

  13. Validation of an analytical method to determine sulfamides in kidney by HPLC-DAD and PARAFAC2 with first-order derivative chromatograms.

    PubMed

    García, I; Ortiz, M C; Sarabia, L; Aldama, J M

    2007-03-28

    Six sulfamides were extracted from kidney and analysed by high-performance liquid chromatography with diode array detection (HPLC-DAD): sulfadiazine, sulfamethazine, sulfamethoxypyridazine, sulfamethoxazole, sulfadimethoxine and sulfaquinoxaline. Two main difficulties arose in identifying and quantifying the analytes. Firstly, the chromatographic peaks of the matrix interferences overlapped with those of the analytes. The uniqueness property of PARAFAC2 solved this problem. Secondly, the gradient elution caused a baseline drift. The first-order derivative of the chromatograms minimized its effect. The analytical method was validated. As the performance criteria detailed in the European Decision 2002/657/EC are based on specific signals, this paper generalizes those criteria for higher-order and non-specific signals. In this sense the proposed methodology is general and can be applied to any chromatographic method (HPLC or GC) with a detector that provide a multivariate signal (MS, DAD, EC, etc.). PMID:17386777

  14. Correlation between mixed-function oxidase enzyme induction and aflatoxin B1-induced unscheduled DNA synthesis in the chick embryo, in vivo.

    PubMed

    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 P1-450-associated enzyme activities. Aflatoxin B1 (AFB1) was injected 24 hr later (7 DI), followed by a 5-hr continuous 3H-thymidine exposure. The livers were removed, prepared for autoradiography, and hepatocytes were scored for an increase in grains/nucleus, indicative of UDS. Aflatoxin B1 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. PMID:6420149

  15. 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. PMID:21637527

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

    PubMed Central

    2009-01-01

    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 ΦST 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. PMID:21637527

  17. [Determination of markers from characteristic HPLC chromatogram of phenols in three official origins of Ephedrae Herba and quantitative analysis of four phenols].

    PubMed

    Zuo, Xue; Hong, Hao; Zang, Xin-yu; Xu, Feng; Shang, Ming-ying; Wang, Xuan; Cai, Shao-qing

    2015-12-01

    This study is to establish the characteristic HPLC chromatogram of phenols in Ephedrae Herba, from which to pick out the marker peaks, followed by the analysis of the regularity of their distribution and content in the herbaceous stems of Ephedra sinica, E. intermedia and E. equisetina. The HPLC-DAD method for the characteristic chromatogram as well as quantitative analysis was established. The separation was carried out on a YMC-Pack ODS-A column (4.6 mm x 250 mm, 5 µm), eluted with the mobile phases as 0.01% formic acid aqueous solution (A) and acetonitrile (B) in a linear gradient (0-10 min, 17% B; 10-25 min, 17%-19% B; 25- 33 min, 19%-48% B; 33-35 min, 48%-51% B; 35-44 min, 51% B). The flow rate was kept at 1.0 mL · min⁻¹. The column tem- perature was 40 °C, and the detection wavelength was set at 350 nm (0-16 min) and 330 nm (16-44 min). Forty-six batches of collected samples from three official origins of Ephedrae Herba were detected, whose liquid chromatograms proven to be helpful to the differentiation of different origins. With principal component analysis and the analysis of distribution of peak area, twelve key peaks from the chromatogram were discussed in details on their contributions to the characteristics and differences of three official origins of the herb: peak area of peak 10, 11, 12 were found out to be significantly higher in E. equisetina than in other two origins, whose sum (higher than 146 mAU in E. equisetina) was useful for the discrimination between E. equisetina and the other two origins; peak area of 1 and 4 were respectively higher in E. sinica and E. intermedia than in other official origins, indicating their important effect on the differen- tiation of corresponding origins; peak 8 and 9 were picked out as two characteristic common peaks in three official origins of the herb, whose peak area showed little difference among different origins; further, peak area of other key peaks in the chromatogram also showed some difference

  18. 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. PMID:27155593

  19. Effects of pretreatment with pyrazole and inducers of mixed function oxidases on DNA repair elicited by dimethylnitrosamine in rat hepatocytes in vivo and in vitro.

    PubMed

    Kornbrust, D; Dietz, D

    1985-12-17

    Experiments were performed to investigate the relationship between the rate of oxidative metabolism of dimethylnitrosamine (DMN) by rat liver microsomes (i.e., DMN demethylase activity, DMNd) and its genotoxicity in liver, as assessed by the in vitro and in vivo/in vitro rat hepatocyte primary culture/DNA repair (HPC/DR) assays. Pretreatment of rats with pyrazole (PYR) resulted in a 4-fold increase in DMNd and a 3-fold greater DNA repair response to in vivo administration of 5 mg DMN/kg body weight. Pretreatment with phenobarbital (PB), dichlorodiphenyltrichloroethane (DDT), 3-methylcholanthrene (3-MC), beta-naphthoflavone (beta-NF) or Aroclor 1254 (ARO) produced a variable degree of inhibition of DMNd and had no significant effects on the response to DMN in the in vivo/in vitro HPC/DR assay. DNA repair elicited by DMN in vitro was decreased in hepatocytes from rats pretreated with 3-MC, while PB, DDT, beta-NF and ARO pretreatments had little effect on the response. In contrast, PYR pretreatment produced a 4.5-6.7-fold increase in the in vitro DNA repair response to DMN, and extended detection of positive responses to lower concentrations. Most of the inducers had no effect on DNA repair elicited by the direct acting alkylator, methyl methanesulfonate (MMS). Thus, the pretreatment-related changes in DMN-induced DNA repair were probably due to alterations in DMNd rather than to effects on the DNA repair capacity of the hepatocytes. PMID:4075445

  20. Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs

    PubMed Central

    Vestheim, Hege; Jarman, Simon N

    2008-01-01

    Background Identification of DNA sequence diversity is a powerful means for assessing the species present in environmental samples. The most common molecular strategies for estimating taxonomic composition depend upon PCR with universal primers that amplify an orthologous DNA region from a range of species. The diversity of sequences within a sample that can be detected by universal primers is often compromised by high concentrations of some DNA templates. If the DNA within the sample contains a small number of sequences in relatively high concentrations, then less concentrated sequences are often not amplified because the PCR favours the dominant DNA types. This is a particular problem in molecular diet studies, where predator DNA is often present in great excess of food-derived DNA. Results We have developed a strategy where a universal PCR simultaneously amplifies DNA from food items present in DNA purified from stomach samples, while the predator's own DNA is blocked from amplification by the addition of a modified predator-specific blocking primer. Three different types of modified primers were tested out; one annealing inhibiting primer overlapping with the 3' end of one of the universal primers, another annealing inhibiting primer also having an internal modification of five dI molecules making it a dual priming oligo, and a third elongation arrest primer located between the two universal primers. All blocking primers were modified with a C3 spacer. In artificial PCR mixtures, annealing inhibiting primers proved to be the most efficient ones and this method reduced predator amplicons to undetectable levels even when predator template was present in 1000 fold excess of the prey template. The prey template then showed strong PCR amplification where none was detectable without the addition of blocking primer. Our method was applied to identifying the winter food of one of the most abundant animals in the world, the Antarctic krill, Euphausia superba. Dietary

  1. [HPLC specific chromatogram spectrum-effect relationship for Shuanghuanglian on MDCK cell injury induced by influenza A virus (H1N1)].

    PubMed

    Liu, Ting; Wang, Hai-dan; Di, Liu-qing; Kang, An; Zhao, Xiao-li; Zhu, Xuan-xuan; Li, Jun-song

    2015-11-01

    To establish HPLC specific chromatogram and its correlation with the protection effect of Shuanghuanglian on MDCK (Madin-Darby canine kidney) cell injury induced by influenza A virus( H1N1). Nine recipes of Shuanghuanglian based on the official prescription were prepared according to orthogonal test for HPLC analysis and MDCK cells protection experiment separately (cytopathic effect (CPE) method was used for observing the virus infectivity and MTT staining results were used as the determining indexes for drug concentration selection and analyzing cell viability). The results suggested that all the other Shuang-Huang-Lian recipes except recipe1 demonstrate protecting effect on MDCK cell injury induced by influenza A virus (P < 0.01, P < 0.001). Stepwise regression analysis was used for analyzing the relationships between HPLC fingerprint and the protecting effect of Shuanghuanglian on influenza A virus induced MDCK cell injury. Peak 2, 3, 6, 8 and 12 were found to be strongly related with anti-influenza A virus efficacy. Stepwise regression analysis of recipes data and efficacy data showed that Lonicerae Japonicae Flos and Forsythiae Fructus were positively associated with the protecting effect of cells injury. From HPLC fingerprints, we found that peak 2, 3, 12 were from Lonicerae Japonicae Flos and peak 6, 8 were from Forsythiae Fructus. Four peaks were identified through comparing the retention time between the standard and Shuanghuanglian recipes, and they were chlorogenicacid, cryptochlorogenic acid, forsythoside B and 3,4-dicaffeoylquinic acid respectively. Caffeic acid derivatives in Lonicerae Japonicae Flos and Forsythiae Fructus were found to be greatly correlated with anti-influenza A virus efficacy and maybe the substance basis of Shuanghuanglian. PMID:27071255

  2. 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.

  3. 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.

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

    PubMed

    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 L(2-)=(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. PMID:25725448

  5. 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. PMID:26818185

  6. 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

    2015-11-01

    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. PMID:26057093

  7. Multiplexed Sequence Encoding: A Framework for DNA Communication.

    PubMed

    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

  8. 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

  9. 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.

  10. 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. PMID:26848778

  11. 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

  12. Third generation fluoroquinolones antibacterial drug based mixed-ligand Cu(II) complexes: structure, antibacterial activity, superoxide dismutase activity and DNA-interaction approach.

    PubMed

    Patel, Mohan N; Parmar, Pradhuman A; Gandhi, Deepen S

    2011-04-01

    The copper(II) complexes of the type [Cu(SPF)(A(n))Cl]/[Cu(PFL)(A(n))Cl] (where SPF is sparfloxacin, PFL is pefloxacin and A(n) is 2,2'-dipyridylamine/pyridine-2-carboxalehyde/thiophene-2-carboxaldehyde) were synthesised and were found to have a pyramidal geometry with a square base. The superoxide dismutase (SOD) like activity of the complexes were measured using an NBT/NADH/PMS system, these were expressed in terms of the concentration of complex which termianates the formation of formazan by 50% (IC₅₀ value) and found to range from 0.781 to 1.354 μM. The interactions of the complexes with DNA were studied by absorption titration, viscosity measurement and gel electrophoresis under physiological conditions. The antimicrobial efficiency of the complexes were tested on five different microorganisms and showed good biological activity. PMID:20583870

  13. 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).

  14. 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. PMID:23463388

  15. A nontargeted screening method for covalent DNA adducts and DNA modification selectivity using liquid chromatography-tandem mass spectrometry.

    PubMed

    Yao, Chunhe; Feng, Yong-Lai

    2016-10-01

    A method for nontargeted screening for covalent DNA adducts was developed using combination of neutral loss scan and product ion scan in a hybrid linear-ion-trap - triple quadrupole mass spectrometer system. DNA 2'-deoxynucleosides and adducts eluted from liquid chromatography were first analyzed in neutral loss mode to screen for the neutral loss of the deoxyribose moiety ([M+H-116](+)) from the protonated molecular ion ([M+H](+)). The product ion scan was subsequently used to elucidate the structures for the molecular ions observed from the peaks in the neutral loss scan chromatogram. The synthesized DNA adducts were used to evaluate the developed method by reaction of 20-mer DNA oligonucleotide with two direct agents respectively, specifically phenyl glycidyl ether and styrene-7,8-oxide. The modification selectivity of two compounds to the four nitrogenous bases on DNA sequence was also investigated in this study. The results showed that the two compounds had different modification selectivity to the four bases. Both compounds could modify all four nitrogenous bases (i.e. adenine, guanine, thymine, and cytosine) on DNA sequences to form various covalent DNA adducts. While phenyl glycidyl ether modified almost all of thymidine on DNA sequence, styrene-7,8-oxide, on the other hand, modified only a small portion of thymidine. The developed method proved possibly a potential tool for screening of unknown DNA adducts as exposure biomarkers of contaminants to human in the environment. PMID:27474284

  16. A [4+2] mixed ligand approach to ruthenium DNA metallointercalators [Ru(tpa)(N-N)](PF(6))(2) using a tris(2-pyridylmethyl)amine (tpa) capping ligand.

    PubMed

    Kraft, Sabine Seeberg née; Bischof, Caroline; Loos, Annette; Braun, Sebastian; Jafarova, Nigar; Schatzschneider, Ulrich

    2009-08-01

    A series of five tris(2-pyridylmethyl)amine (tpa) ruthenium complexes [Ru(tpa)(N-N)](PF(6))(2) with N-N=bpy (2,2'-bipyridine), phen (1,10-phenanthroline), dpq (dipyrido[3,2-d:2',3'-f]quinoxaline), dppz (dipyrido[3,2-a;2',3'-c]phenazine), and dppn (4,5,9,16-tetraazadibenzo[a,c]naphthacene) was prepared and characterized by NMR, UV-Visible (UV/Vis), and fluorescence spectroscopy as well as cyclic voltammetry. Structures optimized with density functional theory methods (DFT, BP86, TZVP) without constraints show C(1) symmetry while in solution, the (1)H and (13)C NMR spectra are in accordance with an average C(s) symmetry. This is thought to be due to a low energy barrier for flipping of the equatorial pyridine ring from one side of the N-N plane to the other. The electronic structure of the compounds was studied with DFT and a change in the highest occupied molecular orbital (HOMO) character from Ru t(2g) for the bpy, phen, and dpq to N-N ligand-based for the dppz and dppn complexes was found. TDDFT calculations showed dominant N-N-based intra-ligand charge transfer (ILCT) transitions in the latter two complexes mixed with metal-to-ligand charge transfer (MLCT) bands found for all five compounds. DNA binding of the complexes was studied with UV/Vis titrations, the fluorescent ethidium bromide displacement assay, and CD spectroscopy. The affinity increases with the aromatic surface area of of the bidentate N-N ligand in the order bpyDNA. PMID:19540597

  17. Separation system suitability (3S): a new criterion of chromatogram classification in HPLC based on cross-evaluation of separation capacity/peak symmetry and its application to complex mixtures of anthraquinones.

    PubMed

    Nowik, Witold; Héron, Sylvie; Bonose, Myriam; Tchapla, Alain

    2013-10-01

    A comparison of chromatograms obtained in a series of separation conditions for a given complex mixture may be done with a series of chromatographic descriptors. In this study, we used two descriptors: the number of critical pairs and symmetry of peaks, further rescaled and converted to the corresponding critical pairs' coefficient (CPc) and symmetry coefficient (Sc). Considering the difficulty of appreciating global separation quality using CPc and Sc criteria separately, as their respective values are usually uncorrelated, a double-criteria cross-evaluation system was required. For that purpose we tested the commonly used multi-criteria decision-making method - Derringer's desirability function (D) - as well as the recently introduced sum of ranking differences (SRD). To facilitate the graphical comparison of both approaches, the desirability function (D) was used in the inverse form (Dinv). The advantages and drawbacks of both evaluation methods, especially the respective under- or over-evaluation of outliers, caused us to introduce a new ranking approach, separation system suitability (3S). The obtained suitability rankings for the three tested approaches (Dinv, SRD and 3S) are different; nevertheless, 3S appears to be the most balanced and the easiest to interpret as well. The approach developed for selection of suitable systems was applied to the problem of separation of complex mixtures through the analysis of a series of standards of anthraquinone derivatives. To judge the pertinence of this evaluation, a sample containing a number of natural anthraquinones extracted from the bark of Indian mulberry (Morinda citrifolia) was analysed. In conclusion, the proposed methodology for the cross-evaluation of the series of chromatograms using single specific descriptors (CPc and Sc) through a global composite descriptor (3S) significantly simplifies the decision that separation systems are the most suitable for the separation of complex target mixtures of compounds

  18. Mixed Dementia

    MedlinePlus

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

  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. Cleaving DNA with DNA

    NASA Astrophysics Data System (ADS)

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

    1998-03-01

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

  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. PMID:22417888

  2. [Mixed marriages].

    PubMed

    Harmsen, C N

    1998-08-01

    The author examines the extent and characteristics of mixed marriages in the Netherlands. "Nine out of ten married persons born in Turkey or Morocco have a partner who was born in the same country. The majority of married Surinamese also have a partner originating from the same country. Those who spend (a part of) their youth in Indonesia (the former Dutch East Indies), on the other hand, are mostly married to someone born in the Netherlands." (EXCERPT) PMID:12294179

  3. DNA repair

    SciTech Connect

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

    1988-01-01

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

  4. Mixed results with mixed disulfides.

    PubMed

    Brigelius-Flohé, Regina

    2016-04-01

    A period of research with Helmut Sies in the 1980s is recalled. Our experiments aimed at an in-depth understanding of metabolic changes due to oxidative challenges under near-physiological conditions, i.e. perfused organs. A major focus were alterations of the glutathione and the NADPH/NADP(+) system by different kinds of oxidants, in particular formation of glutathione mixed disulfides with proteins. To analyze mixed disulfides, a test was adapted which is widely used until today. The observations in perfused rat livers let us believe that glutathione-6-phosphate dehydrogenase (G6PDH), i.a. might be activated by glutathionylation. Although we did not succeed to verify this hypothesis for the special case of G6PDH, the regulation of enzyme/protein activities by glutathionylation today is an accepted posttranslational mechanism in redox biology in general. Our early experimental approaches are discussed in the context of present knowledge. PMID:27095221

  5. Numts: an impediment to DNA barcoding of Polyclinids, Tunicata.

    PubMed

    Ahmed, N Shabeer; Jaffar Ali, H Abdul

    2016-09-01

    The mitochondrial cytochrome c oxidase subunit I (COI) gene, a widely accepted molecular marker for species identification and classification, has been questioned because of the presence of Numts. In this study we found the presence of Numts in the COI chromatogram of two tunicates, Polyclinum indicum and Polyclinum madrasensis belonging to the genus Polyclinum. Numts were also present in our sequence (Accession Number: KJ944391) and in other sequences belonging to genus Polyclinum in the GenBank record. The GeneBank database of genus Polyclinum contains COI-like sequences and COI pseudogenes, but no record of COI gene from Polyclinids. The prevalence of Numts in Polyclinids belonging to Tunicata, is an impediment to DNA barcoding studies of Polyclinum species. PMID:25815560

  6. A rapid DNA digestion system.

    PubMed

    Fu, Lung-Ming; Lin, Che-Hsin

    2007-04-01

    This paper presents a novel microfluidic DNA digestion system incorporating a high performance micro-mixer. Through the appropriate control of fixed and periodic switching DC electric fields, electrokinetic forces are established to mix the DNA and restriction enzyme samples and to drive them through the reaction column of the device. The experimental and numerical results show that a mixing performance of 98% can be achieved within a mixing channel of length 1.6 mm when a 150 V/cm driving voltage and a 5 Hz switching frequency are applied. The relationship between the mixing performance, switching frequency, and main applied electric field is derived. It is found that the optimal switching frequency depends upon the magnitude of the main applied electric field. The successful digestion of lambda-DNA using Eco RI restriction enzyme is demonstrated. The DNA-enzyme reaction is completed within 15 min in the proposed microfluidic system, compared to 50 min in a conventional large-scale system. Hence, the current device provides a valuable tool for rapid lambda-DNA digestion, while its mixer system delivers a simple yet effective solution for mixing problems in the micro-total-analysis-systems field. PMID:17195107

  7. 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. PMID:26607320

  8. 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. PMID:24309206

  9. 11q23 Translocations split the [open quotes]AT-hook[close quotes] cruciform DNA-binding region and the transcriptional repression domain from the activation domain of the mixed-lineage leukemia (MLL) gene

    SciTech Connect

    Zeleznik-Le, N.J.; Harden, A.M.; Rowley, J.D. )

    1994-10-25

    Translocations involving chromosome band 11q23, found in acute lymphoid and myeloid leukemias, disrupt the MLL gene. This gene encodes a putative transcription factor with homology to the zinc fingers and other domains of the Drosophila trithorax gene product and to the [open quotes]AT-hook[close quotes] motif of high mobility group proteins. To map potential transcriptional activation or repression domains of the MLL protein, yeast GAL4 DNA-binding domain and MLL hybrid protein-expressing plasmids were cotransfected with chloramphenicol acetyltransferase reporter plasmids in a transient transfection system. We found that MLL contains a strong activation domain and a repression domain. The former, located telomeric (3[prime]) to the breakpoint region, activated transcription 18-fold to >200-fold, depending on the promoter and cell line used for transfection. A repression domain that repressed transcription 4-fold was located centromeric (5[prime]) to the breakpoint region of MLL. The MLL AT-hook domain protein was expressed in bacteria and was utilized in a gel mobility shift assay to assess DNA-binding activity. The MLL AT-hook domain could bind cruciform DNA, recognizing structure rather than sequence of the target DNA. In translocations involving MLL, loss of an activation domain with retention of a repression domain and a DNA-binding domain on the der(11) chromosome could alter the expression of downstream target genes, suggesting a potential mechanism of action for MLL in leukemia. 35 refs., 5 figs., 1 tab.

  10. 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)

  11. DNA Banking

    SciTech Connect

    Reilly, P.R. )

    1992-11-01

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

  12. Methodology: simplified preparation of a DNA ladder using PCR.

    PubMed

    Wang, T-Y; Wang, L; Wang, F

    2011-01-01

    Serving as a DNA molecular weight standard, the DNA ladder has been widely used in molecular biology applications. We developed a simple method for the preparation of a DNA marker, which involves designing primers to amplify 100- to 1000-bp DNA fragments using lambda DNA as a template for polymerase chain reaction, followed by extraction with phenol/chloroform, precipitation with ethanol and mixing. Fragments of 100- to 1000-bp DNA were successfully amplified; the sequences showed 100% identity with lambda DNA. This prepared DNA marker displayed clear bands, indicating that it can be used for molecular studies. PMID:21863555

  13. 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.

  14. Microfluidic mixing technology for biological applications

    NASA Astrophysics Data System (ADS)

    Jang, Ling-Sheng

    Mixing plays a significant role in most biological analysis systems. An example that motivates this thesis is the purification or "clean-up" of sequencing reaction products prior to sequencing. Magnetic beads, DNA, and reagents must be quickly and thoroughly mixed to process samples in an automated, high-throughput system. Efficient mixing is achieved by layering and folding the fluids being mixed to decrease the characteristic length over which diffusion must act to create a locally equilibrated homogenous mixture. At the microscale this challenge is amplified by the characteristics of low Reynolds number flows present in microfluidic environments where flows are laminar and no turbulent mixing is present. Many mixing techniques have been developed to achieve thorough mixing of different fluids in Microsystems. However, mixing based on circulatory flow patterns has not been reported. We have developed a new mixing technique using circulatory flow patterns generated by PZT (lead-zirconate-titanate) vibration. A micromixer based on PZT was fabricated to demonstrate the principle of mixing using circulatory flow patterns. The circulatory flow patterns were observed at different driving frequencies using fluorescent beads. A protocol was developed to quantify the mixing performance using fluorescein. Efficient mixing was achieved by alternating between two different driving frequencies to produce two circulatory flow patterns that mix all regions in the mixing chamber. In addition, a simulation model was created to predict the mode shapes of the structure with fluid included in the model using CFD-ACE+. Empirical characterization of two-circulatory flow was performed using the confocal laser-scanning microscope to understand the underlying mechanism and generation of circulatory flow. The preliminary analysis suggests that circulatory flow is driven by fluid streaming which is believed to result from the propagation of acoustic waves induced by PZT vibration or to be

  15. Housing Mix, School Mix: Barriers to Success

    ERIC Educational Resources Information Center

    Camina, M. M.; Iannone, P.

    2014-01-01

    Recent UK policy has emphasised both the development of socially mixed communities and the creation of balanced school intakes. In this paper, we use a case study of an area of mixed tenure in eastern England to explore policy in practice and the extent to which mechanisms of segregation impact on both the creation of socially mixed neighbourhoods…

  16. Programmable Quantitative DNA Nanothermometers.

    PubMed

    Gareau, David; Desrosiers, Arnaud; Vallée-Bélisle, Alexis

    2016-07-13

    Developing molecules, switches, probes or nanomaterials that are able to respond to specific temperature changes should prove of utility for several applications in nanotechnology. Here, we describe bioinspired strategies to design DNA thermoswitches with programmable linear response ranges that can provide either a precise ultrasensitive response over a desired, small temperature interval (±0.05 °C) or an extended linear response over a wide temperature range (e.g., from 25 to 90 °C). Using structural modifications or inexpensive DNA stabilizers, we show that we can tune the transition midpoints of DNA thermometers from 30 to 85 °C. Using multimeric switch architectures, we are able to create ultrasensitive thermometers that display large quantitative fluorescence gains within small temperature variation (e.g., > 700% over 10 °C). Using a combination of thermoswitches of different stabilities or a mix of stabilizers of various strengths, we can create extended thermometers that respond linearly up to 50 °C in temperature range. Here, we demonstrate the reversibility, robustness, and efficiency of these programmable DNA thermometers by monitoring temperature change inside individual wells during polymerase chain reactions. We discuss the potential applications of these programmable DNA thermoswitches in various nanotechnology fields including cell imaging, nanofluidics, nanomedecine, nanoelectronics, nanomaterial, and synthetic biology. PMID:27058370

  17. Mixing and Transport.

    PubMed

    Chang, Chein-Chi; Chapman, Tom; Siverts-Wong, Elena; Wei, Li; Mei, Ying

    2016-10-01

    This section covers research published during the calendar year 2015 on mixing and transport processes. The review covers mixing of anaerobic digesters, mixing of heat transfer, and environmental fate and transport. PMID:27620101

  18. STATIC AND KINETIC SITE-SPECIFIC PROTEIN-DNA PHOTOCROSSLINKING: ANALYSIS OF BACTERIAL TRANSCRIPTION INITIATION COMPLEXES

    PubMed Central

    Naryshkin, Nikolai; Druzhinin, Sergei; Revyakin, Andrei; Kim, Younggyu; Mekler, Vladimir; Ebright, Richard H.

    2009-01-01

    Static site-specific protein-DNA photocrosslinking permits identification of protein-DNA interactions within multiprotein-DNA complexes. Kinetic site-specific protein-DNA photocrosslinking--involving rapid-quench-flow mixing and pulsed-laser irradiation--permits elucidation of pathways and kinetics of formation of protein-DNA interactions within multiprotein-DNA complexes. We present detailed protocols for application of static and kinetic site-specific protein-DNA photocrosslinking to bacterial transcription initiation complexes. PMID:19378179

  19. 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

  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. DNA ALTERATIONS

    EPA Science Inventory

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

  2. 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.

  3. [DNA computing].

    PubMed

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

    2011-01-01

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

  4. 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

  5. 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.

  6. 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)

  7. 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.

  8. 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. PMID:26244884

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

    PubMed Central

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

    2015-01-01

    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 1H 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. PMID:26244884

  10. Unravelling DNA

    NASA Astrophysics Data System (ADS)

    Conroy, Rs; Danilowicz, C.

    2004-04-01

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

  11. 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.

  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. 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 ...

  14. ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility.

    PubMed

    Otto, T D; Vasconcellos, E A; Gomes, L H F; Moreira, A S; Degrave, W M; Mendonça-Lima, L; Alves-Ferreira, M

    2008-01-01

    Optimizing and monitoring the data flow in high-throughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a "technological platform". Infrastructure includes a 48-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project. The pipeline (named ChromaPipe for Chromatogram Pipeline) is available for download by the scientific community at the url http://bioinfo.pdtis.fiocruz.br/ChromaPipe/. The support for assembly is also configured as a web service: http://bioinfo.pdtis.fiocruz.br/Assembly/. PMID:18949705

  15. 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

  16. 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.

  17. Foundations of chaotic mixing.

    PubMed

    Wiggins, Stephen; Ottino, Julio M

    2004-05-15

    The simplest mixing problem corresponds to the mixing of a fluid with itself; this case provides a foundation on which the subject rests. The objective here is to study mixing independently of the mechanisms used to create the motion and review elements of theory focusing mostly on mathematical foundations and minimal models. The flows under consideration will be of two types: two-dimensional (2D) 'blinking flows', or three-dimensional (3D) duct flows. Given that mixing in continuous 3D duct flows depends critically on cross-sectional mixing, and that many microfluidic applications involve continuous flows, we focus on the essential aspects of mixing in 2D flows, as they provide a foundation from which to base our understanding of more complex cases. The baker's transformation is taken as the centrepiece for describing the dynamical systems framework. In particular, a hierarchy of characterizations of mixing exist, Bernoulli --> mixing --> ergodic, ordered according to the quality of mixing (the strongest first). Most importantly for the design process, we show how the so-called linked twist maps function as a minimal picture of mixing, provide a mathematical structure for understanding the type of 2D flows that arise in many micromixers already built, and give conditions guaranteeing the best quality mixing. Extensions of these concepts lead to first-principle-based designs without resorting to lengthy computations. PMID:15306478

  18. Mixing and compaction temperatures for Superpave mixes

    NASA Astrophysics Data System (ADS)

    Yildirim, Yetkin

    According to Superpave mixture design, gyratory specimens are mixed and compacted at equiviscous binder temperatures corresponding to viscosities of 0.17 and 0.28 Pa.s. respectively. These were the values previously used in the Marshal mix design method to determine optimal mixing and compaction temperatures. In order to estimate the appropriate mixing and compaction temperatures for Superpave mixture design, a temperature-viscosity relationship for the binder needs to be developed (ASTM D 2493, Calculation of Mixing and Compaction Temperatures). The current approach is simple and provides reasonable temperatures for unmodified binders. However, some modified binders have exhibited unreasonably high temperatures for mixing and compaction using this technique. These high temperatures can result in construction problems, damage of asphalt, and production of fumes. Heating asphalt binder to very high temperatures during construction oxidizes the binder and separates the polymer from asphalt binder. It is known that polymer modified asphalt binders have many benefits to the roads, such as; increasing rutting resistance, enhancing low temperature cracking resistance, improving traction, better adhesion and cohesion, elevating tensile strength which are directly related to the service life of the pavement. Therefore, oxidation and separation of the polymer from the asphalt binder results in reduction of the service life. ASTM D 2493 was established for unmodified asphalt binders which are Newtonian fluids at high temperatures. For these materials, viscosity does not depend on shear rate. However, most of the modified asphalt binders exhibit a phenomenon known as pseudoplasticity, where viscosity does depend on shear rate. Thus, at the high shear rates occurring during mixing and compaction, it is not necessary to go to very high temperatures. This research was undertaken to determine the shear rate during compaction such that the effect of this parameter could be

  19. 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'.

  20. Peculiarities of the incorporation of (/sup 3/H)thymidine into AT-rich regions of DNA during replicative synthesis

    SciTech Connect

    Khudolii, G.A.; Khakimov, K.A.; Gorelova, T.V.; Akif'ev, A.P.

    1985-11-01

    The authors studied the role of the AT-rich regions in DNA replication in vivo. The authors selected cells of humans and Drosophila - organisms belonging to different types of alternation of unique and repetitive sequences - as the objects of investigation. The authors then studied the behavior of the AT-rich sequences in replication by the method of thermoelution of (/sup 3/H)thymidine-labeled DNA, fragmented by ultrasound to 350 nucleotide pairs. By measuring the amount of DNA and the amount of the label in the fractions, the authors were able to construct curves of the change in the specific activity of DNA as a function of the temperature of elution from HAP and, consequently, as a function of the AT composition. The authors call them differential temperature chromatograms (DTC). Human peripheral blood lymphocytes were cultured according to the standard procedure with PHA (Difco P). A culture of D. melanogaster cells was labeled with (/sup 3/H)thymidine in the logarithmic phase of growth for 1.2 and 42 h. At the end of the labeling, cell DNA was isolated from the lymphocytes and cell and nuclear DNA from a Drosophila tissue culture by the standard methods.

  1. DNA codes

    SciTech Connect

    Torney, D. C.

    2001-01-01

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

  2. DNA computing.

    PubMed

    Gibbons, A; Amos, M; Hodgson, D

    1997-02-01

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

  3. 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)

  4. 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)

  5. DNA Methylation

    PubMed Central

    Marinus, M.G.; Løbner-Olesen, A.

    2014-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential and in C. crescentus, it is important for temporal gene expression which, in turn, is required for coordinating chromosome initiation, replication and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage; decrease transformation frequency in certain bacteria; decrease the stability of short direct repeats; are necessary for site-directed mutagenesis; and to probe eukaryotic structure and function. PMID:26442938

  6. 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.

  7. Synthesis, characterization and thermal studies of binary and/or mixed ligand complexes of Cd(II), Cu(II), Ni(II) and Co(III) based on 2-(Hydroxybenzylidene) thiosemicarbazone: DNA binding affinity of binary Cu(II) complex

    NASA Astrophysics Data System (ADS)

    Saif, M.; Mashaly, Mahmoud M.; Eid, Mohamed F.; Fouad, R.

    A new series of metal complexes of Cd(II), Cu(II), Ni(II) and Co(III) with Schiff base ligand, H2L, 2-(Hydroxybenzylidene) thiosemicarbazone were synthesized. The mixed ligand complexes were prepared by using glycine (Gly), 2-aminopyridine (2-Ampy) and 1,10-phenanthroline (Phen) as secondary ligands. The structure of these complexes was identified and confirmed by elemental analysis, molar conductivity, UV-Vis, FT-IR and 1H NMR spectroscopy and magnetic moment measurements as well as TG-DSC technique. The discussions of the prepared complexes indicate that the ligand behaves as a monoanionic tridentate ligand through ONS donor sites. Thermal studies suggested a mechanism for the degradation of the metal complexes as a function of temperature supporting the chelation modes and showed the possibility of obtaining new complexes pyrolytically in the solid state which cannot be synthesized from the solution. The absorption studies support that the binary Cu(II) complex exhibits a significant binding affinity to HS-DNA through intercalative mode.

  8. Synthesis, characterization and thermal studies of binary and/or mixed ligand complexes of Cd(II), Cu(II), Ni(II) and Co(III) based on 2-(Hydroxybenzylidene) thiosemicarbazone: DNA binding affinity of binary Cu(II) complex.

    PubMed

    Saif, M; Mashaly, Mahmoud M; Eid, Mohamed F; Fouad, R

    2012-06-15

    A new series of metal complexes of Cd(II), Cu(II), Ni(II) and Co(III) with Schiff base ligand, H(2)L, 2-(Hydroxybenzylidene) thiosemicarbazone were synthesized. The mixed ligand complexes were prepared by using glycine (Gly), 2-aminopyridine (2-Ampy) and 1,10-phenanthroline (Phen) as secondary ligands. The structure of these complexes was identified and confirmed by elemental analysis, molar conductivity, UV-Vis, FT-IR and (1)H NMR spectroscopy and magnetic moment measurements as well as TG-DSC technique. The discussions of the prepared complexes indicate that the ligand behaves as a monoanionic tridentate ligand through ONS donor sites. Thermal studies suggested a mechanism for the degradation of the metal complexes as a function of temperature supporting the chelation modes and showed the possibility of obtaining new complexes pyrolytically in the solid state which cannot be synthesized from the solution. The absorption studies support that the binary Cu(II) complex exhibits a significant binding affinity to HS-DNA through intercalative mode. PMID:22446784

  9. Incorporating multiple mixed stocks in mixed stock analysis: 'many-to-many' analyses.

    PubMed

    Bolker, Benjamin M; Okuyama, Toshinori; Bjorndal, Karen A; Bolten, Alan B

    2007-02-01

    Traditional mixed stock analyses use morphological, chemical, or genetic markers measured in several source populations and in a single mixed population to estimate the proportional contribution of each source to the mixed population. In many systems, however, different individuals from a particular source population may go to a variety of mixed populations. Now that data are becoming available from (meta)populations with multiple mixed stocks, the need arises to estimate contributions in this 'many-to-many' scenario. We suggest a Bayesian hierarchical approach, an extension of previous Bayesian mixed stock analysis algorithms, that can estimate contributions in this case. Applying the method to mitochondrial DNA data from green turtles (Chelonia mydas) in the Atlantic gives results that are largely consistent with previous results but makes some novel points, e.g. that the Florida, Bahamas and Corisco Bay foraging grounds have greater contributions than previously thought from distant foraging grounds. More generally, the 'many-to-many' approach gives a more complete understanding of the spatial ecology of organisms, which is especially important in species such as the green turtle that exhibit weak migratory connectivity (several distinct subpopulations at one end of the migration that mix in unknown ways at the other end). PMID:17284204

  10. Theory for Neutrino Mixing

    NASA Astrophysics Data System (ADS)

    He, Xiao-Gang

    2016-07-01

    Since the discovery of neutrino oscillations, for which Takaaki Kajita and Arthur B. McDonald were awarded the 2015 Nobel prize in physics, tremendous progresses have been made in measuring the mixing angles which determine the oscillation pattern. A lot of theoretical efforts have been made to understand how neutrinos mix with each other. Present data show that in the standard parameterization of the mixing matrix, θ23 is close to π/4 and the CP violating phase is close to ‑ π/2. In this talk I report results obtained in arXiv:1505.01932 (Phys. Lett. B750(2015)620) and arXive:1404.01560 (Chin. J. Phys.53(2015)100101) and discuss some implications for theoretical model buildings for such mixing pattern. Specific examples for neutrino mixing based on A4 family symmetry are given.

  11. High-mix insulins

    PubMed Central

    Kalra, Sanjay; Farooqi, Mohammad Hamed; El-Houni, Ali E.

    2015-01-01

    Premix insulins are commonly used insulin preparations, which are available in varying ratios of different molecules. These drugs contain one short- or rapid-acting, and one intermediate- or long-acting insulin. High-mix insulins are mixtures of insulins that contain 50% or more than 50% of short-acting insulin. This review describes the clinical pharmacology of high-mix insulins, including data from randomized controlled trials. It suggests various ways, in which high-mix insulin can be used, including once daily, twice daily, thrice daily, hetero-mix, and reverse regimes. The authors provide a rational framework to help diabetes care professionals, identify indications for pragmatic high-mix use. PMID:26425485

  12. 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

  13. Stabilized, Freeze-Dried PCR Mix for Detection of Mycobacteria

    PubMed Central

    Klatser, Paul R.; Kuijper, Sjoukje; van Ingen, Cor W.; Kolk, Arend H. J.

    1998-01-01

    We report here the development of a freeze-drying procedure allowing stabilization at ambient temperature of preoptimized, premixed, and predispensed PCR mixes aimed at the detection of mycobacteria in clinical materials. The freeze-dried mixes retained activity at 4°C and at 20°C for 1 year and for 3 months at 37°C, as judged by their performance with 50 and 500 fg of purified Mycobacterium bovis BCG target DNA. PMID:9620427

  14. 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

  15. 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.

  16. DNA Microarrays

    NASA Astrophysics Data System (ADS)

    Nguyen, C.; Gidrol, X.

    Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

  17. Validation and scale-up of plasmid DNA purification by phenyl-boronic acid chromatography.

    PubMed

    Gomes, A Gabriela; Azevedo, Ana M; Aires-Barros, M Raquel; Prazeres, D Miguel F

    2012-11-01

    This study addresses the feasibility of scaling-up the removal of host cell impurities from plasmid DNA (pDNA)-containing Escherichia coli lysates by phenyl-boronic (PB) acid chromatography using columns packed with 7.6 and 15.2 cm(3) of controlled porous glass beads (CPG) derivatized with PB ligands. Equilibration was performed with water at 10 cm(3) /min and no conditioning of the lysate feed was required. At a ratio of lysate feed to adsorbent volume of 1.3, 93-96% of pDNA was recovered in the flow through while 66-71% of impurities remained bound (~2.5-fold purification). The entire sequence of loading, washing, elution, and re-equilibration was completed in 20 min. Run-to-run consistency was observed in terms of chromatogram features and performance (yield, purification factor, agarose electrophoresis) across the different amounts of adsorbent (0.75-15.2 cm(3) ) by performing successive injections of lysates prepared independently and containing 3.7 or 6.1 kbp plasmids. The column productivity at large scale was 4 dm(3) of alkaline lysate per hour per dm(3) of PB-CPG resin. The method is rapid, reproducible, simple, and straightforward to scale-up. Furthermore, it is capable of handling heavily contaminated samples, constituting a good alternative to purification techniques such as isopropanol precipitation, aqueous two-phase systems, and tangential flow filtration. PMID:23175141

  18. Changes in DNA methyltransferase induced by treatment with N-2-acetylaminofluorene.

    PubMed

    Bravo, L M; Salas, C E

    1989-11-01

    We have compared the levels of DNA methyltransferases from rat liver and spleen in both sexes following a single injection of N-2-acetylaminofluorene (AAF). Enzyme extracts from treated animals were obtained at different intervals (2-34 days) after treatment. The extracts were assayed in the presence of chicken erythrocyte DNA and S-adenosyl-L-[Me-3H]methionine. A 55% increase in male rat-liver methyltransferase activity measured by Me-3H incorporation into DNA occurred on day 14. By contrast, female methyltransferase after a similar period revealed a 33% decrease in activity. Between days 21 and 34, there is a progressive return to normal methyltransferase levels. Spleen-derived enzyme studied between days 7 and 14, showed a decrease in methylating activity in both sexes. After replacing corn seed oil by ethanol as the vehicle for AAF injection, we observed a change in liver methyltransferase 48 h after injection. Quantification of radioactive eluates in m5C fractions together with the increase in the integrated area identified as m5C in HPLC chromatograms allowed positive identification of methylated products. PMID:2811914

  19. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide.

    PubMed

    Huang, Jiahao; Wang, Zhenyu; Kim, Jang-Kyo; Su, Xuefen; Li, Zhigang

    2015-12-15

    We propose a simple and fast method for detecting arbitrary DNA mutations. Single-stranded DNA probes labeled with fluorescein amidite (FAM-ssDNA), ethidium bromide (EB), and graphene oxide (GO) are employed in the sensing system. The detection is achieved in two steps. In the first step, the sensing system contains FAM-ssDNA probes and EB molecules. It exhibits different fluorescence emissions in the presence of perfectly matched, mismatched, and random DNA sequences. With the addition of GO in the second step, the fluorescence signal for perfectly matched and random DNA does not vary greatly, which, however, experiences a significant change for mismatched DNA targets. The signal ratio before and after the addition of GO can clearly distinguish mutations from normal and random DNA sequences. The detection method works well regardless of the mutation positions and only requires "mix-and-detect" steps, which are completed within 15 min. PMID:26559174

  20. Remotely controllable mixing system

    NASA Technical Reports Server (NTRS)

    Belew, R. R. (Inventor)

    1986-01-01

    This invention relates to a remotely controllable mixing system in which a plurality of mixing assemblies are arranged in an annular configuration, and wherein each assembly employs a central chamber and two outer, upper and lower chambers. Valves are positioned between chambers, and these valves for a given mixing assembly are operated by upper and lower control rotors, which in turn are driven by upper and lower drive rotors. Additionally, a hoop is compressed around upper control rotors and a hoop is compressed around lower control rotors to thus insure constant frictional engagement between all control rotors and drive rotors. The drive rollers are driven by a motor.

  1. 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.

  2. Wrinkled DNA.

    PubMed Central

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

    1983-01-01

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

  3. Optical DNA

    NASA Astrophysics Data System (ADS)

    Vijaywargi, Deepak; Lewis, Dave; Kirovski, Darko

    A certificate of authenticity (COA) is an inexpensive physical object with a random and unique structure S which is hard to near-exactly replicate. An inexpensive device should be able to scan object’s physical “fingerprint,” a set of features that represents S. In this paper, we explore one set of requirements that optical media such as DVDs should satisfy, to be considered as COAs. As manufacturing of such media produces inevitable errors, we use the locations and count of these errors as a “fingerprint” for each optical disc: its optical DNA. The “fingerprint” is signed using publisher’s private-key and the resulting signature is stored onto the optical medium using a post-production process. Standard DVD players with altered firmware that includes publisher’s public-key, should be able to verify the authenticity of DVDs protected with optical DNA. Our key finding is that for the proposed protocol, only DVDs with exceptional wear-and-tear characteristics would result in an inexpensive and viable anti-counterfeiting technology.

  4. 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.

  5. 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.

  6. More evidence for non-maternal inheritance of mitochondrial DNA?

    PubMed Central

    Bandelt, H; Kong, Q; Parson, W; Salas, A

    2005-01-01

    Background: A single case of paternal co-transmission of mitochondrial DNA (mtDNA) in humans has been reported so far. Objective: To find potential instances of non-maternal inheritance of mtDNA. Methods: Published medical case studies (of single patients) were searched for irregular mtDNA patterns by comparing the given haplotype information for different clones or tissues with the worldwide mtDNA database as known to date—a method that has proved robust and reliable for the detection of flawed mtDNA sequence data. Results: More than 20 studies were found reporting clear cut instances with mtDNAs of different ancestries in single individuals. As examples, cases are reviewed from recent published reports which, at face value, may be taken as evidence for paternal inheritance of mtDNA or recombination. Conclusions: Multiple types (or recombinant types) of quite dissimilar mitochondrial DNA from different parts of the known mtDNA phylogeny are often reported in single individuals. From re-analyses and corrigenda of forensic mtDNA data, it is apparent that the phenomenon of mixed or mosaic mtDNA can be ascribed solely to contamination and sample mix up. PMID:15923271

  7. In vitro selection and characterization of catalytic DNA in model biological systems

    NASA Astrophysics Data System (ADS)

    Slimmer, Scott Collins

    This work reports the in vitro selection and characterization of a metal cofactor independent DNAzyme with RNA phosphoesterase activity. The majority of DNAzymes with catalytic RNA phosphoesterase activity are dependent upon divalent metal ion cofactors. The family of DNAzymes described in this research is functional in the absence of divalent cations. The most prevalent sequence in the selection population was chosen for further study. In contrast to previous studies which have reported divalent cation independent DNAzyme activity between pH 5.0 and pH 9.0, the catalytic activity of the DNAzyme reported here is extremely pH-dependent with maximum activity between pH 4.0 and pH 5.0. The catalytic activity of this DNAzyme appears to be dependent on the presence of organic anion cofactors including acetic acid, formic acid, citric acid, and MES. This research also details the first attempt to obtain useful information from heterogeneous DNA sequencing data. A sample of the selection population from each of the twelve rounds of in vitro selection was heterogeneously sequenced without any prior separation or purification. The observed concurrence of qualitative changes in the heterogeneous sequencing chromatograms with observed changes in the catalytic activity of the population is evidence of the ability of heterogeneous DNA sequencing to successfully monitor the evolution of DNA populations during in vitro selection. The ability to successfully analyze heterogeneous DNA samples containing multiple DNA sequences using a single sequencing experiment may play an important role in driving the development of new DNA sequencing technologies and shaping the future of genomic research.

  8. Rapid and sensitive PCR-dipstick DNA chromatography for multiplex analysis of the oral microbiota.

    PubMed

    Tian, Lingyang; Sato, Takuichi; 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

  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. /sup 32/P-postlabeling analysis of aromatic DNA adducts in fish from polluted areas

    SciTech Connect

    Dunn, B.P.; Black, J.J.; Maccubbin, A.

    1987-12-15

    Brown bullheads (Ictalurus nebulosus) were sampled from sites in the Buffalo and Detroit Rivers where fish are exposed to high levels of sediment bound polycyclic aromatic hydrocarbons, and suffer from an elevated frequency of liver cancer. DNA was isolated from the livers of these wild fish and from control specimens which were raised in clean aquariums. DNA was enzymatically digested to normal and adducted nucleotides, and hydrophobic/bulky adducts were enriched in the digests either by preparative reverse-phase high-pressure liquid chromatography, or selective nuclease P1 dephosphorylation of normal nucleotides. Aromatic DNA-carcinogen adducts were then quantitated using /sup 32/P-postlabeling analysis. Using both adduct enrichment procedures, chromatograms derived from DNA of fish from polluted areas showed a diffuse diagonal radioactive zone not present in DNA from aquarium raised fish. The diagonal zone appeared to consist at least in part of multiple overlapping discrete adduct spots which could be partially separated by gradient high-pressure liquid chromatography prior to /sup 32/P-postlabeling analysis, and most of which were more strongly retained on a reverse-phase column than the major benzo(a)pyrene-DNA adduct. The behavior of the adducts in the diagonal radioactive zone and of their unlabeled precursors is consistent with their identification as nucleotide adducts of a variety of bulky hydrophobic aromatic environmental compounds. Total pollution-related adduct levels as analyzed by HPLC adduct enrichment and /sup 32/P-postlabeling were 70.1 +/- 29 (SD) nmol/mol normal nucleotide in fish from the Buffalo River, and 52 and 56 nmol/mol for two specimens from the Detroit River.

  11. DNA mimicry by proteins.

    PubMed

    Dryden, D T F; Tock, M R

    2006-04-01

    It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins. PMID:16545103

  12. 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. PMID:26776022

  13. 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.

  14. 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.

  15. Imaging of DNA/Nanosphere Condensates

    NASA Astrophysics Data System (ADS)

    Krishnan, R.

    2005-03-01

    DNA forms condensates in a variety of environments. In chromatin, DNA is condensed around 10-nm-diameter, positively-charged histone complexes. To model chromatin formation in cells, lambda-phage (16 microns long) and herring sperm (0.03 to1 micron) DNAs were mixed with polystyrene nanospheres of diameter 40nm and 930nm containing 1.8x10^4 and 2.6x10^8 positive surface charges, respectively, to form condensates. Sphere concentrations were 1-2 times the isoelectric concentration. Condensation vs time was imaged at various concentrations, pH's, viscosities, and ionic strengths. Bright-field and fluorescence (YOYO-1 dye bound to DNA) images were recorded. In general HS DNA aggregate size increased with time. Except in 0.5-0.8 M KCl, herring sperm DNA formed one huge aggregate (100's of microns) and depleted other areas, both in 10% and 20% glycerol. Phage DNA samples rapidly formed longer, fiber-like aggregates. Within 2 hours it formed ordered structures and in most samples, empty, apparently depleted regions were found in the viewing area. Shapes of the phage-DNA aggregates in 20% glycerol, in contrast, formed small clumps like HS DNA.

  16. 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

  17. 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.

  18. [Mixed states and schizophrenia].

    PubMed

    Fakra, E; Belzeaux, R; Pringuey, D; Cermolacce, M; Corréard, N; Micoulaud-Franchi, J-A; Azorin, J-M

    2013-12-01

    Because of their compilation of contrasted symptoms and their variable clinical presentation, mixed episodes have been withdrawn from the DSM. However, mixed states question not only the bonds between depression and mania, but also the distinction between bipolar disorders and schizophrenia. Indeed, doubts about the dichotomy introduced by Kraepelin between bipolar disorders and schizophrenia is as old as the nosolgy itself, as attest the later works of this author revealing his hesitations on his own classification. But findings here reviewed issued from recent technical advances, particularly in the imaging and genetic fields, offer a better understanding of the boundaries between these two disorders. Yet, when confronted to an acute episode, clinicians may find it challenging to distinguish a mixed state from a schizophrenic relapse. Indeed, there is no pathognomonic manifestation allowing to retain a diagnosis with confidence. The physician will therefore have to identify a pattern of signs, which will orient his assessment with no certainty. Thus, negative rather than affective or psychotic symptomatology appears to be useful in discriminating schizophrenia (or schizoaffective) disorders from mixed mania. However, a conclusion during this acute stage appears in definitive a formal exercise, first because the final diagnosis will only be ascertained once the symptoms are amended, and second because, according to our classifications, a mood episode, including mania and mixed mania, can be observed without ruling out the diagnosis of schizophrenia. PMID:24359851

  19. Mitochondrial DNA replacement versus nuclear DNA persistence

    NASA Astrophysics Data System (ADS)

    Serva, Maurizio

    2006-10-01

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

  20. 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.

  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. Sperm DNA oxidative damage and DNA adducts.

    PubMed

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

    2015-12-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps=0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps=0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps=0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on sperm

  3. 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.

  4. 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.

  5. Rapid mixing kinetic techniques.

    PubMed

    Martin, Stephen R; Schilstra, Maria J

    2013-01-01

    Almost all of the elementary steps in a biochemical reaction scheme are either unimolecular or bimolecular processes that frequently occur on sub-second, often sub-millisecond, time scales. The traditional approach in kinetic studies is to mix two or more reagents and monitor the changes in concentrations with time. Conventional spectrophotometers cannot generally be used to study reactions that are complete within less than about 20 s, as it takes that amount of time to manually mix the reagents and activate the instrument. Rapid mixing techniques, which generally achieve mixing in less than 2 ms, overcome this limitation. This chapter is concerned with the use of these techniques in the study of reactions which reach equilibrium; the application of these methods to the study of enzyme kinetics is described in several excellent texts (Cornish-Bowden, Fundamentals of enzyme kinetics. Portland Press, 1995; Gutfreund, Kinetics for the life sciences. Receptors, transmitters and catalysis. Cambridge University Press, 1995).There are various ways to monitor changes in concentration of reactants, intermediates and products after mixing, but the most common way is to use changes in optical signals (absorbance or fluorescence) which often accompany reactions. Although absorbance can sometimes be used, fluorescence is often preferred because of its greater sensitivity, particularly in monitoring conformational changes. Such methods are continuous with good time resolution but they seldom permit the direct determination of the concentrations of individual species. Alternatively, samples may be taken from the reaction volume, mixed with a chemical quenching agent to stop the reaction, and their contents assessed by techniques such as HPLC. These methods can directly determine the concentrations of different species, but are discontinuous and have a limited time resolution. PMID:23729251

  6. 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.

  7. DNA polymerases and cancer

    PubMed Central

    Lange, Sabine S.; Takata, Kei-ichi; Wood, Richard D.

    2013-01-01

    There are fifteen different DNA polymerases encoded in mammalian genomes, which are specialized for replication, repair or the tolerance of DNA damage. New evidence is emerging for lesion-specific and tissue-specific functions of DNA polymerases. Many point mutations that occur in cancer cells arise from the error-generating activities of DNA polymerases. However, the ability of some of these enzymes to bypass DNA damage may actually defend against chromosome instability in cells and at least one DNA polymerase, POLζ, is a suppressor of spontaneous tumorigenesis. Because DNA polymerases can help cancer cells tolerate DNA damage, some of these enzymes may be viable targets for therapeutic strategies. PMID:21258395

  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. 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.

  10. 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.

  11. Mixed waste characterization strategy

    SciTech Connect

    Baldwin, C.E.; Stakebake, J.; Peters, M.

    1992-01-01

    Radioactive mixed wastes containing a radioactive component subject to the Atomic Energy Act (AEA) and hazardous waste subject to resource Conservation and Recovery Act (RCRA) are generated, treated, and stored at the Rocky Flats Plant (RFP) and are subject to federal and state statutory and regulatory requirements. The US Environmental Protection Agency (EPA) and the Colorado Department of Health (CDH) are the two primary regulatory agencies which enforce these requirements. This paper describes the mechanism by which RFP will characterize mixed wastes within the LDR provisions of RCRA and the LDR FFCA as well as for meeting the waste acceptance criteria for disposal.

  12. Mixed waste characterization strategy

    SciTech Connect

    Baldwin, C.E.; Stakebake, J.; Peters, M.

    1992-08-01

    Radioactive mixed wastes containing a radioactive component subject to the Atomic Energy Act (AEA) and hazardous waste subject to resource Conservation and Recovery Act (RCRA) are generated, treated, and stored at the Rocky Flats Plant (RFP) and are subject to federal and state statutory and regulatory requirements. The US Environmental Protection Agency (EPA) and the Colorado Department of Health (CDH) are the two primary regulatory agencies which enforce these requirements. This paper describes the mechanism by which RFP will characterize mixed wastes within the LDR provisions of RCRA and the LDR FFCA as well as for meeting the waste acceptance criteria for disposal.

  13. MixDown

    Energy Science and Technology Software Center (ESTSC)

    2010-01-01

    MixDown is a meta-build tool that orchestrates and manages the building of multiple 3rd party libraries. It can manage the downloading, uncompressing, unpacking, patching, configuration, build, and installation of 3rd party libraries using a variety of configuration and build tools. As a meta-build tool, it relies on 3rd party tools such as GNU Autotools, make, Cmake, scons, etc. to actually confugure and build libraries. MixDown includes an extensive database of settings to be used formore » general machines and specific leadership class computing resources.« less

  14. Turbulence and Interfacial Mixing

    SciTech Connect

    Glimm, James; Li, Xiaolin

    2005-03-15

    The authors study mix from analytical and numerical points of view. These investigations are linked. The analytical studies (in addition to laboratory experiments) provide bench marks for the direct simulation of mix. However, direct simulation is too detailed to be useful and to expensive to be practical. They also consider averaged equations. Here the major issue is the validation of the closure assumptions. They appeal to the direct simulation methods for this step. They have collaborated with several NNSA teams; moreover, Stony Brook alumni (former students, faculty and research collaborators) presently hold staff positions in NNSA laboratories.

  15. 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.

  16. 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.

  17. Josephson junction mixing.

    NASA Technical Reports Server (NTRS)

    Thompson, E. D.

    1973-01-01

    A theory is presented which, though too simple to explain quantitative details in the Josephson junction mixing response, is sufficient for explaining qualitatively the results observed. Crucial to the theory presented, and that which differentiates it from earlier ones, is the inclusion of harmonic voltages across the ideal Josephson element.

  18. Mixed valent metals.

    PubMed

    Riseborough, P S; Lawrence, J M

    2016-08-01

    We review the theory of mixed-valent metals and make comparison with experiments. A single-impurity description of the mixed-valent state is discussed alongside the description of the nearly-integer valent or Kondo limit. The degeneracy N of the f-shell plays an important role in the description of the low-temperature Fermi-liquid state. In particular, for large N, there is a rapid cross-over between the mixed-valent and the Kondo limit when the number of f electrons is changed. We discuss the limitations on the application of the single-impurity description to concentrated compounds such as those caused by the saturation of the Kondo effect and those due to the presence of magnetic interactions between the impurities. This discussion is followed by a description of a periodic lattice of mixed-valent ions, including the role of the degeneracy N. The article concludes with a comparison of theory and experiment. Topics covered include the single-impurity Anderson model, Luttinger's theorem, the Friedel sum rule, the Schrieffer-Wolff transformation, the single-impurity Kondo model, Kondo screening, the Wilson ratio, local Fermi-liquids, Fermi-liquid sum rules, the Noziéres exhaustion principle, Doniach's diagram, the Anderson lattice model, the Slave-Boson method, etc. PMID:27376888

  19. 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.

  20. Progress in mix modeling

    SciTech Connect

    Harrison, A.K.

    1997-03-14

    We have identified the Cranfill multifluid turbulence model (Cranfill, 1992) as a starting point for development of subgrid models of instability, turbulent and mixing processes. We have differenced the closed system of equations in conservation form, and coded them in the object-oriented hydrodynamics code FLAG, which is to be used as a testbed for such models.

  1. 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…

  2. Mixed valent metals

    NASA Astrophysics Data System (ADS)

    Riseborough, P. S.; Lawrence, J. M.

    2016-08-01

    We review the theory of mixed-valent metals and make comparison with experiments. A single-impurity description of the mixed-valent state is discussed alongside the description of the nearly-integer valent or Kondo limit. The degeneracy N of the f-shell plays an important role in the description of the low-temperature Fermi-liquid state. In particular, for large N, there is a rapid cross-over between the mixed-valent and the Kondo limit when the number of f electrons is changed. We discuss the limitations on the application of the single-impurity description to concentrated compounds such as those caused by the saturation of the Kondo effect and those due to the presence of magnetic interactions between the impurities. This discussion is followed by a description of a periodic lattice of mixed-valent ions, including the role of the degeneracy N. The article concludes with a comparison of theory and experiment. Topics covered include the single-impurity Anderson model, Luttinger’s theorem, the Friedel sum rule, the Schrieffer–Wolff transformation, the single-impurity Kondo model, Kondo screening, the Wilson ratio, local Fermi-liquids, Fermi-liquid sum rules, the Noziéres exhaustion principle, Doniach’s diagram, the Anderson lattice model, the Slave-Boson method, etc.

  3. Mixing of Supersonic Streams

    NASA Technical Reports Server (NTRS)

    Hawk, Clark W.; Landrum, D. Brian; Turner, Matthew; Wagner, David K.; Lambert, James

    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. 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. Initial cold flow testing of the model is underway to determine both, the behavior of the ingested air in the duct and to validate the mixing diagnostics. During the tests, each of the two rocket nozzles ejected up to two pounds mass per second into the 13.6 square inch duct. The tests showed that the mass flow of the rockets was great enough to cause the entrained air to go sonic at the strut, which is the location of the rocket nozzles. More tests are necessary to determine whether the entrained air chokes due to the reduction in the area of the duct at the strut (a physical choke), or because of the addition of mass inside the duct at the nozzle exit (a Fabri choke). The initial tests of the mixing diagnostics are showing promise.

  4. Mixed Markov models

    PubMed Central

    Fridman, Arthur

    2003-01-01

    Markov random fields can encode complex probabilistic relationships involving multiple variables and admit efficient procedures for probabilistic inference. However, from a knowledge engineering point of view, these models suffer from a serious limitation. The graph of a Markov field must connect all pairs of variables that are conditionally dependent even for a single choice of values of the other variables. This makes it hard to encode interactions that occur only in a certain context and are absent in all others. Furthermore, the requirement that two variables be connected unless always conditionally independent may lead to excessively dense graphs, obscuring the independencies present among the variables and leading to computationally prohibitive inference algorithms. Mumford [Mumford, D. (1996) in ICIAM 95, eds. Kirchgassner, K., Marenholtz, O. & Mennicken, R. (Akademie Verlag, Berlin), pp. 233–256] proposed an alternative modeling framework where the graph need not be rigid and completely determined a priori. Mixed Markov models contain node-valued random variables that, when instantiated, augment the graph by a set of transient edges. A single joint probability distribution relates the values of regular and node-valued variables. In this article, we study the analytical and computational properties of mixed Markov models. In particular, we show that positive mixed models have a local Markov property that is equivalent to their global factorization. We also describe a computationally efficient procedure for answering probabilistic queries in mixed Markov models. PMID:12829802

  5. Color mixing models

    NASA Astrophysics Data System (ADS)

    Harrington, Steven J.

    1992-05-01

    In black-and-white printing the page image can be represented within a computer as an array of binary values indicating whether or not pixels should be inked. The Boolean operators of AND, OR, and EXCLUSIVE-OR are often used when adding new objects to the image array. For color printing the page may be represented as an array of continuous tone color values, and the generalization of these logic functions to gray-scale or full-color images is, in general, not defined or understood. When incrementally composing a page image new colors can replace old in an image buffer, or new colors and old can be combined according to some mixing function to form a composite color which is stored. This paper examines the properties of the Boolean operations and suggests full-color mixing functions which preserve the desired properties. These functions can be used to combine colored images, giving various transparency effects. The relationships between the mixing functions and physical models of color mixing are also discussed.

  6. 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)

  7. 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.

  8. Direct nanomaterial-DNA contact effects on DNA and mutation induction.

    PubMed

    Thongkumkoon, P; Sangwijit, K; Chaiwong, C; Thongtem, S; Singjai, P; Yu, L D

    2014-04-01

    The toxicity of nanomaterials has been well known, but mechanisms involved have been little known. This study was aimed at looking at direct interaction between nanomaterials and naked DNA for some fundamental understanding. Two different types of nanomaterials, carbon nanotubes (CNTs) and tungsten trioxide (WO₃) nanoplates, were simply mixed with naked DNA plasmid, respectively, in two different contact modes, dry or wet (in solution), for varied time periods. DNA topological forms were analyzed for changes using gel electrophoresis and fluoro-spectrometry. The nanomaterial-contacted DNA was transferred into bacteria Escherichia coli (E. coli) cells for mutation observation. Certain types and degrees of DNA damage were observed, such as single strand break and double strand break, and bacterial mutation was confirmed. The DNA damage increased with the contacting time in an exponential manner and increased more rapidly in the initial stage for the wet contact. The nanomaterials-contacted DNA transferred bacteria had about less than 10% survival but almost 100% mutation for the surviving cells. The CNTs were more offensive than the metal oxide nanomaterials. The mutation spectrum from the DNA sequencing analysis showed that DNA point mutation was dominated by transversion, which was dominated by guanine changes in the wet contact condition while by cytosine changes in the dry contact condition. The point mutation occurrence in the wet contact was more than in the dry contact, confirming the wet contact more active and thus dangerous than dry contact. This experiment, although as a model study, revealed that direct simple contacts between nanomaterials and DNA could cause DNA changes and thus induce mutations which might potentially lead to cancers, diseases and genetic changes. This could be a mechanism for nanomaterial genotoxicity to the cells and also provided a caution to applications in using nanomaterials for DNA delivery. PMID:24503012

  9. 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.

  10. Unitarity constraints on trimaximal mixing

    SciTech Connect

    Kumar, Sanjeev

    2010-07-01

    When the neutrino mass eigenstate {nu}{sub 2} is trimaximally mixed, the mixing matrix is called trimaximal. The middle column of the trimaximal mixing matrix is identical to tribimaximal mixing and the other two columns are subject to unitarity constraints. This corresponds to a mixing matrix with four independent parameters in the most general case. Apart from the two Majorana phases, the mixing matrix has only one free parameter in the CP conserving limit. Trimaximality results in interesting interplay between mixing angles and CP violation. A notion of maximal CP violation naturally emerges here: CP violation is maximal for maximal 2-3 mixing. Similarly, there is a natural constraint on the deviation from maximal 2-3 mixing which takes its maximal value in the CP conserving limit.

  11. 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.

  12. [Mixed leg ulcers].

    PubMed

    Willenberg, Torsten

    2011-03-01

    Coexisting peripheral arterial disease is not uncommon (15 - 21 %) in patients with ulcera cruris primarily based on a venous etiology. Patient's history, clinical examination and detection of ABI as well as duplex scan will establish diagnosis of mixed arterial-venous ulcera. Clinical significance of coexisting arterial disease is often difficult to define and should be evaluated by a vascular specialist. The concept of treatment of mixed ulcers should always include the arterial component. Frequently peripheral arterial perfusion and healing can be improved by minimal invasive, endovascular revascularization. Compression therapy is the corner stone in treatment of venous disease and should be complemented by contemporary two piece graduated compression systems if ulcera are present. According to circumstances ablation of varicose veins must be considered. PMID:21360460

  13. Nozzle mixing apparatus

    SciTech Connect

    Mensink, D.L.

    1992-12-31

    This invention is comprised of a nozzle device for causing two fluids to mix together. In particular, a spray nozzle comprise two hollow, concentric housings, an inner housing and an outer housing. The inner housing has a channel formed therethrough for a first fluid. Its outer surface cooperates with the interior surface of the outer housing to define the second channel for a second fluid. The outer surface of the inner housing and the inner surface of the outer housing each carry a plurality of vanes that interleave but do not touch, each vane of one housing being between two vanes of the other housing. The vanes are curved and the inner surface of the outer housing and the outer surface of the inner housing converge to narrow the second channel. The shape of second channel results in a swirling, accelerating second fluid that will impact the first fluid just past the end of the nozzle where mixing will take place.

  14. 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.

  15. 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.

  16. Turbulent mixing and beyond.

    PubMed

    Abarzhi, S I; Sreenivasan, K R

    2010-04-13

    Turbulence is a supermixer. Turbulent mixing has immense consequences for physical phenomena spanning astrophysical to atomistic scales under both high- and low-energy-density conditions. It influences thermonuclear fusion in inertial and magnetic confinement systems; governs dynamics of supernovae, accretion disks and explosions; dominates stellar convection, planetary interiors and mantle-lithosphere tectonics; affects premixed and non-premixed combustion; controls standard turbulent flows (wall-bounded and free-subsonic, supersonic as well as hypersonic); as well as atmospheric and oceanic phenomena (which themselves have important effects on climate). In most of these circumstances, the mixing phenomena are driven by non-equilibrium dynamics. While each article in this collection dwells on a specific problem, the purpose here is to seek a few unified themes amongst diverse phenomena. PMID:20211872

  17. Sonocatalytic degradation of azo fuchsine in the presence of the Co-doped and Cr-doped mixed crystal TiO2 powders and comparison of their sonocatalytic activities.

    PubMed

    Wang, Jun; Lv, Yanhui; Zhang, Zhaohong; Deng, Yingqiao; Zhang, Liquan; Liu, Bin; Xu, Rui; Zhang, Xiangdong

    2009-10-15

    In order to degrade some pollutants effectively under ultrasonic irradiation, the Co-doped and Cr-doped mixed crystal TiO(2) powders, with high sonocatalytic activity, were prepared as sonocatalyst. The Co-doped and Cr-doped mixed crystal TiO(2) powders as sonocatalyst were prepared through sol-gel and heat-treated methods from tetrabutylorthotitanate, and then were characterized by XRD and TG-DTA technologies. In order to compare and evaluate the sonocatalytic activity of the Co-doped and Cr-doped mixed crystal TiO(2) powders, the low power ultrasound was as an irradiation source and the azo fuchsine was chosen as a model compound to be degraded. The degradation process was investigated by UV-vis, TOC, ion chromatogram and HPLC techniques. The results indicated that the sonocatalytic activity of Cr-doped mixed crystal TiO(2) powder was higher than that of Co-doped and undoped mixed crystal TiO(2) powder during the sonocatalytic degradation of the azo fuchsine in aqueous solution. These results may be of great significance for driving sonocatalytic method to treat non- or low-transparent industrial wastewaters. PMID:19467773

  18. 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.

  19. 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.

  20. 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

  1. Next Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy

    PubMed Central

    Huang, Taosheng

    2015-01-01

    This protocol is to describe the methodology to characterize mitochondria DNA (mtDNA) heteroplasmy with parallel sequencing. Mitochondria play a very important role in important cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondria genomes. The mutant mtDNA and the wild type may co-exist as heteroplasmy, and cause human disease. The purpose of this methodology is to simultaneously determine mtDNA sequence and to quantify the heteroplasmy level. The protocol includes two-fragment mitochondria genome DNA PCR amplification. The PCR product is then mixed at an equimolar ratio. The samples will be barcoded and sequenced with high-throughput next-generation sequencing technology. We found that this technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree of heteroplasmic level. PMID:21975941

  2. 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.

  3. LCAT DNA shearing.

    PubMed

    Okabe, Yuka; Lee, Abraham P

    2014-04-01

    We present a novel method to fragment DNA by using lateral cavity acoustic transducers (LCATs). DNA solution is placed within a microfluidic device containing LCATs. The LCATs cause microstreaming, which fragments DNA within the solution without any need for purification or downstream processing. The LCAT-based DNA fragmentation method offers an easy-to-use, low-cost, low-energy way to fragment DNA that is amenable to integration on microfluidic platforms to further automate DNA processing. Furthermore, the LCAT microdevice requires less than 10 µL of sample, and no external equipment is needed besides a piezoelectric transducer. PMID:23850863

  4. 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.

  5. Mix/Cast Contamination Control

    NASA Technical Reports Server (NTRS)

    Wallentine, M.

    2005-01-01

    Presented is a training handbook for Mix/Cast Contamination Control; a part of a series of training courses to qualify access to Mix/Cast facilities. Contents: List Contamination Control Requirements; Identify foreign objects debris (FOD), Control Areas and their guidelines; Describe environmental monitoring; List Contamination Control Initiatives; Describe concern for Controlled Materials; Identify FOD Controlled Areas in Mix/Cast.

  6. 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

    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.

  7. 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. PMID:26905597

  8. 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.

  9. 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

  10. 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)

  11. 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)

  12. HPV DNA test

    MedlinePlus

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

  13. 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.

  14. 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.

  15. 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.

  16. Is DNA a language?

    PubMed

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

    1997-01-01

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

  17. Inference of Mix from Experimental Data and Theoretical Mix Models

    SciTech Connect

    Welser-Sherrill, L.; Haynes, D. A.; Cooley, J. H.; Mancini, R. C.; Haan, S. W.; Golovkin, I. E.

    2007-08-02

    The mixing between fuel and shell materials in Inertial Confinement Fusion implosion cores is a topic of great interest. Mixing due to hydrodynamic instabilities can affect implosion dynamics and could also go so far as to prevent ignition. We have demonstrated that it is possible to extract information on mixing directly from experimental data using spectroscopic arguments. In order to compare this data-driven analysis to a theoretical framework, two independent mix models, Youngs' phenomenological model and the Haan saturation model, have been implemented in conjunction with a series of clean hydrodynamic simulations that model the experiments. The first tests of these methods were carried out based on a set of indirect drive implosions at the OMEGA laser. We now focus on direct drive experiments, and endeavor to approach the problem from another perspective. In the current work, we use Youngs' and Haan's mix models in conjunction with hydrodynamic simulations in order to design experimental platforms that exhibit measurably different levels of mix. Once the experiments are completed based on these designs, the results of a data-driven mix analysis will be compared to the levels of mix predicted by the simulations. In this way, we aim to increase our confidence in the methods used to extract mixing information from the experimental data, as well as to study sensitivities and the range of validity of the mix models.

  18. 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.

  19. Oxidative DNA Damage and Nucleotide Excision Repair

    PubMed Central

    Melis, Joost P.M.; Luijten, Mirjam

    2013-01-01

    Abstract Significance: Oxidative DNA damage is repaired by multiple, overlapping DNA repair pathways. Accumulating evidence supports the hypothesis that nucleotide excision repair (NER), besides base excision repair (BER), is also involved in neutralizing oxidative DNA damage. Recent Advances: NER includes two distinct sub-pathways: transcription-coupled NER (TC-NER) and global genome repair (GG-NER). The CSA and CSB proteins initiate the onset of TC-NER. Recent findings show that not only CSB, but also CSA is involved in the repair of oxidative DNA lesions, in the nucleus as well as in mitochondria. The XPG protein is also of importance for the removal of oxidative DNA lesions, as it may enhance the initial step of BER. Substantial evidence exists that support a role for XPC in NER and BER. XPC deficiency not only results in decreased repair of oxidative lesions, but has also been linked to disturbed redox homeostasis. Critical Issues: The role of NER proteins in the regulation of the cellular response to oxidative (mitochondrial and nuclear) DNA damage may be the underlying mechanism of the pathology of accelerated aging in Cockayne syndrome patients, a driving force for internal cancer development in XP-A and XP-C patients, and a contributor to the mixed exhibited phenotypes of XP-G patients. Future Directions: Accumulating evidence indicates that DNA repair factors can be involved in multiple DNA repair pathways. However, the distinct detailed mechanism and consequences of these additional functions remain to be elucidated and can possibly shine a light on clinically related issues. Antioxid. Redox Signal. 18, 2409–2419. PMID:23216312

  20. DNAzymes in DNA Nanomachines and DNA Analysis

    NASA Astrophysics Data System (ADS)

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

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

  1. Correlating lepton mixing angles and mixing maxtrix with Wolfenstein parameters

    NASA Astrophysics Data System (ADS)

    Zhang, Xinyi; Ma, Bo-Qiang

    2012-11-01

    Inspired by a new relation θ13PMNS=θC/2 observed from the relatively large θ13PMNS, we find that the combination of this relation with the quark-lepton complementarity and the self-complementarity results in correlations of the lepton mixing angles with the quark mixing angles. We find that the three mixing angles in the Pontecorvo-Maki-Nakagawa-Sakata (PMNS) matrix are all related to the Wolfenstein parameter λ in the quark mixing, so they are also correlated. Consequently, the PMNS matrix can be parameterized by λ, A, and a Dirac CP-violating phase δ. Such parametrizations for the PMNS matrix have the same explicitly hierarchical structure as the Wolfenstein parametrization for the Cabibbo-Kobayashi-Maskawa matrix in the quark mixing, and the bimaximal mixing pattern is deduced at the leading order. We also discuss implications of these phenomenological relations in parametrizations.

  2. Experimental phase diagram of negatively supercoiled DNA measured by magnetic tweezers and fluorescence

    NASA Astrophysics Data System (ADS)

    Vlijm, Rifka; Mashaghi, Alireza; Bernard, Stéphanie; Modesti, Mauro; Dekker, Cees

    2015-02-01

    The most common form of DNA is the well-known B-structure of double-helix DNA. Many processes in the cell, however, exert force and torque, inducing structural changes to the DNA that are vital to biological function. Virtually all DNA in cells is in a state of negative supercoiling, with a DNA structure that is complex. Using magnetic tweezers combined with fluorescence imaging, we here study DNA structure as a function of negative supercoiling at the single-molecule level. We classify DNA phases based on DNA length as a function of supercoiling, down to a very high negative supercoiling density σ of -2.5, and forces up to 4.5 pN. We characterize plectonemes using fluorescence imaging. DNA bubbles are visualized by the binding of fluorescently labelled RPA, a eukaryotic single-strand-binding protein. The presence of Z-DNA, a left-handed form of DNA, is probed by the binding of Zα77, the minimal binding domain of a Z-DNA-binding protein. Without supercoiling, DNA is in the relaxed B-form. Upon going toward negative supercoiling, plectonemic B-DNA is being formed below 0.6 pN. At higher forces and supercoiling densities down to about -1.9, a mixed state occurs with plectonemes, multiple bubbles and left-handed L-DNA. Around σ = -1.9, a buckling transition occurs after which the DNA end-to-end length linearly decreases when applying more negative turns, into a state that we interpret as plectonemic L-DNA. By measuring DNA length, Zα77 binding, plectoneme and ssDNA visualisation, we thus have mapped the co-existence of many DNA structures and experimentally determined the DNA phase diagram at (extreme) negative supercoiling.The most common form of DNA is the well-known B-structure of double-helix DNA. Many processes in the cell, however, exert force and torque, inducing structural changes to the DNA that are vital to biological function. Virtually all DNA in cells is in a state of negative supercoiling, with a DNA structure that is complex. Using magnetic tweezers

  3. 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)

  4. Nation's water picture mixed

    NASA Astrophysics Data System (ADS)

    The nation's water picture for April showed mixed trends: More than half of the index gaging stations reported normal streamflow conditions during the month, while the spring snowmelt boosted streamflow in the Northeast and Northwest to well above normal levels. Parts of the Southeast, however, from West Virginia south to the Carolinas, reported well-below normal streamflow conditions, according to a month-end check on water resources conditions by the U.S. Geological Survey, Department of the Interior.After nearly 2 years of drought conditions the three major reservoirs supplying New York City reached full storage capacity and were spilling during April. Combined contents of the three reservoirs on May 1, 1982, was 272 billion gallons, 101% of their full usable capacity. The full reservoirs and the generally good surface and groundwater conditions throughout the Delaware River basin allowed the Delaware River Basin Commission to lift its drought emergency warning on April 27.

  5. Holographic mixing quantified

    SciTech Connect

    Batell, Brian; Gherghetta, Tony

    2007-08-15

    We compute the precise elementary/composite field content of mass eigenstates in holographic duals of warped models in a slice of AdS{sub 5}. This is accomplished by decomposing the bulk fields not in the usual Kaluza-Klein basis, but rather into a holographic basis of 4D fields, corresponding to purely elementary source or conformal field theory (CFT) composite fields. Generically, this decomposition yields kinetic and mass mixing between the elementary and composite sectors of the holographic theory. Depending on where the bulk zero mode is localized, the elementary/composite content may differ radically, which we show explicitly for several examples including the bulk Randall-Sundrum graviton, bulk gauge boson, and Higgs boson.

  6. 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.

  7. 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.

  8. 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.

  9. DNA in Nanoscale Electronics

    NASA Astrophysics Data System (ADS)

    Slinker, Jason

    2012-10-01

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

  10. DNA structure and function.

    PubMed

    Travers, Andrew; Muskhelishvili, Georgi

    2015-06-01

    The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase. PMID:25903461

  11. 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

  12. Internet-accessible DNA sequence database for identifying fusaria from human and animal infections.

    PubMed

    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

    2010-10-01

    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

  13. Human DNA repair genes.

    PubMed

    Wood, R D; Mitchell, M; Sgouros, J; Lindahl, T

    2001-02-16

    Cellular DNA is subjected to continual attack, both by reactive species inside cells and by environmental agents. Toxic and mutagenic consequences are minimized by distinct pathways of repair, and 130 known human DNA repair genes are described here. Notable features presently include four enzymes that can remove uracil from DNA, seven recombination genes related to RAD51, and many recently discovered DNA polymerases that bypass damage, but only one system to remove the main DNA lesions induced by ultraviolet light. More human DNA repair genes will be found by comparison with model organisms and as common folds in three-dimensional protein structures are determined. Modulation of DNA repair should lead to clinical applications including improvement of radiotherapy and treatment with anticancer drugs and an advanced understanding of the cellular aging process. PMID:11181991

  14. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology.

    PubMed

    Hadrys, H; Balick, M; Schierwater, B

    1992-05-01

    Molecular genetic markers have been developed into powerful tools to analyse genetic relationships and genetic diversity. As an extension to the variety of existing techniques using polymorphic DNA markers, the Random Amplified Polymorphic DNA (RAPD) technique may be used in molecular ecology to determine taxonomic identity, assess kinship relationships, analyse mixed genome samples, and create specific probes. Main advantages of the RAPD technology include (i) suitability for work on anonymous genomes, (ii) applicability to problems where only limited quantities of DNA are available, (iii) efficiency and low expense. PMID:1344984

  15. Mixing entropy in Dean flows

    NASA Astrophysics Data System (ADS)

    Fodor, Petru; Vyhnalek, Brian; Kaufman, Miron

    2013-03-01

    We investigate mixing in Dean flows by solving numerically the Navier-Stokes equation for a circular channel. Tracers of two chemical species are carried by the fluid. The centrifugal forces, experienced as the fluid travels along a curved trajectory, coupled with the fluid incompressibility induce cross-sectional rotating flows (Dean vortices). These transversal flows promote the mixing of the chemical species. We generate images for different cross sections along the trajectory. The mixing efficiency is evaluated using the Shannon entropy. Previously we have found, P. S. Fodor and M. Kaufman, Modern Physics Letters B 25, 1111 (2011), this measure to be useful in understanding mixing in the staggered herringbone mixer. The mixing entropy is determined as function of the Reynolds number, the angle of the cross section and the observation scale (number of bins). Quantitative comparison of the mixing in the Dean micromixer and in the staggered herringbone mixer is attempted.

  16. 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

  17. DNA methylation in plants.

    PubMed

    Vanyushin, B F

    2006-01-01

    DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA

  18. 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.

  19. Forensic DNA analysis.

    PubMed

    McDonald, Jessica; Lehman, Donald C

    2012-01-01

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

  20. Enantioselective sulfoxidation reaction catalyzed by a G-quadruplex DNA metalloenzyme.

    PubMed

    Cheng, Mingpan; Li, Yinghao; Zhou, Jun; Jia, Guoqing; Lu, Sheng-Mei; Yang, Yan; Li, Can

    2016-07-26

    Enantioselective sulfoxidation reaction is achieved for the first time by a DNA metalloenzyme assembled with the human telomeric G-quadruplex DNA and Cu(ii)-4,4'-bimethyl-2,2'-bipyridine complex, and the mixed G-quadruplex architectures are responsible for the catalytic enantioselectivity and activity. PMID:27359255

  1. Rigid-body molecular dynamics of DNA inside a nucleosome.

    PubMed

    Fathizadeh, Arman; Berdy Besya, Azim; Reza Ejtehadi, Mohammad; Schiessel, Helmut

    2013-03-01

    The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use Kramers theory to calculate nucleosome sliding caused by such defects. It is shown that the twist defect scenario together with the sequence-dependent elasticity of DNA can explain the slow time scales observed for nucleosome mobility along DNA. With this method we also show how the twist defect mechanism leads to a higher mobility of DNA in the presence of sin mutations near the dyad axis. Finally, by performing simulations on 5s rDNA, 601, and telomeric base pair sequences, it is demonstrated that the current model is a powerful tool to predict nucleosome positioning. PMID:23475204

  2. Mixed additive models

    NASA Astrophysics Data System (ADS)

    Carvalho, Francisco; Covas, Ricardo

    2016-06-01

    We consider mixed models y =∑i =0 w Xiβi with V (y )=∑i =1 w θiMi Where Mi=XiXi⊤ , i = 1, . . ., w, and µ = X0β0. For these we will estimate the variance components θ1, . . ., θw, aswell estimable vectors through the decomposition of the initial model into sub-models y(h), h ∈ Γ, with V (y (h ))=γ (h )Ig (h )h ∈Γ . Moreover we will consider L extensions of these models, i.e., y˚=Ly+ɛ, where L=D (1n1, . . ., 1nw) and ɛ, independent of y, has null mean vector and variance covariance matrix θw+1Iw, where w =∑i =1 n wi .

  3. Mixed waste analysis

    SciTech Connect

    Reynolds, J.J.; Turner, C.A.

    1993-12-31

    Improved superpower relations followed by the Soviet Union`s collapse acted as catalysts for changing the mission at Rocky Flats. Now, environmental concerns command as much attention as production capability. As a result, laboratory instruments once dedicated to plutonium production have a new purpose - the analysis of mixed wastes. Waste drums destined for WIPP require headspace analysis by GS/MS (gas chromatography/mass spectrometry) for volatile and semi-volatile organic compounds (VOC and SVOC). Flame AA analysis provides information on inorganic constituents. EPA guidelines for waste analysis (SW-846) overlook the obstacles of glove box manipulations. Sometimes, SW-846 guidelines conflict with the Rocky Flats waste minimization effort. However, the EPA encourages SW-846 adaptations if experimental data confirms the results. For water and soil samples, AA analysis of laboratory control samples show method capability inside a glove box. Non-radioactive drum headspace samples use a revised version of USEPA compendium method TO-14. Radioactive drum headspace samples require new instrumentation and change to SW-846 methods.

  4. 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.

  5. Maximum mixing method

    NASA Astrophysics Data System (ADS)

    Hjorth, Jens

    The unique feature of MEM is that C(-1)(z) = exp(z) amplifies all scales equally. Narayan & Nityananda (1986) have shown that this leads to Gaussian deconvolved peaks. In MMM different scales are treated differently, depending on the choice of C. This gives different peak shapes, but also allows one to experiment with the degree of peak sharpening as a function of peak height. In fact, despite its strong information-theoretic background, MEM is known to redistribute flux incorrectly during deconvolution, thus making the method problematic if the goal is to get correct intensities out. MMM could remedy this problem by using an alternative to the entropy. In conclusion, some ideas connecting the physics of blurring with a proposed reconstruction scheme, dubbed Maximum Mixing Method, have been presented. It has been shown that this physically motivated, non-information theoretic, non-probabilistic, non-Bayesian approach can be turned into a powerful deconvolution technique, competitive with, and having as a special case, the Maximum Entropy Method. Further work within the proposed framework is required to fully explore the consequences of the theory. A paper including proofs and examples is in preparation.

  6. Measures on mixing angles

    SciTech Connect

    Gibbons, Gary W.; Gielen, Steffen; Pope, C. N.; Turok, Neil

    2009-01-01

    We address the problem of the apparently very small magnitude of CP violation in the standard model, measured by the Jarlskog invariant J. In order to make statements about probabilities for certain values of J, we seek to find a natural measure on the space of Kobayashi-Maskawa matrices, the double quotient U(1){sup 2}/SU(3)/U(1){sup 2}. We review several possible, geometrically motivated choices of the measure, and compute expectation values for powers of J for these measures. We find that different choices of the measure generically make the observed magnitude of CP violation appear finely tuned. Since the quark masses and the mixing angles are determined by the same set of Yukawa couplings, we then do a second calculation in which we take the known quark mass hierarchy into account. We construct the simplest measure on the space of 3x3 Hermitian matrices which reproduces this known hierarchy. Calculating expectation values for powers of J in this second approach, we find that values of J close to the observed value are now rather likely, and there does not seem to be any fine-tuning. Our results suggest that the choice of Kobayashi-Maskawa angles is closely linked to the observed mass hierarchy. We close by discussing the corresponding case of neutrinos.

  7. 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

  8. Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

    PubMed Central

    Deagle, Bruce E; Eveson, J Paige; Jarman, Simon N

    2006-01-01

    Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ) can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide). This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will allow researchers to

  9. 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

  10. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals.

    PubMed

    Foote, Andrew D; Thomsen, Philip Francis; 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

  11. 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 ...

  12. 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.

  13. DNA profiles from fingermarks.

    PubMed

    Templeton, Jennifer E L; Linacre, Adrian

    2014-11-01

    Criminal investigations would be considerably improved if DNA profiles could be routinely generated from single fingermarks. Here we report a direct DNA profiling method that was able to generate interpretable profiles from 71% of 170 fingermarks. The data are based on fingermarks from all 5 digits of 34 individuals. DNA was obtained from the fingermarks using a swab moistened with Triton-X, and the fibers were added directly to one of two commercial DNA profiling kits. All profiles were obtained without increasing the number of amplification cycles; therefore, our method is ideally suited for adoption by the forensic science community. We indicate the use of the technique in a criminal case in which a DNA profile was generated from a fingermark on tape that was wrapped around a drug seizure. Our direct DNA profiling approach is rapid and able to generate profiles from touched items when current forensic practices have little chance of success. PMID:25391915

  14. Electrocatalysis in DNA Sensors.

    PubMed

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

    2014-12-14

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

  15. DNA Media Storage

    PubMed Central

    Bogard, Christy M.; Rouchka, Eric C.

    2010-01-01

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

  16. DNA Media Storage.

    PubMed

    Bogard, Christy M; Rouchka, Eric C

    2007-09-01

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

  17. Ribonucleotides in Bacterial DNA

    PubMed Central

    Schroeder, Jeremy W.; Randall, Justin R.; Matthews, Lindsay A.; Simmons, Lyle A.

    2014-01-01

    In all living cells, DNA is the storage medium for genetic information. Being quite stable, DNA is well-suited for its role in storage and propagation of information, but RNA is also covalently included in DNA through various mechanisms. Recent studies also demonstrate useful aspects of including ribonucleotides in the genome during repair. Therefore, our understanding of the consequences of RNA inclusion into bacterial genomic DNA is just beginning, but with its high frequency of occurrence the consequences and potential benefits are likely to be numerous and diverse. In this review, we discuss the processes that cause ribonucleotide inclusion in genomic DNA, the pathways important for ribonucleotide removal and the consequences that arise should ribonucleotides remain nested in genomic DNA. PMID:25387798

  18. 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

  19. 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.

  20. SOURCE ASSESSMENT: ASPHALT HOT MIX

    EPA Science Inventory

    This report summarizes data on air emissions from the asphalt hot mix industry. A representative asphalt hot mix plant was defined, based on the results of an industrial survey, to assess the severity of emissions from this industry. Source severity was defined as the ratio of th...

  1. 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…

  2. DNA-based machines.

    PubMed

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications. PMID:24647836

  3. 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. PMID:27421219

  4. CHARACTERIZING PULSATING MIXING OF SLURRIES

    SciTech Connect

    Bamberger, Judith A.; Meyer, Perry A.

    2007-12-01

    This paper describes the physical properties for defining the operation of a pulse jet mixing system. Pulse jet mixing operates with no moving parts located in the vessel to be mixed. Pulse tubes submerged in the vessel provide a pulsating flow due to a controlled combination of applied pressure to expel the fluid from the pulse tube nozzle followed by suction to refill the pulse tube through the same nozzle. For mixing slurries nondimensional parameters to define mixing operation include slurry properties, geometric properties and operational parameters. Primary parameters include jet Reynolds number and Froude number; alternate parameters may include particle Galileo number, particle Reynolds number, settling velocity ratio, and hindered settling velocity ratio. Rating metrics for system performance include just suspended velocity, concentration distribution as a function of elevation, and blend time.

  5. 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...

  6. 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.

  7. Tiny telomere DNA

    PubMed Central

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

    2002-01-01

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

  8. DNA Damage Response

    PubMed Central

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

    2011-01-01

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

  9. Replicative DNA polymerases.

    PubMed

    Johansson, Erik; Dixon, Nicholas

    2013-06-01

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

  10. 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

  11. Turbidity Current Head Mixing

    NASA Astrophysics Data System (ADS)

    Hernandez, David; Sanchez, Miguel Angel; Medina, Pablo

    2010-05-01

    coastal diffusion using image analysis. Applied Scientific Research 59,.191-204. 1998. [5] J.M. Redondo. Turbulent mixing in the Atmosphere and Ocean. Fluid Physics. 584-597. World Scientific. New York. 1994

  12. Nanoparticle bridge DNA biosensor

    NASA Astrophysics Data System (ADS)

    Huang, Hong-Wen

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

  13. Effect of sperm DNA vaccine on fertility of female mice.

    PubMed

    Naz, Rajesh K

    2006-07-01

    Our laboratory has identified a sperm-specific dodecamer peptide sequence, designated as YLP(12), vaccination with which causes a long-term reversible immunocontraceptive effect in female mice. In the present study, the effects of YLP(12) DNA vaccine were examined. YLP(12) 36 bp cDNA was cloned into pVAX1 vector to prepare the DNA vaccine. Two additional vaccine constructs were made by in frame cloning of one and two CpG repeats in the YLP(12)-cDNA vaccine. Five groups of female mice were immunized intradermally by using gene gun with YLP(12)-cDNA, YLP(12)-cDNA-CpG, YLP(12)-cDNA-CpG-CpG, YLP(12)-cDNA mixed with exogenous synthetic CpG oligodeoxynucleotide (ODN), or vector DNA alone, respectively. Vaccination with all three constructs and the YLP(12) vaccine mixed with exogenous ODN raised antibody response both in the sera as well as locally in the vaginal tract. There was no antibody response in the mice injected with the vector alone. In sera, the highest titers were obtained for the IgG class for all constructs and formulation followed by IgA class. In vaginal washings the highest titers were obtained for the IgA class followed by IgG class. Within the IgG class, the titers for the IgG2a subclass were significantly greater than the IgG1 subclass. Immunization with all constructs and formulation caused a significant (P < 0.05 to <0.001) reduction (20-43%) in fertility of female mice. The highest reductions were seen in mice immunized with YLP(12)-cDNA-CpG-CpG (two repeats) (43% reduction) and with the YLP(12) vaccine administered with exogenous CpG ODN (42% reduction). T lymphocytes obtained from DNA-vaccinated mice showed clearly distinguished comparative RT-PCR analysis of cytokine mRNA expression for Th1 and Th2 immune responses compared to T lymphocytes obtained from control animals injected with vector DNA. Expression of both Th1 cytokines (IL-2 and IFN-gamma) and Th2 cytokines (IL-4 and IL-10) was enhanced after DNA vaccination as compared to controls, with

  14. 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

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

    PubMed

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

    2009-04-01

    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. PMID:19392360

  16. Detection of Non-PCR Amplified S. enteritidis Genomic DNA from Food Matrices Using a Gold-Nanoparticle DNA Biosensor: A Proof-of-Concept Study

    PubMed Central

    Vetrone, Sylvia A.; Huarng, Michael C.; Alocilja, Evangelyn C.

    2012-01-01

    Bacterial pathogens pose an increasing food safety and bioterrorism concern. Current DNA detection methods utilizing sensitive nanotechnology and biosensors have shown excellent detection, but require expensive and time-consuming polymerase chain reaction (PCR) to amplify DNA targets; thus, a faster, more economical method is still essential. In this proof-of-concept study, we investigated the ability of a gold nanoparticle-DNA (AuNP-DNA) biosensor to detect non-PCR amplified genomic Salmonella enterica serovar Enteritidis (S. enteritidis) DNA, from pure or mixed bacterial culture and spiked liquid matrices. Non-PCR amplified DNA was hybridized into sandwich-like structures (magnetic nanoparticles/DNA/AuNPs) and analyzed through detection of gold voltammetric peaks using differential pulse voltammetry. Our preliminary data indicate that non-PCR amplified genomic DNA can be detected at a concentration as low as 100 ng/mL from bacterial cultures and spiked liquid matrices, similar to reported PCR amplified detection levels. These findings also suggest that AuNP-DNA biosensors are a first step towards a viable detection method of bacterial pathogens, in particular, for resource-limited settings, such as field-based or economically limited conditions. Future efforts will focus on further optimization of the DNA extraction method and AuNP-biosensors, to increase sensitivity at lower DNA target concentrations from food matrices comparable to PCR amplified DNA detection strategies. PMID:23112611

  17. Accurate quantification of supercoiled DNA by digital PCR.

    PubMed

    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

  18. 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

  19. 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...

  20. 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...

  1. 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…

  2. MICROWAVE RESONANCES IN DNA

    EPA Science Inventory

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

  3. Replicating repetitive DNA.

    PubMed

    Tognetti, Silvia; Speck, Christian

    2016-05-27

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

  4. Hydrogels: DNA bulks up

    NASA Astrophysics Data System (ADS)

    Labean, Thom

    2006-10-01

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

  5. Translesion DNA synthesis

    PubMed Central

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

    2014-01-01

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

  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. DNA as information.

    PubMed

    Wills, Peter R

    2016-03-13

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

  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. Nanofluidic mixing via hybrid surface

    SciTech Connect

    Ye, Ziran; Li, Shunbo; Zhou, Bingpu; Hui, Yu Sanna; Shen, Rong; Wen, Weijia

    2014-10-20

    We report the design and fabrication of the nanofluidic mixer comprising hybrid hydrophobic/hydrophilic micro-patterns on the top and bottom walls of the nanochannel. The unique feature of such mixer is that, without any geometric structure inside the nanochannel, the mixing can be realized solely by the hybrid surfaces. Besides, the mixing length in nanomixer has been significantly shortened comparing to micromixer. We attribute the mixing achievement to be caused by the convection and chaotic flows of two fluids along the hybrid surface due to the large surface-to-volume ratio of the nanochannel.

  10. [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). PMID:26093140

  11. 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.

  12. Premeltons in DNA.

    PubMed

    Sobell, Henry M

    2016-03-01

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

  13. Efficient in vivo gene transfection by stable DNA/PEI complexes coated by hyaluronic acid.

    PubMed

    Ito, Tomoko; Iida-Tanaka, Naoko; Koyama, Yoshiyuki

    2008-05-01

    Plasmid DNA was mixed with polyethyleneimine (PEI) and hyaluronic acid (HA) to afford ternary complexes with negative surface charge regardless of the mixing order. They showed reduced non-specific interactions with blood components. When DNA and PEI were mixed at a high concentration such as that used in in vivo experiments, they soon aggregated, and large particles were formed. On the other hand, pre-addition of HA to DNA prior to PEI effectively diminished the aggregation, and 10% (in volume) of the complexes remained as small particles with a diameter below 80 nm. Those negatively charged small ternary complexes induced a much stronger extra-gene expression in tumor than binary DNA/PEI complex after intratumoral or intravenous injection into the mice bearing B16 cells. PMID:18446606

  14. Advances in DNA photonics

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

  15. Archaeal DNA replication.

    PubMed

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

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

  16. DNA Align Editor: DNA Alignment Editor Tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  17. Liposome-mediated DNA immunisation via the subcutaneous route.

    PubMed

    Perrie, Y; McNeil, S; Vangala, A

    2003-01-01

    Compared to naked DNA immunisation, entrapment of plasmid-based DNA vaccines into liposomes by the dehydration-rehydration method has shown to enhance both humoural and cell-mediated immune responses to encoded antigens administered by a variety of routes. In this paper, we have investigated the application of liposome-entrapped DNA and their cationic lipid composition on such potency after subcutaneous immunisation. Plasmid pI.18Sfi/NP containing the nucleoprotein (NP) gene of A/Sichuan/2/87 (H3N2) influenza virus in the pI.18 expression vector was incorporated by the dehydration-rehydration method into liposomes composed of 16 micromol egg phosphatidylcholine (PC), 8 micromoles dioleoyl phosphatidylethanolamine (DOPE) or cholesterol (Chol) and either the cationic lipid 1,2-diodeoyl-3-(trimethylammonium) propane (DOTAP) or cholesteryl 3-N-(dimethyl amino ethyl) carbamate (DC-Chol). This method, entailing mixing of small unilamellar vesicles (SUV) with DNA, followed by dehydration and rehydration, yielded incorporation values of 90-94% of the DNA used. Mixing or rehydration of preformed cationic liposomes with 100 microg plasmid DNA also led to similarly high complexation values (92-94%). In an attempt to establish differences in the nature of DNA association with these various liposome preparations their physico-chemical characteristics were investigated. Studies on vesicle size, zeta potential and gel electrophoresis in the presence of the anion sodium dodecyl sulphate (SDS) indicate that, under the conditions employed, formulation of liposomal DNA by the dehydration-rehydration generated submicron size liposomes incorporating most of the DNA in a manner that prevents DNA displacement through anion competition. The bilayer composition of these dehydration-rehydration vesicles (DRV(DNA)) can also further influence these physico-chemical characteristics with the presence of DOPE within the liposome bilayer resulting in a reduced vesicle zeta potential. Subcutaneous

  18. DNA typing of epithelial cells after strangulation.

    PubMed

    Wiegand, P; Kleiber, M

    1997-01-01

    DNA typing was carried out on epithelial cells which were transferred from the hands of the suspect onto the neck of the victim. In an experimental study 16 suspect-victim combinations were investigated for estimating the typing success. Alternatively to an attack against the neck, the upper arm was used for "strangulation". PCR typing was carried out using the short tandem repeat systems (STRs) HumCD4, HumVWF31A (VWA) and Hum-FIBRA (FGA) and the success rate was > 70% for all 3 systems. In most of the cases mixed patterns containing the phenotype of the suspect and the victim were obtained. In a case where strangulation was the cause of death, epithelial cells could be removed from the neck of the victim. The DNA pattern of the suspect could be successfully amplified using four STRs, demonstrating the applicability of this approach for practical casework. PMID:9274940

  19. 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

  20. 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.

  1. 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

    2015-01-01

    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

  2. Relationship inference based on DNA mixtures.

    PubMed

    Kaur, Navreet; Bouzga, Mariam M; Dørum, Guro; Egeland, Thore

    2016-03-01

    Today, there exists a number of tools for solving kinship cases. But what happens when information comes from a mixture? DNA mixtures are in general rarely seen in kinship cases, but in a case presented to the Norwegian Institute of Public Health, sample DNA was obtained after a rape case that resulted in an unwanted pregnancy and abortion. The only available DNA from the fetus came in form of a mixture with the mother, and it was of interest to find the father of the fetus. The mother (the victim), however, refused to give her reference data and so commonly used methods for paternity testing were no longer applicable. As this case illustrates, kinship cases involving mixtures and missing reference profiles do occur and make the use of existing methods rather inconvenient. We here present statistical methods that may handle general relationship inference based on DNA mixtures. The basic idea is that likelihood calculations for mixtures can be decomposed into a series of kinship problems. This formulation of the problem facilitates the use of kinship software. We present the freely available R package relMix which extends on the R version of Familias. Complicating factors like mutations, silent alleles, and θ-correction are then easily handled for quite general family relationships, and are included in the statistical methods we develop in this paper. The methods and their implementations are exemplified on the data from the rape case. PMID:26541994

  3. Cobalt oxyhydroxide nanoflake based fluorescence sensing platform for label-free detection of DNA.

    PubMed

    Chang, Yaqing; Zhang, Zhe; Liu, Huiqing; Wang, Nan; Tang, Jilin

    2016-08-01

    Detection of specific DNA sequences is critical in life science. In this study, we investigated the interaction of cobalt oxyhydroxide (CoOOH) nanoflakes with DNA and their fluorescence quenching mechanism of a FAM-labeled single-stranded DNA (ssDNA) probe. ssDNA could adsorb on the CoOOH surface via electrostatic interactions and therefore the fluorescence of FAM was quenched. However, upon addition of targets, ssDNA was hybridized with target DNA and the formed double-stranded DNA (dsDNA) had much weaker affinity to CoOOH, resulting in the retaining of fluorescence. Based on the affinity difference of CoOOH nanoflakes to ssDNA and dsDNA and fluorescence resonance energy transfer based fluorescence quenching, a mix-and-detect method was proposed for homogeneous detection of DNA. The proposed method is simple and can be finished in a few minutes with high sensitivity. Furthermore, it displays a wide linear range from 1 to 50 nM with a detection limit of 0.5 nM and is capable of detecting DNA in real biological samples. PMID:27251111

  4. 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)

  5. 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)

  6. 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.

  7. 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.

  8. Crossflow Mixing of Noncircular Jets

    NASA Technical Reports Server (NTRS)

    Liscinsky, D. S.; True, B.; Holdeman, J. D.

    1995-01-01

    An experimental investigation has been conducted of the isothermal mixing of a turbulent jet injected perpendicular to a uniform crossflow through several different types of sharp-edged orifices. Jet penetration and mixing was studied using planar Mie scattering to measure time-averaged mixture fraction distributions of circular, square, elliptical, and rectangular orifices of equal geometric area injected into a constant velocity crossflow. Hot-wire anemometry was also used to measure streamwise turbulence intensity distributions at several downstream planes. Mixing effectiveness was determined using (1) a spatial unmixedness parameter based on the variance of the mean jet concentration distributions and (2) by direct comparison of the planar distributions of concentration and of turbulence intensity. No significant difference in mixing performance was observed for the six configurations based on comparison of the mean properties.

  9. 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.

  10. 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

    2016-07-01

    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

  11. 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

  12. Perspectives on dilution jet mixing

    NASA Technical Reports Server (NTRS)

    Holdeman, J. D.

    1986-01-01

    A microcomputer code which displays 3-D oblique and 2-D plots of the temperature distribution downstream of jets mixing with a confined crossflow has been used to investigate the effects of varying the several independent flow and geometric parameters on the mixing. Temperature profiles calculated with this empirical model are presented to show the effects of orifice size and spacing, momentum flux ratio, density ratio, variable temperature mainstream, flow area convergence, orifice aspect ratio, and opposed and axially staged rows of jets.

  13. An Overview of Neutrino Mixing

    NASA Astrophysics Data System (ADS)

    Altarelli, G.

    2013-08-01

    We present a concise review of the recent important experimental developments on neutrino mixing (hints for sterile neutrinos, large θ13, possible non maximal θ23, approaching sensitivity on δ) and their implications on models of neutrino mixing. The new data disfavour many models but the surviving ones still span a wide range going from Anarchy (no structure, no symmetry in the lepton sector) to a maximum of symmetry, as for the models based on discrete non-abelian flavour groups.

  14. Perspectives On Dilution Jet Mixing

    NASA Technical Reports Server (NTRS)

    Holdeman, J. D.; Srinivasan, R.

    1990-01-01

    NASA recently completed program of measurements and modeling of mixing of transverse jets with ducted crossflow, motivated by need to design or tailor temperature pattern at combustor exit in gas turbine engines. Objectives of program to identify dominant physical mechanisms governing mixing, extend empirical models to provide near-term predictive capability, and compare numerical code calculations with data to guide future analysis improvement efforts.

  15. Analysis of stratified flow mixing

    NASA Astrophysics Data System (ADS)

    Soo, S. L.; Lyczkowski, R. W.

    1985-06-01

    The Creare 1/5-scale Phase II experiments which model fluid and thermal mixing of relatively cold high pressure injection (PHI) water into a cold leg of a full-scale pressurized water reactor (PWR) having loop flow are analyzed and found that they cannot achieve complete similarity with respect to characteristic Reynolds and Froude numbers and developing hydrodynamic entry length. Several analyses show that these experiments fall into two distinct regimes of mixing: momentum controlled and gravity controlled (stratification).

  16. Analysis of stratified flow mixing

    SciTech Connect

    Soo, S.L.; Lyckowski, R.W.

    1985-11-01

    The Creare one-fifth-scale Phase II experiments which model fluid and thermal mixing of relatively cold high-pressure injection water into a cold leg of a full-scale pressurized water reactor having loop flow, are analyzed. It is found that they cannot achieve complete similarity with respect to characteristic Reynolds and Froude numbers and developing hydrodynamic entry length. Several analyses show that these experiments fall into two distinct regimes of mixing: momentum and gravity controlled (stratification).

  17. On Infinite-Volume Mixing

    NASA Astrophysics Data System (ADS)

    Lenci, Marco

    2010-09-01

    In the context of the long-standing issue of mixing in infinite ergodic theory, we introduce the idea of mixing for observables possessing an infinite-volume average. The idea is borrowed from statistical mechanics and appears to be relevant, at least for extended systems with a direct physical interpretation. We discuss the pros and cons of a few mathematical definitions that can be devised, testing them on a prototypical class of infinite measure-preserving dynamical systems, namely, the random walks.

  18. Mixing of discontinuously deforming media

    NASA Astrophysics Data System (ADS)

    Smith, L. D.; Rudman, M.; Lester, D. R.; Metcalfe, G.

    2016-02-01

    Mixing of materials is fundamental to many natural phenomena and engineering applications. The presence of discontinuous deformations—such as shear banding or wall slip—creates new mechanisms for mixing and transport beyond those predicted by classical dynamical systems theory. Here, we show how a novel mixing mechanism combining stretching with cutting and shuffling yields exponential mixing rates, quantified by a positive Lyapunov exponent, an impossibility for systems with cutting and shuffling alone or bounded systems with stretching alone, and demonstrate it in a fluid flow. While dynamical systems theory provides a framework for understanding mixing in smoothly deforming media, a theory of discontinuous mixing is yet to be fully developed. New methods are needed to systematize, explain, and extrapolate measurements on systems with discontinuous deformations. Here, we investigate "webs" of Lagrangian discontinuities and show that they provide a template for the overall transport dynamics. Considering slip deformations as the asymptotic limit of increasingly localised smooth shear, we also demonstrate exactly how some of the new structures introduced by discontinuous deformations are analogous to structures in smoothly deforming systems.

  19. Mixing of discontinuously deforming media.

    PubMed

    Smith, L D; Rudman, M; Lester, D R; Metcalfe, G

    2016-02-01

    Mixing of materials is fundamental to many natural phenomena and engineering applications. The presence of discontinuous deformations-such as shear banding or wall slip-creates new mechanisms for mixing and transport beyond those predicted by classical dynamical systems theory. Here, we show how a novel mixing mechanism combining stretching with cutting and shuffling yields exponential mixing rates, quantified by a positive Lyapunov exponent, an impossibility for systems with cutting and shuffling alone or bounded systems with stretching alone, and demonstrate it in a fluid flow. While dynamical systems theory provides a framework for understanding mixing in smoothly deforming media, a theory of discontinuous mixing is yet to be fully developed. New methods are needed to systematize, explain, and extrapolate measurements on systems with discontinuous deformations. Here, we investigate "webs" of Lagrangian discontinuities and show that they provide a template for the overall transport dynamics. Considering slip deformations as the asymptotic limit of increasingly localised smooth shear, we also demonstrate exactly how some of the new structures introduced by discontinuous deformations are analogous to structures in smoothly deforming systems. PMID:26931594

  20. 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.

  1. Reversible DNA compaction.

    PubMed

    González-Pérez, Alfredo

    2014-01-01

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

  2. Tracking Mitochondrial DNA In Situ.

    PubMed

    Ligasová, Anna; Koberna, Karel

    2016-01-01

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

  3. 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.

  4. A simple and practical method that prepares high molecular weight DNA ladders.

    PubMed

    Zhang, Jun-He; Yang, Rui; Wang, Tian-Yun; Dong, Wei-Hua; Wang, Fang; Wang, Li

    2012-11-01

    The purpose of the current study was to report a simple and practical method to prepare high molecular weight (mw) DNA ladders. The method involves 1,000-4,000-base pairs (bp) DNA fragments being amplified by polymerase chain reaction (PCR), using λ DNA as a template. The constructed plasmids are digested by restriction endonucleases to produce 5-, 6-, 8- and 10-kb DNA fragments, followed by purification and precipitation with ethanol, and mixed proportionally. The 1,000-4,000-bp DNA fragments were successfully generated by PCR and 5-, 6-, 8- and 10-kb DNA fragments were obtained through the digestion of the plasmids. The bands of the prepared high mw DNA ladder were clear and may aid future molecular biology studies. PMID:22948498

  5. 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.

  6. 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

  7. DNA Mismatch Repair

    PubMed Central

    MARINUS, M. G.

    2014-01-01

    DNA mismatch repair functions to correct replication errors in newly synthesized DNA and to prevent recombination between related, but not identical (homeologous), DNA sequences. The mechanism of mismatch repair is best understood in Escherichia coli and is the main focus of this review. The early genetic studies of mismatch repair are described as a basis for the subsequent biochemical characterization of the system. The effects of mismatch repair on homologous and homeologous recombination are described. The relationship of mismatch repair to cell toxicity induced by various drugs is included. The VSP (Very Short Patch) repair system is described in detail. PMID:26442827

  8. 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.

  9. Allergen extracts for immunotherapy: to mix or not to mix?

    PubMed

    Nony, Emmanuel; Martelet, Armelle; Jain, Karine; Moingeon, Philippe

    2016-03-01

    Allergen immunotherapy (AIT) is established as a curative treatment for allergic rhinitis, asthma, as well as insect venom allergy. AIT is based on the administration of natural allergen extracts via the subcutaneous or sublingual routes to reorient the immune system towards tolerogenic mechanisms. In this regard, since many patients are poly-allergic, mixtures of allergen extracts are often used with a potential risk to cause allergen degradation, thereby affecting treatment efficacy. Herein, we discuss the advantages and drawbacks of mixing homologous (i.e., related) or heterogeneous (i.e., unrelated) allergen extracts. We provide evidence for incompatibilities between mixes of grass pollen and house dust mite extracts containing bodies and feces, and summarize critical points to consider when mixing allergen extracts for AIT. PMID:26652799

  10. 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.

  11. Expansion of the DNA Alphabet beyond Natural DNA Recognition.

    PubMed

    Tateishi-Karimata, Hisae; Sugimoto, Naoki

    2016-07-15

    Simple and inexpensive DNA fibres: New, stable DNA structures are created by the binding of a small molecule to poly(A). Because these DNA fibres are formed from inexpensive materials by using very simple methods, DNA materials suitable for practical use such as information storage should be possible in the near future. PMID:27061868

  12. DNA computing in microreactors

    NASA Astrophysics Data System (ADS)

    Wagler, Patrick; van Noort, Danny; McCaskill, John S.

    2001-11-01

    The goal of this research is to improve the modular stability and programmability of DNA-based computers and in a second step towards optical programmable DNA computing. The main focus here is on hydrodynamic stability. Clockable microreactors can be connected in various ways to solve combinatorial optimisation problems, such as Maximum Clique or 3-SAT. This work demonstrates by construction how one micro-reactor design can be programmed to solve any instance of Maximum Clique up to its given maximum size (N). It reports on an implementation of the architecture proposed previously. This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem. In this pilot study we are tackling a graph for the Maximum Clique problem with NDNA solution space will be presented, which is symbolized by a set of bit-strings (words).

  13. 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.

  14. 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

  15. 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.

  16. 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)

  17. Harnessing DNA intercalation.

    PubMed

    Persil, Ozgül; Hud, Nicholas V

    2007-10-01

    Numerous small molecules are known to bind to DNA through base pair intercalation. Fluorescent dyes commonly used for nucleic acid staining, such as ethidium, are familiar examples. Biological and physical studies of DNA intercalation have historically been motivated by mutation and drug discovery research. However, this same mode of binding is now being harnessed for the creation of novel molecular assemblies. Recent studies have used DNA scaffolds and intercalators to construct supramolecular assemblies that function as fluorescent 'nanotags' for cell labeling. Other studies have demonstrated how intercalators can be used to promote the formation of otherwise unstable nucleic acid assemblies. These applications illustrate how intercalators can be used to facilitate and expand DNA-based nanotechnology. PMID:17825446

  18. DNA damage tolerance.

    PubMed

    Branzei, Dana; Psakhye, Ivan

    2016-06-01

    Accurate chromosomal DNA replication is fundamental for optimal cellular function and genome integrity. Replication perturbations activate DNA damage tolerance pathways, which are crucial to complete genome duplication as well as to prevent formation of deleterious double strand breaks. Cells use two general strategies to tolerate lesions: recombination to a homologous template, and trans-lesion synthesis with specialized polymerases. While key players of these processes have been outlined, much less is known on their choreography and regulation. Recent advances have uncovered principles by which DNA damage tolerance is regulated locally and temporally - in relation to replication timing and cell cycle stage -, and are beginning to elucidate the DNA dynamics that mediate lesion tolerance and influence chromosome structure during replication. PMID:27060551

  19. 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.

  20. Patterning nanocrystals using DNA

    SciTech Connect

    Williams, Shara Carol

    2003-09-01

    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

  1. 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.

  2. DNA-Nanoparticle Tinkertoys.

    PubMed

    Chandrasekaran, Arun Richard

    2016-06-16

    Nanoparticle superlattices can be self-assembled by using DNA linkers, which gives control over their size, shape, and composition. Recently, such programmable atom equivalents have been tailored to respond to chemical stimuli and result in specific crystalline lattices. Moreover, the molecular recognition properties and the robustness of designed DNA nanostructures have been used in combination with metallic nanoparticles for the production of the elusive diamond superlattice. PMID:27080095

  3. Ribonucleotide triggered DNA damage and RNA-DNA damage responses

    PubMed Central

    Wallace, Bret D; Williams, R Scott

    2014-01-01

    Research indicates that the transient contamination of DNA with ribonucleotides exceeds all other known types of DNA damage combined. The consequences of ribose incorporation into DNA, and the identity of protein factors operating in this RNA-DNA realm to protect genomic integrity from RNA-triggered events are emerging. Left unrepaired, the presence of ribonucleotides in genomic DNA impacts cellular proliferation and is associated with chromosome instability, gross chromosomal rearrangements, mutagenesis, and production of previously unrecognized forms of ribonucleotide-triggered DNA damage. Here, we highlight recent findings on the nature and structure of DNA damage arising from ribonucleotides in DNA, and the identification of cellular factors acting in an RNA-DNA damage response (RDDR) to counter RNA-triggered DNA damage. PMID:25692233

  4. Probing Protein-DNA Interactions by Unzipping DNA

    NASA Astrophysics Data System (ADS)

    Wang, Michelle

    2003-03-01

    Protein-DNA interactions are essential to cellular processes. In replication, transcription, recombination, DNA repair, and DNA packaging, proteins bind to DNA as activators or repressors, to recruit other proteins, or to carry out various catalytic activities. I will present Unzipping Force Analysis of Protein Association (UFAPA) as a novel and versatile method for detection of the position and dynamic nature of protein-DNA interactions. A single DNA double helix was unzipped in the presence of DNA-binding proteins using a feedback-enhanced optical trap. When the unzipping fork in a DNA reached a bound protein molecule, we observed a dramatic increase in the tension in the DNA, followed by a sudden tension reduction. Analysis of the unzipping force throughout an unbinding "event" revealed information about the spatial location and dynamic nature of the protein-DNA complex.

  5. Birth of Lepton Flavor Mixing

    NASA Astrophysics Data System (ADS)

    Kobayashi, Makoto

    The history of the lepton flavor mixing could be traced back to the early 60s, when Maki, Nakagawa and Sakata (MNS) discussed the neutrino mixing. Their work emerged in the course of the developments of the composite model of elementary particles which was initiated by Sakata. In Sakata's model, the weak interaction of the hadrons can be described by two types of transitions among the fundamental triplet baryons. This pattern of the weak interaction of the hadrons is similar to that of leptons provided that the neutrino consists of a single species. From this similarity, Maki, Nakagawa, Ohnuki and Sakata proposed the so-called Nagoya model, in which the fundamental triplet baryons are regarded as composite states of the leptons and a hypothetical object called B-matter. Although the Nagoya model did not make a remarkable success, when existence of two kinds of neutrinos was discovered in 1962, Maki, Nakagawa and Sakata precisely formulated lepton flavor mixing to associate leptons with the fundamental baryons in the framework of the Nagoya model. To recognize their contributions, the flavor mixing matrix of the lepton sector is called the MNS matrix. See also: M. Kobayashi, "Neutrino mass and mixing -- The beginning and future", Nucl. Phys. B (Proc. Suppl.) Vol. 235-236, (2013), pp. 4-7.

  6. A novel DNA-binding protein from Campylobacter jejuni bacteriophage NCTC12673.

    PubMed

    Arutyunov, Denis; Szymanski, Christine M

    2015-11-01

    We previously suggested that the double-stranded genomic DNA of Campylobacter jejuni bacteriophage NCTC12673 was complexed with proteins. Mass spectrometry of peptides obtained from tryptic digests of purified phage DNA indicated that phage protein Gp001 co-purified with the DNA. Gp001 is an acidic protein that lacks any obvious homology or conserved domains found in known DNA-binding proteins. The DNA-binding ability of recombinant Gp001 was examined using an electrophoretic mobility shift assay. Slow DNA-Gp001 complex formation was observed at pH 5.5, but not at neutral or basic pH. This nucleoprotein complex had difficulty entering agarose gels used in the assay while proteinase K pretreatment released the DNA from the complex. No mobility shift was observed when the DNA was immediately subjected to electrophoresis after mixing with Gp001, even if both components were separately pre-incubated at pH 5.5. The complexed DNA was unable to transform chemically competent Escherichia coli cells and was less susceptible to degradation by nucleases. The formation of Gp001-DNA complexes at low pH may provide a mechanism for maintaining DNA integrity while the phage pursues its host through the gastrointestinal tract. Also, this feature can potentially be used to improve DNA delivery protocols applied in gene therapy. PMID:26363017

  7. DNA microdevice for electrochemical detection of Escherichia coli 0157:H7 molecular markers.

    PubMed

    Berganza, J; Olabarria, G; García, R; Verdoy, D; Rebollo, A; Arana, S

    2007-04-15

    An electrochemical DNA sensor based on the hybridization recognition of a single-stranded DNA (ssDNA) probe immobilized onto a gold electrode to its complementary ssDNA is presented. The DNA probe is bound on gold surface electrode by using self-assembled monolayer (SAM) technology. An optimized mixed SAM with a blocking molecule preventing the nonspecific adsorption on the electrode surface has been prepared. In this paper, a DNA biosensor is designed by means of the immobilization of a single stranded DNA probe on an electrochemical transducer surface to recognize specifically Escherichia coli (E. coli) 0157:H7 complementary target DNA sequence via cyclic voltammetry experiments. The 21 mer DNA probe including a C6 alkanethiol group at the 5' phosphate end has been synthesized to form the SAM onto the gold surface through the gold sulfur bond. The goal of this paper has been to design, characterise and optimise an electrochemical DNA sensor. In order to investigate the oligonucleotide probe immobilization and the hybridization detection, experiments with different concentration of DNA and mismatch sequences have been performed. This microdevice has demonstrated the suitability of oligonucleotide Self-assembled monolayers (SAMs) on gold as immobilization method. The DNA probes deposited on gold surface have been functional and able to detect changes in bases sequence in a 21-mer oligonucleotide. PMID:17084071

  8. Geographic distribution of co-dominant DNA stemlines in breast carcinoma

    SciTech Connect

    Visscher, D.; Dolan, P.; Ottosen, S.; Crissman, J.

    1995-09-01

    Breast carcinomas often contain multiple DNA stemlines in flow cytometric DNA histograms. However, due to mixing during tissue disaggregation the microanatomical relationship between the cells which comprise distinct stemlines is unclear. We performed image cytophotometric DNA analysis (IA) on two separate areas of intact tissue sections of 19 breast carcinomas which were selected on the basis of flow cytometric (FCM) DNA content heterogeneity (i.e., multiple stemlines). For comparison, similar analyses were performed on seven tumors with unimodal FCM DNA histograms. Six of the 7 tumors (86%) with unimodal FCM histograms were also unimodal in both IA DNA histograms. Among tumors with heterogeneous FCM DNA histograms, the presence of multiple stemlines was confirmed in IA DNA histograms in 16/19. In nine of these 16 cases, multiple DNA stemlines having similar DNA indices were present in both areas of neoplasm examined with IA. The remaining seven cases displayed unimodal IA histograms in both areas, however DNA indices differed between the two histograms. These findings imply that cell populations corresponding to flow cytometrically detected DNA stemlines are often intimately admixed, even within geographically separated portions of breast tumors. This pattern suggests that productive interactions between genetically distinct tumor populations may lead to stable co-dominance of ancestral clones during progression of some breast carcinomas. 12 refs., 4 tabs.

  9. 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. PMID:22406690

  10. Ancient dirt DNA

    NASA Astrophysics Data System (ADS)

    Willerslev, E.

    2007-12-01

    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 genomic studies 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 discoveries of DNA preserved in ancient sediments, coprolites, and fossil ice (Ancient Dirt DNA). These findings promise to make possible the reconstructions of entire ecosystems through time and allow for studies of past population genetics in cases where fossils are rare. The advantages and pitfalls connected to the Ancient Dirt DNA approach will be discussed as will recently obtained data relating to Greenland environmental history, long-term bacterial survival and the first human migration into the Americas.

  11. 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

  12. Vibrational structure of DNA

    NASA Astrophysics Data System (ADS)

    Gómez C, S.; Rey-González, R. R.

    2003-10-01

    DNA has been object of more extensive research in last years. Human genome may be the main work. On the other hand, DNA has been used as physical system in opposite to its biological character. Examples of this are electronic, thermally and Ramman spectroscopy studies, in others. However, some DNA physical features are unclear, they deserve more work in a effort to understand them. In this work we are interesting on the vibrational properties of DNA. We model it as a lineal chain constituted by three different mass. We use two different constant forces into the Dynamical Matrix formalism. Two masses represent the real mass of DNA bases plus the glucose mass and the third represents the phosphate mass. In this model, DNA unit cell is composed by four masses The dispersion relation shows one acoustical and three optical branches. Also, there is a wide gap between the first and second optical branches. These features are confirmed by the density of states. Also we consider disorder effects in the proposal to do a more realistic model. In this case our results suggest a behavior as diatomic chain where the central and wide gap is preserved.

  13. Evaluation of DNA extraction methods for freshwater eukaryotic microalgae.

    PubMed

    Eland, Lucy E; Davenport, Russell; Mota, Cesar R

    2012-10-15

    The use of molecular methods to investigate microalgal communities of natural and engineered freshwater resources is in its infancy, with the majority of previous studies carried out by microscopy. Inefficient or differential DNA extraction of microalgal community members can lead to bias in downstream community analysis. Three commercially available DNA extraction kits have been tested on a range of pure culture freshwater algal species with diverse cell walls and mixed algal cultures taken from eutrophic waste stabilization ponds (WSP). DNA yield and quality were evaluated, along with DNA suitability for amplification of 18S rRNA gene fragments by polymerase chain reaction (PCR). QiagenDNeasy(®) Blood and Tissue kit (QBT), was found to give the highest DNA yields and quality. Denaturant Gradient Gel Electrophoresis (DGGE) was used to assess the diversity of communities from which DNA was extracted. No significant differences were found among kits when assessing diversity. QBT is recommended for use with WSP samples, a conclusion confirmed by further testing on communities from two tropical WSP systems. The fixation of microalgal samples with ethanol prior to DNA extraction was found to reduce yields as well as diversity and is not recommended. PMID:22853974

  14. 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.

  15. DNA/Fusogenic Lipid Nanocarrier Assembly: Millisecond Structural Dynamics.

    PubMed

    Angelov, Borislav; Angelova, Angelina; Filippov, Sergey K; Narayanan, Theyencheri; Drechsler, Markus; Štěpánek, Petr; Couvreur, Patrick; Lesieur, Sylviane

    2013-06-01

    Structural changes occurring on a millisecond time scale during uptake of DNA by cationic lipid nanocarriers are monitored by time-resolved small-angle X-ray scattering (SAXS) coupled to a rapid-mixing stopped-flow technique. Nanoparticles (NPs) of nanochannel organization are formed by PEGylation, hydration, and dispersion of a lipid film of the fusogenic lipid monoolein in a mixture with positively charged (DOMA) and PEGylated (DOPE-PEG2000) amphiphiles and are characterized by the inner cubic structure of very large nanochannels favorable for DNA upload. Ultrafast structural dynamics of complexation and assembly of these cubosome particles with neurotrophic plasmid DNA (pDNA) is revealed thanks to the high brightness of the employed synchrotron X-ray beam. The rate constant of the pDNA/lipid NP complexation is estimated from dynamic roentgenograms recorded at 4 ms time resolution. pDNA upload into the vastly hydrated channels of the cubosome carriers leads to a fast nanoparticle-nanoparticle structural transition and lipoplex formation involving tightly packed pDNA. PMID:26283134

  16. Preparation of high-molecular-weight DNA from Drosophila embryos.

    PubMed

    Karpen, Gary H

    2009-07-01

    Standard methods for extracting DNA from cells or organisms (e.g., phenol extraction and ethanol precipitation) produce fragments with an average size of 50-200 kb under optimal conditions. The shearing forces that are applied to DNA in solution during mechanical vortexing or mixing and pipetting produce frequent double-stranded breaks. To prepare high-molecular-weight (HMW) DNA, it is necessary to guard against such damaging forces by performing all extractions and manipulations on DNA that is embedded within a protective matrix. Preparation of HMW DNA from Drosophila embryos is described in detail here because, in our hands, it is the simplest and most reliable protocol and can be used for large- or small-scale preparations. The overall strategy is to purify nuclei, gently embed them in molten agarose, and then extract proteins and perform other enzymatic reactions by transferring the solidified agarose block into the appropriate solutions. Salts, soaps, and enzymes act on the DNA by diffusing through the agarose matrix, while the matrix protects the DNA from shearing forces. PMID:20147219

  17. Investigation of Turbulent Mixing Processes

    NASA Technical Reports Server (NTRS)

    Viktorin, K.

    1946-01-01

    With water as driving medium and delivered medium in a device similar to a simple jet apparatus, the pressure and velocity fields of the mixing zone were explored with a pitot bar; the ratio of delivered to driving volume ranged between the values 0, 1, 2, and 4. An attempt was also made to analyze the mixing flow mathematically by integration of the equation of motion, with the aid of conventional formulas for the turbulent shearing stress, but this succeeded only approximately for the very simplified case that a driving jet is introduced in an unlimited parallel flow, while the pressure over the whole mixing field is assumed to be constant. In spite of these dissimilar assumptions for the theory and the experiment, the form of the measured and the computed velocity profiles indicates a very high degree of approximation. The pressure rise, which was approximated by Flugel's formulas, disclosed good agreement with the measured values.

  18. Fluid mixing from viscous fingering.

    PubMed

    Jha, Birendra; Cueto-Felgueroso, Luis; Juanes, Ruben

    2011-05-13

    Mixing efficiency at low Reynolds numbers can be enhanced by exploiting hydrodynamic instabilities that induce heterogeneity and disorder in the flow. The unstable displacement of fluids with different viscosities, or viscous fingering, provides a powerful mechanism to increase fluid-fluid interfacial area and enhance mixing. Here we describe the dissipative structure of miscible viscous fingering, and propose a two-equation model for the scalar variance and its dissipation rate. Our analysis predicts the optimum range of viscosity contrasts that, for a given Péclet number, maximizes interfacial area and minimizes mixing time. In the spirit of turbulence modeling, the proposed two-equation model permits upscaling dissipation due to fingering at unresolved scales. PMID:21668165

  19. Supramolecular Complexes of DNA

    NASA Astrophysics Data System (ADS)

    Zuber, G.; Scherman, D.

    Deoxyribose nucleic acid or DNA is a linear polymer in the form of a double strand, synthesised by sequential polymerisation of a large number of units chosen from among the nucleic bases called purines (adenosine A and guanosine G) and pyrimidines (cytosine C and thymidine T). DNA contains all the genetic information required for life. It exists in the form of a limited number (a few dozen) of very big molecules, called chromosomes. This genetic information is first of all transcribed. In this process, a restricted fragment of the DNA called a gene is copied in the form of ribonucleic acid, or RNA. This RNA is itself a polymer, but with a single strand in which the sequence of nucleic acids is schematically analogous to the sequence on one of the two strands of the transcribed DNA. Finally, this RNA is translated into a protein, yet another linear polymer. The proteins make up the main part of the active constituents ensuring the survival of the cell. Any loss of information, either by mutation or by deletion of the DNA, will cause an imbalance in the cell's metabolism that may in turn lead to incurable pathologies. Several strategies have been developed to reduce the consequences of such genetic deficiencies or, more generally, to act, by amplifying or suppressing them, on the mechanisms leading from the reading of the genetic information to the production of proteins: Strategies aiming to introduce synthetic DNA or RNA, which selectively block the expression of certain genes, are now being studied by an increasing number of research scientists and pharmacologists. They use antisense oligodeoxyribonucleotides or interfering oligoribonucleotides and they already have clinical applications. This kind of therapy is often called gene pharmacology. Other, more ambitious strategies aim to repair in situ mutated or incomplete DNA within the chromosomes themselves, by introducing short sequences of DNA or RNA which recognise and take the place of mutations. This is the

  20. Mixing in magnetized turbulent media

    SciTech Connect

    Sur, Sharanya; Scannapieco, Evan; Pan, Liubin E-mail: evan.scannapieco@asu.edu

    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 {sup –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 {sup –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.

  1. 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.

  2. Nonideal Rayleigh–Taylor mixing

    PubMed Central

    Lim, Hyunkyung; Iwerks, Justin; Glimm, James; Sharp, David H.

    2010-01-01

    Rayleigh–Taylor mixing is a classical hydrodynamic instability that 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 nonideal (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 nonuniqueness 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 nonunique 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 Prandtl 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 play a 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. PMID:20615983

  3. Ion mixing of semiconductor superlattices

    SciTech Connect

    Xia, W.; Hsu, S.N.; Han, C.C.; Pappert, S.A.; Zhu, B.; Cozzolino, C.; Yu, P.K.L.; Lau, S.S. . Dept. of Electrical and Computer Engineering); Poker, D.B.; White, C.W. ); Schwarz, S.A. )

    1990-01-01

    Compositional disordering of III-V compound superlattice structures has received considerable attention recently due to its potential application for photonic devices. The conventional method in induce compositional disorder is to implant a moderate dose of impurity ions ({approximately} 10 {sup 15} /cm{sup 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 five 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. 49 refs., 6 figs.

  4. 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...

  5. Evaluating Mixed Research Studies: A Mixed Methods Approach

    ERIC Educational Resources Information Center

    Leech, Nancy L.; Dellinger, Amy B.; Brannagan, Kim B.; Tanaka, Hideyuki

    2010-01-01

    The purpose of this article is to demonstrate application of a new framework, the validation framework (VF), to assist researchers in evaluating mixed research studies. Based on an earlier work by Dellinger and Leech, a description of the VF is delineated. Using the VF, three studies from education, health care, and counseling fields are…

  6. 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…

  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. 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.

  9. 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.

  10. Analysis of stratified flow mixing

    SciTech Connect

    Soo, S.L.; Lyczkowski, R.W.

    1985-01-01

    The Creare 1/5-scale Phase II experiments which model fluid and thermal mixing of relatively cold high pressure injection (HPI) water into a cold leg of a full-scale pressurized water reactor (PWR) having loop flow are analyzed and found that they cannot achieve complete similarity with respect to characteristic Reynolds and Froude numbers and developing hydrodynamic entry length. Several analyses show that these experiments fall into two distinct regimes of mixing: momentum controlled and gravity controlled (stratification). 18 refs., 9 figs.

  11. DNA Knots: Theory and Experiments

    NASA Astrophysics Data System (ADS)

    Sumners, D. W.

    Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

  12. Abnormal response to DNA crosslinking agents of Fanconi anemia fibroblasts can be corrected by transfection with normal human DNA.

    PubMed

    Diatloff-Zito, C; Papadopoulo, D; Averbeck, D; Moustacchi, E

    1986-09-01

    Primary skin fibroblast cell lines from patients with Fanconi anemia were cotransfected with UV-irradiated pSV2neo plasmids and high molecular weight DNA from normal human cells. Restoration of a normal cellular resistance to mitomycin C (MMC) was observed provided that a Fanconi anemia cell line is selected for DNA-mediated transformation (neo gene) and that at least two successive rounds of transfection are performed. Cells were selected by taking advantage of the higher proliferation rate and plating efficiency of the MMC resistant transformants. As estimated from reconstruction experiments, the frequency of transfer of MMC resistance lies between 1 and 30 X 10(-7). The MMC resistance phenotype was maintained for at least 10 generations following transfection. Evidence for DNA-mediated transformation also includes the recovery of a normal pattern of DNA semiconservative synthesis after treatment with 8-methoxypsoralen and 365-nm UV irradiation, and the presence of exogenous pSV2neo DNA sequences was shown by Southern blot analysis. The acquired MMC resistance is probably due to the presence of DNA from normal cells. Indeed, sensitivity to MMC was maintained when Fanconi anemia cells were cotransfected with the UV-irradiated pSV2neo plasmid mixed with their own DNA or with yeast or salmon sperm DNA. These negative results also render unlikely the selection of spontaneous MMC resistant revertants in transfection of Fanconi anemia cells with normal DNA. These experiments establish the prerequisites for the isolation of the gene(s) involved in the response to DNA crosslinking lesions in human cells. PMID:3092225

  13. DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion

    SciTech Connect

    Tarahovsky, Yury S.; Koynova, Rumiana; MacDonald, Robert C.

    2010-01-18

    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.

  14. 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

  15. 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. PMID

  16. Identification of tissue-specific cell death using methylation patterns of circulating DNA.

    PubMed

    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

    2016-03-29

    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

  17. Human DNA polymerase α in binary complex with a DNA:DNA template-primer

    PubMed Central

    Coloma, Javier; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K.

    2016-01-01

    The Polα/primase complex assembles the short RNA-DNA fragments for priming of lagging and leading strand DNA replication in eukaryotes. As such, the Polα polymerase subunit encounters two types of substrates during primer synthesis: an RNA:DNA helix and a DNA:DNA helix. The engagement of the polymerase subunit with the DNA:DNA helix has been suggested as the of basis for primer termination in eukaryotes. However, there is no structural information on how the Polα polymerase subunit actually engages with a DNA:DNA helix during primer synthesis. We present here the first crystal structure of human Polα polymerase subunit in complex with a DNA:DNA helix. Unexpectedly, we find that portion of the DNA:DNA helix in contact with the polymerase is not in a B-form but in a hybrid A-B form. Almost all of the contacts observed previously with an RNA primer are preserved with a DNA primer – with the same set of polymerase residues tracking the sugar-phosphate backbone of the DNA or RNA primer. Thus, rather than loss of specific contacts, the free energy cost of distorting DNA from B- to hybrid A-B form may augur the termination of primer synthesis in eukaryotes. PMID:27032819

  18. Scalar entrainment in the mixing layer

    NASA Technical Reports Server (NTRS)

    Sandham, N. D.; Mungal, M. G.; Broadwell, J. E.; Reynolds, W. C.

    1988-01-01

    New definitions of entrainment and mixing based on the passive scalar field in the plane mixing layer are proposed. The definitions distinguish clearly between three fluid states: (1) unmixed fluid, (2) fluid engulfed in the mixing layer, trapped between two scalar contours, and (3) mixed fluid. The difference betwen (2) and (3) is the amount of fluid which has been engulfed during the pairing process, but has not yet mixed. Trends are identified from direct numerical simulations and extensions to high Reynolds number mixing layers are made in terms of the Broadwell-Breidenthal mixing model. In the limit of high Peclet number (Pe = ReSc) it is speculated that engulfed fluid rises in steps associated with pairings, introducing unmixed fluid into the large scale structures, where it is eventually mixed at the Kolmogorov scale. From this viewpoint, pairing is a prerequisite for mixing in the turbulent plane mixing layer.

  19. Dynamic Modulation of DNA Hybridization Using Allosteric DNA Tetrahedral Nanostructures.

    PubMed

    Song, Ping; Li, Min; Shen, Juwen; Pei, Hao; Chao, Jie; Su, Shao; Aldalbahi, Ali; Wang, Lihua; Shi, Jiye; Song, Shiping; Wang, Lianhui; Fan, Chunhai; Zuo, Xiaolei

    2016-08-16

    The fixed dynamic range of traditional biosensors limits their utility in several real applications. For example, viral load monitoring requires the dynamic range spans several orders of magnitude; whereas, monitoring of drugs requires extremely narrow dynamic range. To overcome this limitation, here, we devised tunable biosensing interface using allosteric DNA tetrahedral bioprobes to tune the dynamic range of DNA biosensors. Our strategy takes the advantage of the readily and flexible structure design and predictable geometric reconfiguration of DNA nanotechnology. We reconfigured the DNA tetrahedral bioprobes by inserting the effector sequence into the DNA tetrahedron, through which, the binding affinity of DNA tetrahedral bioprobes can be tuned. As a result, the detection limit of DNA biosensors can be programmably regulated. The dynamic range of DNA biosensors can be tuned (narrowed or extended) for up to 100-fold. Using the regulation of binding affinity, we realized the capture and release of biomolecules by tuning the binding behavior of DNA tetrahedral bioprobes. PMID:27435955

  20. Strandwise translocation of a DNA glycosylase on undamaged DNA

    SciTech Connect

    Qi, Yan; Nam, Kwangho; Spong, Marie C.; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L.

    2012-05-14

    Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

  1. Active DNA demethylation by DNA repair: Facts and uncertainties.

    PubMed

    Schuermann, David; Weber, Alain R; Schär, Primo

    2016-08-01

    Pathways that control and modulate DNA methylation patterning in mammalian cells were poorly understood for a long time, although their importance in establishing and maintaining cell type-specific gene expression was well recognized. The discovery of proteins capable of converting 5-methylcytosine (5mC) to putative substrates for DNA repair introduced a novel and exciting conceptual framework for the investigation and ultimate discovery of molecular mechanisms of DNA demethylation. Against the prevailing notion that DNA methylation is a static epigenetic mark, it turned out to be dynamic and distinct mechanisms appear to have evolved to effect global and locus-specific DNA demethylation. There is compelling evidence that DNA repair, in particular base excision repair, contributes significantly to the turnover of 5mC in cells. By actively demethylating DNA, DNA repair supports the developmental establishment as well as the maintenance of DNA methylation landscapes and gene expression patterns. Yet, while the biochemical pathways are relatively well-established and reviewed, the biological context, function and regulation of DNA repair-mediated active DNA demethylation remains uncertain. In this review, we will thus summarize and critically discuss the evidence that associates active DNA demethylation by DNA repair with specific functional contexts including the DNA methylation erasure in the early embryo, the control of pluripotency and cellular differentiation, the maintenance of cell identity, and the nuclear reprogramming. PMID:27247237

  2. Electroeluting DNA fragments.

    PubMed

    Zarzosa-Alvarez, Ana L; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L; Bermudez-Cruz, Rosa M

    2010-01-01

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The electroelution procedure allows one to purify very clean DNA to be used in a large number of applications (sequencing, radiolabeling, enzymatic restriction, enzymatic modification, cloning etc). This procedure consists in placing DNA band-containing agarose or acrylamide slices into sample wells of the electroeluter, then applying current will make the DNA fragment to leave the agarose and thus be trapped in a cushion salt to be recovered later by ethanol precipitation. PMID:20834225

  3. Dynamical Behavior of DNA

    NASA Astrophysics Data System (ADS)

    Kumar, Shankar

    1990-01-01

    The crystal structure of the DNA-EcoRI complex (Kim et al., 1990) revealed the existence of a 'kink' (or a disruption of the helical symmetry) in the DNA. Part of this work was an investigation of whether or not the kinked structure is a physically meaningful metastable state that is intrinsic to DNA. By using the "All Atom" hamiltonian of Weiner et al (1986) it has been found that the kink is not a metastable feature of the DNA. Rapid scanning of conformational space is indispensable in statistical mechanical studies of proteins and DNA. The Quasi-Optimized-Monte-Carlo (or QOMC) method is more efficient than the conventional Metropolis Monte Carlo method in the simulated annealing calculations reported here. It is also shown here that using altered masses in Molecular Dynamics calculations enhances sampling efficiency. The Multiple Histogram technique (Ferrenberg, 1989) has been applied for the first time on complex biomolecular hamiltonians. This method is superior to the classical perturbation and multistage sampling techniques for calculating free energy differences and generating potential of mean force profiles for suitably chosen reaction coordinates. This was demonstrated by using the multiple histogram method to generate the potential of mean force for the pseudorotation phase angle of the sugar ring in adenosine.

  4. Chromatin and DNA replication.

    PubMed

    MacAlpine, David M; Almouzni, Geneviève

    2013-08-01

    The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as genes and regulatory elements. This is achieved via the dynamic nucleoprotein organization of eukaryotic DNA into chromatin. The basic unit of chromatin, the nucleosome, comprises a core particle with 147 bp of DNA wrapped 1.7 times around an octamer of histones. The nucleosome is a highly versatile and modular structure, both in its composition, with the existence of various histone variants, and through the addition of a series of posttranslational modifications on the histones. This versatility allows for both short-term regulatory responses to external signaling, as well as the long-term and multigenerational definition of large functional chromosomal domains within the nucleus, such as the centromere. Chromatin organization and its dynamics participate in essentially all DNA-templated processes, including transcription, replication, recombination, and repair. Here we will focus mainly on nucleosomal organization and describe the pathways and mechanisms that contribute to assembly of this organization and the role of chromatin in regulating the DNA replication program. PMID:23751185

  5. 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).

  6. The Mystery of Neutrino Mixings

    NASA Astrophysics Data System (ADS)

    Altarelli, Guido

    2013-07-01

    In the last years we have learnt a lot about neutrino masses and mixings. Neutrinos are not all massless but their masses are very small. Probably masses are small because neutrinos are Majorana particles with masses inversely proportional to the large scale M of lepton number (L) violation, which turns out to be compatible with the GUT scale. We have understood that there is no contradiction between large neutrino mixings and small quark mixings, even in the context of GUTs and that neutrino masses fit well in the SUSY GUT picture. Out of equilibrium decays with CP and L violation of heavy RH neutrinos can produce a B-L asymmetry, then converted near the weak scale by instantons into an amount of B asymmetry compatible with observations (baryogenesis via leptogenesis). It appears that active neutrinos are not a significant component of Dark Matter in the Universe. A long list of models have been formulated over the years to understand neutrino masses and mixings. With the continuous improvement of the data most of the models have been discarded by experiment. The surviving models still span a wide range going from a maximum of symmetry, with discrete non-abelian flavour groups, to the opposite extreme of anarchy.

  7. 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…

  8. 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…

  9. VLSI mixed signal processing system

    NASA Technical Reports Server (NTRS)

    Alvarez, A.; Premkumar, A. B.

    1993-01-01

    An economical and efficient VLSI implementation of a mixed signal processing system (MSP) is presented in this paper. The MSP concept is investigated and the functional blocks of the proposed MSP are described. The requirements of each of the blocks are discussed in detail. A sample application using active acoustic cancellation technique is described to demonstrate the power of the MSP approach.

  10. [Mixed approaches in nursing science].

    PubMed

    Dupin, Cécile-Marie

    2015-06-01

    Mixed methods research uses methodologies from quantitative and qualitative approaches in a single project. Thanks to the integration of the results of the studies, complex phenomena can be explored. The designs are based on specific criteria of rigour. Strategies exist for the design of this type of research. PMID:26146330

  11. 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)

  12. 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...

  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. Chaotic mixing across oceanic jets

    SciTech Connect

    Miller, P.; Jones, C.K.; Haller, G.; Pratt, L. |

    1996-06-01

    The perspective of geometric dynamical systems is used to study the transport of fluid across oceanic jets. We study the mixing associated with the simplest analytical models for jets, namely, neutral modes superimposed on a base mean flow, where the base flow and the neutral modes are approximately potential vorticity conserving. The base jet plus a single neutral mode is an integrable flow in the appropriate moving frame, and heteroclinic orbits act as impenetrable boundaries separating different regions of phase space. Superimposing more than one neutral mode results in the breakup of these heteroclinic orbits and associated chaotic mixing. Using a cusped jet model we study the case where the perturbation is periodic in time. We present numerical simulations of the Poincar{acute e} map along with calculations of the Melnikov integral which characterizes the exchange rate across such boundaries. The analytical and numerical results show that these models explain mixing along the edges of the jet, but do not appear to explain mixing across the body of the jet. {copyright} {ital 1996 American Institute of Physics.}

  15. Generalized perturbations in neutrino mixing

    NASA Astrophysics Data System (ADS)

    Liao, Jiajun; Marfatia, D.; Whisnant, K.

    2015-10-01

    We derive expressions for the neutrino mixing parameters that result from complex perturbations on (1) the Majorana neutrino mass matrix (in the basis of charged lepton mass eigenstates) and on (2) the charged lepton mass matrix, for arbitrary initial (unperturbed) mixing matrices. In the first case, we find that the phases of the elements of the perturbation matrix, and the initial values of the Dirac and Majorana phases, strongly impact the leading-order corrections to the neutrino mixing parameters and phases. For experimentally compatible scenarios wherein the initial neutrino mass matrix has μ -τ symmetry, we find that the Dirac phase can take any value under small perturbations. Similarly, in the second case, perturbations to the charged lepton mass matrix can generate large corrections to the mixing angles and phases of the Pontecorvo-Maki-Nakagawa-Sakata (PMNS) matrix. As an illustration of our generalized procedure, we apply it to a situation in which nonstandard scalar and nonstandard vector interactions simultaneously affect neutrino oscillations.

  16. 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)

  17. Reductant injection and mixing system

    DOEpatents

    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.

  18. Integrated microfluidic systems for DNA analysis.

    PubMed

    Njoroge, Samuel K; Chen, Hui-Wen; Witek, Małgorzata A; Soper, Steven A

    2011-01-01

    The potential utility of genome-related research in terms of evolving basic discoveries in biology has generated widespread use of DNA diagnostics and DNA forensics and driven the accelerated development of fully integrated microfluidic systems for genome processing. To produce a microsystem with favorable performance characteristics for genetic-based analyses, several key operational elements must be strategically chosen, including device substrate material, temperature control, fluidic control, and reaction product readout. As a matter of definition, a microdevice is a chip that performs a single processing step, for example microchip electrophoresis. Several microdevices can be integrated to a single wafer, or combined on a control board as separate devices to form a microsystem. A microsystem is defined as a chip composed of at least two microdevices. Among the many documented analytical microdevices, those focused on the ability to perform the polymerase chain reaction (PCR) have been reported extensively due to the importance of this processing step in most genetic-based assays. Other microdevices that have been detailed in the literature include those for solid-phase extractions, microchip electrophoresis, and devices composed of DNA microarrays used for interrogating DNA primary structure. Great progress has also been made in the areas of chip fabrication, bonding and sealing to enclose fluidic networks, evaluation of different chip substrate materials, surface chemistries, and the architecture of reaction conduits for basic processing steps such as mixing. Other important elements that have been developed to realize functional systems include miniaturized readout formats comprising optical or electrochemical transduction and interconnect technologies. These discoveries have led to the development of fully autonomous and functional integrated systems for genome processing that can supply "sample in/answer out" capabilities. In this chapter, we focus on

  19. Electrostatic sampling of trace DNA from clothing.

    PubMed

    Zieger, Martin; Defaux, Priscille Merciani; Utz, Silvia

    2016-05-01

    During acts of physical aggression, offenders frequently come into contact with clothes of the victim, thereby leaving traces of DNA-bearing biological material on the garments. Since tape-lifting and swabbing, the currently established methods for non-destructive trace DNA sampling from clothing, both have their shortcomings in collection efficiency and handling, we thought about a new collection method for these challenging samples. Testing two readily available electrostatic devices for their potential to sample biological material from garments made of different fabrics, we found one of them, the electrostatic dust print lifter (DPL), to perform comparable to well-established sampling with wet cotton swabs. In simulated aggression scenarios, we had the same success rate for the establishment of single aggressor profiles, suitable for database submission, with both the DPL and wet swabbing. However, we lost a substantial amount of information with electrostatic sampling, since almost no mixed aggressor-victim profiles suitable for database entry could be established, compared to conventional swabbing. This study serves as a proof of principle for electrostatic DNA sampling from items of clothing. The technique still requires optimization before it might be used in real casework. But we are confident that in the future it could be an efficient and convenient contribution to the toolbox of forensic practitioners. PMID:26753871

  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

  1. 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

  2. Advancing taxonomy and bioinventories with DNA barcodes.

    PubMed

    Miller, Scott E; Hausmann, Axel; Hallwachs, Winnie; Janzen, Daniel H

    2016-09-01

    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

  3. 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

  4. 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'. PMID:27325829

  5. 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.

  6. Tunnelling microscopy of DNA

    NASA Astrophysics Data System (ADS)

    Selci, Stefano; Cricenti, Antonio

    1991-01-01

    Uncoated DNA molecules marked with an activated tris (1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with a high resolution Scanning Tunnelling Microscope (STM). The STM operated simultaneously in the constant-current and gap-modulated mode. Highly reproducible STM images have been obtained and interpreted in terms of expected DNA structure. The main periodicity, regularly presented in molecules several hundred Ångstrom long, ranges from 25 Å to 35 Å with an average diameter of 22 Å. Higher resolution images of the minor groove have revealed the phosphate groups along the DNA backbones. Constant-current images of TAPO deposited on gold show a crystalline structure of rows of molecules with a side-by-side spacing of 3 Å.

  7. Transposon facilitated DNA sequencing

    SciTech Connect

    Berg, D.E.; Berg, C.M.; Huang, H.V.

    1990-01-01

    The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.

  8. DNA sequencing: chemical methods

    SciTech Connect

    Ambrose, B.J.B.; Pless, R.C.

    1987-01-01

    Limited base-specific or base-selective cleavage of a defined DNA fragment yields polynucleotide products, the length of which correlates with the positions of the particular base (or bases) in the original fragment. Sverdlov and co-workers recognized the possibility of using this principle for the determination of DNA sequences. In 1977 a fully elaborated method was introduced based on this principle, which allowed routine analysis of DNA sequences over distances greater than 100 nucleotide unite from a defined, radiolabeled terminus. Six procedures for partial cleavage were described. Simultaneous parallel resolution of an appropriate set of partial cleavage mixtures by polyacrylamide gel electrophoresis, followed by visualization of the radioactive bands by autoradiography, allows the deduction of nucleotide sequence.

  9. [DNA methylation in obesity].

    PubMed

    Pokrywka, Małgorzata; Kieć-Wilk, Beata; Polus, Anna; Wybrańska, Iwona

    2014-01-01

    The number of overweight and obese people is increasing at an alarming rate, especially in the developed and developing countries. Obesity is a major risk factor for diabetes, cardiovascular disease, and cancer, and in consequence for premature death. The development of obesity results from the interplay of both genetic and environmental factors, which include sedentary life style and abnormal eating habits. In the past few years a number of events accompanying obesity, affecting expression of genes which are not directly connected with the DNA base sequence (e.g. epigenetic changes), have been described. Epigenetic processes include DNA methylation, histone modifications such as acetylation, methylation, phosphorylation, ubiquitination, and sumoylation, as well as non-coding micro-RNA (miRNA) synthesis. In this review, the known changes in the profile of DNA methylation as a factor affecting obesity and its complications are described. PMID:25531701

  10. 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.

  11. Design and characterization of a novel lipid-DNA complex that resists serum-induced destabilization.

    PubMed

    Lian, Tianshun; Ho, Rodney J Y

    2003-12-01

    Ineffectiveness of cationic lipids to enhance DNA transfection has been attributed to serum-mediated dissociation and perhaps complement activation of lipid-DNA complexes. To overcome these problems, we have developed a novel lipid-DNA complex that greatly reduces serum-mediated dissociation. The complexes were prepared by mixing cationic liposomes containing 1,2-dioleoyl-3-trimethylammonium-propane and dioleoylphosphatidyl-ethanolamine and DNA in ethanolic (20% v/v ethanol) solution containing 5% sucrose followed by dehydration via rotating evaporation. Upon hydration in H(2)O, the lipid-DNA complexes [ethanol-dried lipid-DNA (EDL) complexes] were formed. The complexes exhibit a low positive zeta potential and enhanced transfection efficiency in contrast to the suppressed efficiency detected with admixed lipid-DNA complexes in the presence of serum across several cell lines. This result may be attributed to the inability of serum to dissociate DNA from lipids in EDL complexes. Using displacement of ethidium bromide intercalation analysis, we found that in serum, only 50% of DNA was exposed in the EDL complexes, compared with 100% in the admixed lipid-DNA complexes. The EDL complexes also showed increased resistance to DNase digestion in the presence of negatively charged lipid, while reducing complement activation in serum. The EDL complexes may improve the transfection activity of lipid-DNA complexes in serum and, perhaps, in vivo. PMID:14603483

  12. DNA Before Proteins? Recent Discoveries in Nucleic Acid Catalysis Strengthen the Case

    NASA Astrophysics Data System (ADS)

    Burton, Aaron S.; Lehman, Niles

    2009-02-01

    An RNA-DNA World could arise from an all-RNA system with the development of as few as three ribozymes -- a DNA-dependent RNA polymerase, an RNA-dependent DNA polymerase, and a catalyst for the production of DNA nucleotides. A significant objection to DNA preceding proteins is that RNA has not been shown to catalyze the production of DNA. However, RNA- and DNAzymes have been recently discovered that catalyze chemical reactions capable of forming deoxyribose, such as mixed aldol condensation of 5'-glyceryl- and 3'-glycoaldehyde-terminated DNA strands. Thus, the only remaining obstacles to RNA-catalyzed in vitro DNA synthesis are alterations of substrate and template specificities of known ribozymes. The RNA-DNA World lessens genomic size constraints through a relaxed error threshold, affording the evolutionary time needed to develop protein synthesis. Separation of information from catalyst enables genotype and phenotype to be readily discriminated by absence or presence, respectively, of the 2'-OH. Novel ribozymes that arise through mutation can be preserved in DNA by reverse transcription, which makes them much more likely to be retained than in an RNA-genome milieu. The extra degree of separation between protein and mRNA, in terms of identifying and then retaining a useful enzyme, may have in fact necessitated storing information in DNA prior to the advent of translation.

  13. 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. PMID:26456453

  14. Electrochemical DNA sensor-based strategy for sensitive detection of DNA demethylation and DNA demethylase activity.

    PubMed

    Shen, Qingming; Fan, Mengxing; Yang, Yin; Zhang, Hui

    2016-08-31

    DNA demethylation and demethylase activity play important roles in DNA self-repair, and their detection is key to early diagnosis of fatal diseases. Herein, a facile electrochemical DNA (E-DNA) sensor was developed for the sensitive detection of DNA demethylation and demethylase activity based on an enzyme cleavage strategy. The thiol modified hemi-methylated hairpin probe DNA (pDNA) was self-assembled on a Au electrode surface through the formation of AuS bonds. The hemi-methylated pDNA served as the substrate of DNA demethylase (using methyl-CpG-binding domain protein 2 (MBD2) as an example). Following demethylation, the hairpin stem was then recognized and cleaved by BstUI endonuclease. The ferrocene carboxylic acid (FcA)-tagged pDNA strands were released into the buffer solution from the electrode surface, resulting in a significant decrease of electrochemical signal and providing a means to observe DNA demethylation. The activity of DNA demethylase was analyzed in the concentration ranging from 0.5 to 500 ng mL(-1) with a limit of detection as low as 0.17 ng mL(-1). With high specificity and sensitivity, rapid response, and low cost, this simple E-DNA sensor provides a unique platform for the sensitive detection of DNA demethylation, DNA demethylase activity, and related molecular diagnostics and drug screening. PMID:27506345

  15. DNA templated magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Kinsella, Joseph M.

    Recent discoveries in nanoscience are predicted to potentially revolutionize future technologies in an extensive number of fields. These developments are contingent upon discovering new and often unconventional methods to synthesize and control nanoscale components. Nature provides several examples of working nanotechnology such as the use of programmed self assembly to build and deconstruct complex molecular systems. We have adopted a method to control the one dimensional assembly of magnetic nanoparticles using DNA as a scaffold molecule. With this method we have demonstrated the ability to organize 5 nm particles into chains that stretch up to ˜20 mum in length. One advantage of using DNA compared is the ability of the molecule to interact with other biomolecules. After assembling particles onto DNA we have been able to cleave the molecule into smaller fragments using restriction enzymes. Using ligase enzymes we have re-connected these fragments, coated with either gold or iron oxide, to form long one-dimensional arrangements of the two different types of nanoparticles on a single molecular guide. We have also created a sensitive magnetic field sensor by incorporating magnetic nanoparticle coated DNA strands with microfabricated electrodes. The IV characteristics of the aligned nanoparticles are dependant on the magnitude of an externally applied magnetic field. This transport phenomenon known as tunneling magnetoresistance (TMR) shows room temperature resistance of our devices over 80% for cobalt ferrite coated DNA when a field of 20 kOe is applied. In comparison, studies using two dimensional nanoparticle films of irox oxides xii only exhibit a 35% MR effect. Confinement into one dimension using the DNA guide produces a TMR mechanism which produces significant increases in magnetoresistance. This property can be utilized for applications in magnetic field sensing, data storage, and logic elements.

  16. 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).

  17. Automated DNA sequencing.

    PubMed

    Wallis, Yvonne; Morrell, Natalie

    2011-01-01

    Fluorescent cycle sequencing of PCR products is a multistage process and several methodologies are available to perform each stage. This chapter will describe the more commonly utilised dye-terminator cycle sequencing approach using BigDye® terminator chemistry (Applied Biosystems) ready for analysis on a 3730 DNA genetic analyzer. Even though DNA sequencing is one of the most common and robust techniques performed in molecular laboratories it may not always produce desirable results. The causes of the most common problems will also be discussed in this chapter. PMID:20938839

  18. Ancient human DNA.

    PubMed

    Kirsanow, Karola; Burger, Joachim

    2012-01-20

    The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements. PMID:22169595

  19. Rigidity of melting DNA.

    PubMed

    Pal, Tanmoy; Bhattacharjee, Somendra M

    2016-05-01

    The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation. PMID:27300825

  20. Rigidity of melting DNA

    NASA Astrophysics Data System (ADS)

    Pal, Tanmoy; Bhattacharjee, Somendra M.

    2016-05-01

    The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.

  1. Extraktion von DNA

    NASA Astrophysics Data System (ADS)

    Pöpping, Bert; Unterberger, Claudia

    Eine DNA-gestützte Analytik spielt im Lebensmittelbereich eine große Rolle. So wird die PCR bzw. die Real Time PCR z. B. für den Nachweis von Krankheitserreger in Lebensmitteln, zur Tier- und Pflanzenartendifferenzierung und den Nachweis von gentechnologisch veränderten Organismen eingesetzt [1]. Grundvoraussetzung für die sehr sensitiven molekularbiologischen Methoden ist eine saubere und kontaminationsfreie Nukleinsäure [2]. Die Qualität der Nukleinsäure entscheidet über Erfolg und Misserfolg der anschließenden molekularbiologischen Analytik. Deshalb werden im Bereich der Lebensmittelanalytik hohe Anforderungen an das jeweilige DNA-Extraktionsprotokoll gestellt. Durch die Anwendung eines geeigneten Extraktionsverfahrens soll die nachzuweisende DNA möglichst in hochmolekularer Form und frei von die nachfolgende Analytik hemmenden Substanzen vorliegen [1]. Gerade hier stellt die Natur der Lebensmittelmatrix eine besondere Herausforderung dar. Matrixkomponenten wie Fette, Zucker, Proteine und sekundäre Inhaltsstoffe erschweren die DNA-Extraktion und können, wenn sie nicht durch die Extraktion vollständig entfernt werden, zu einer Inhibierung der PCR führen [3]. Des Weiteren müssen auf der Matrixoberfläche vorhandene DNA-abbauende Enzyme gehemmt werden [1]. Daneben spielt der Einfluss verschiedener chemischer und physikalischer Parameter (pH-Wert, Temperatur, Enzyme, Scherkräfte) bei der Lebensmittelproduktion eine große Rolle für die Qualität der extrahierten DNA. So führen z. B. hohe Temperaturen und saure pH-Werte während der Lebensmittelverarbeitung zu einer Fragmentierung der DNA. Auch die physikalischen und chemischen Bedingungen der verwendeten Extraktionsmethode beeinflussen die Qualität der DNA [2]. Bleiben nach der Extraktion organische Lösungsmittel (Phenol, Ethanol), Enzyme, Proteine oder Salze zurück, können diese ebenfalls eine nachfolgende PCR inhibieren. Um eine Inhibition der PCR auszuschließen, sollten in der

  2. DNA banking and DNA databanking by academic and commercial laboratories

    SciTech Connect

    McEwen, J.E. |; Reilly, P.R.

    1994-09-01

    The advent of DNA-based testing is giving rise to DNA banking (the long-term storage of cells, transformed cell lines, or extracted DNA for subsequent retrieval and analysis) and DNA data banking (the indefinite storage of information derived from DNA analysis). Large scale acquisition and storage of DNA and DNA data has important implications for the privacy rights of individuals. A survey of 148 academically based and commercial DNA diagnostic laboratories was conducted to determine: (1) the extent of their DNA banking activities; (2) their policies and experiences regarding access to DNA samples and data; (3) the quality assurance measures they employ; and (4) whether they have written policies and/or depositor`s agreements addressing specific issues. These issues include: (1) who may have access to DNA samples and data; (2) whether scientists may have access to anonymous samples or data for research use; (3) whether they have plans to contact depositors or retest samples if improved tests for a disorder become available; (4) disposition of samples at the end of the contract period if the laboratory ceases operations, if storage fees are unpaid, or after a death or divorce; (5) the consequence of unauthorized release, loss, or accidental destruction of samples; and (6) whether depositors may share in profits from the commercialization of tests or treatments developed in part from studies of stored DNA. The results suggest that many laboratories are banking DNA, that many have already amassed a large number of samples, and that a significant number plan to further develop DNA banking as a laboratory service over the next two years. Few laboratories have developed written policies governing DNA banking, and fewer still have drafted documents that define the rights and obligations of the parties. There may be a need for increased regulation of DNA banking and DNA data banking and for better defined policies with respect to protecting individual privacy.

  3. Purification and biochemical characterization of DnaK and its transcriptional activator RpoH from Neisseria gonorrhoeae.

    PubMed

    Narayanan, Shalini; Beckham, Simone A; Davies, John K; Roujeinikova, Anna

    2014-12-01

    DnaK plays a central role in stress response in the important human pathogen Neisseria gonorrhoeae. The genes encoding the DnaK chaperone machine (DnaK/DnaJ/GrpE) in N. gonorrhoeae are transcribed from RpoH (σ(32))-dependent promoters. In this study, we cloned, purified and biochemically characterised N. gonorrhoeae DnaK (NgDnaK) and RpoH. The NgDnaK and RpoH sequences are 73 and 50 % identical to the sequences of their respective E. coli counterparts. Similar to EcDnaK, nucleotide-free NgDnaK exists as a mix of monomers, dimers and higher oligomeric species in solution, and dissociates into monomers on addition of ATP. Like E. coli σ(32), RpoH of N. gonorrhoeae is monomeric in solution. Kinetic analysis of the basal ATPase activity of purified NgDnaK revealed a V max of 193 pmol phosphate released per minute per microgram DnaK (which is significantly higher than reported basal ATPase activity of EcDnaK), and the turnover number against ATP was 0.4 min(-1) under our assay conditions. Nucleotide-free NgDnaK bound a short model substrate, NR-peptide, with micromolar affinity close to that reported for EcDnaK. Our analysis showed that interaction between N. gonorrhoeae RpoH and DnaK appears to be ATP-dependent and non-specific, in stark contrast to the E. coli DnaK system where σ(32) and DnaK interact as monomers even in the absence of ATP. Sequence comparison showed that the DnaK-binding site of σ(32) is not conserved in RpoH. Our findings suggest that the mechanism of DnaK/RpoH recognition in N. gonorrhoeae is different from that in E. coli. PMID:25156536

  4. A DNA-Fullerene Conjugate as a Template for Supramolecular Chromophore Assemblies: Towards DNA-Based Solar Cells.

    PubMed

    Ensslen, Philipp; Gärtner, Stefan; Glaser, Konstantin; Colsmann, Alexander; Wagenknecht, Hans-Achim

    2016-01-26

    A fullerene was covalently attached to a (dA)20 template that serves as structural scaffold to self-assemble an ordered and mixed array of ethynyl-pyrene- and ethynyl-Nile-red-nucleoside conjugates. Fluorescence spectroscopy revealed evidence for energy transfer between the two different chromophores. Moreover, fluorescence quenching is significantly enhanced by the attached fullerene in mixed assemblies of different chromophore ratios. This indicates exciton dissociation by electron transfer from the photo-generated exciton on the chromophore stack to the fullerene. The fullerene-DNA-conjugate was integrated as a photo-active layer in solar cells that showed charge-carrier generation in the spectral regime of all three components of the conjugate. This work clearly demonstrates that DNA is suitable as structural element for chromophore assemblies in future organic optoelectronic devices, such as solar cells. PMID:26689149

  5. DNA Nanotechnology for Cancer Therapy

    PubMed Central

    Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

    2016-01-01

    DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients. PMID:27022418

  6. DNA Nanotechnology for Cancer Therapy.

    PubMed

    Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

    2016-01-01

    DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients. PMID:27022418

  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. PMID:21749560

  8. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOEpatents

    Tabor, S.; Richardson, C.

    1997-03-25

    A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

  9. Quantification of human mitochondrial DNA using synthesized DNA standards.

    PubMed

    Kavlick, Mark F; Lawrence, Helen S; Merritt, R Travis; Fisher, Constance; Isenberg, Alice; Robertson, James M; Budowle, Bruce

    2011-11-01

    Successful mitochondrial DNA (mtDNA) forensic analysis depends on sufficient quantity and quality of mtDNA. A real-time quantitative PCR assay was developed to assess such characteristics in a DNA sample, which utilizes a duplex, synthetic DNA to ensure optimal quality assurance and quality control. The assay's 105-base pair target sequence facilitates amplification of degraded DNA and is minimally homologous to nonhuman mtDNA. The primers and probe hybridize to a region that has relatively few sequence polymorphisms. The assay can also identify the presence of PCR inhibitors and thus indicate the need for sample repurification. The results show that the assay provides information down to 10 copies and provides a dynamic range spanning seven orders of magnitude. Additional experiments demonstrated that as few as 300 mtDNA copies resulted in successful hypervariable region amplification, information that permits sample conservation and optimized downstream PCR testing. The assay described is rapid, reliable, and robust. PMID:21883207

  10. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles

    1997-01-01

    Modified gene encoding a modified DNA polymerase wherein the modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase.

  11. Impact of Alternative DNA Structures on DNA Damage, DNA Repair, and Genetic Instability

    PubMed Central

    Wang, Guliang; Vasquez, Karen M.

    2014-01-01

    Repetitive genomic sequences can adopt a number of alternative DNA structures that differ from the canonical B-form duplex (i.e. non-B DNA). These non-B DNA-forming sequences have been shown to have many important biological functions related to DNA metabolic processes; for example, they may have regulatory roles in DNA transcription and replication. In addition to these regulatory functions, non-B DNA can stimulate genetic instability in the presence or absence of DNA damage, via replication-dependent and/or replication-independent pathways. This review focuses on the interactions of non-B DNA conformations with DNA repair proteins and how these interactions impact genetic instability. PMID:24767258

  12. 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.

  13. Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

    PubMed

    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

  14. 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

  15. PREFACE: Turbulent Mixing and Beyond Turbulent Mixing and Beyond

    NASA Astrophysics Data System (ADS)

    Abarzhi, Snezhana I.; Gauthier, Serge; Rosner, Robert

    2008-10-01

    The goals of the International Conference `Turbulent Mixing and Beyond' are to expose the generic problem of Turbulence and Turbulent Mixing in Unsteady Flows to a wide scientific community, to promote the development of new ideas in tackling the fundamental aspects of the problem, to assist in the application of novel approaches in a broad range of phenomena, where the non-canonical turbulent processes occur, and to have a potential impact on technology. The Conference provides the opportunity to bring together scientists from the areas which include, but are not limited to, high energy density physics, plasmas, fluid dynamics, turbulence, combustion, material science, geophysics, astrophysics, optics and telecommunications, applied mathematics, probability and statistics, and to have their attention focused on the long-standing formidable task. The Turbulent Mixing and Turbulence in Unsteady Flows, including multiphase flows, plays a key role in a wide variety of phenomena, ranging from astrophysical to nano-scales, under either high or low energy density conditions. Inertial confinement and magnetic fusion, light-matter interaction and non-equilibrium heat transfer, properties of materials under high strain rates, strong shocks, explosions, blast waves, supernovae and accretion disks, stellar non-Boussinesq and magneto-convection, planetary interiors and mantle-lithosphere tectonics, premixed and non-premixed combustion, oceanography, atmospheric flows, unsteady boundary layers, hypersonic and supersonic flows, are a few examples to list. A grip on unsteady turbulent processes is crucial for cutting-edge technology such as laser-micromachining and free-space optical telecommunications, and for industrial applications in aeronautics. Unsteady Turbulent Processes are anisotropic, non-local and multi-scale, and their fundamental scaling, spectral and invariant properties depart from the classical Kolmogorov scenario. The singular aspects and similarity of the

  16. Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits.

    PubMed

    Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2016-08-22

    Modern electronic microprocessors use semiconductor logic gates organized on a silicon chip to enable efficient inter-gate communication. Here, arrays of communicating DNA logic gates integrated on a single DNA tile were designed and used to process nucleic acid inputs in a reusable format. Our results lay the foundation for the development of a DNA nanoprocessor, a small and biocompatible device capable of performing complex analyses of DNA and RNA inputs. PMID:27430161

  17. 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.

  18. Mixed states in ferromagnetic superconductors

    SciTech Connect

    Matsumoto, H.; Teshima, R.; Umezawa, H.; Tachiki, M.

    1983-01-01

    A detailed study of the mixed state of the ferromagnetic rare-earth compounds RRh/sub 4/B/sub 4/, R/sub x/Mo/sub 6/S/sub 8/, and R/sub x/Mo/sub 6/Se/sub 6/ is presented. The saturation effect of the magnetic moments is taken into account. Depending on the parameters, there are many types of phase transitions between the type-II/2, type-II/1, and type-I mixed states and the paramagnetic Meissner state, ferromagnetic Meissner state, spin-periodic Meissner state, and the self-induced vortex state. It is predicted that the magnetization can exhibit a variety of unusual modes.

  19. Mixing enhancement using axial flow

    NASA Technical Reports Server (NTRS)

    Papamoschou, Dimitri (Inventor)

    2003-01-01

    A method and an apparatus for enhancing fluid mixing. The method comprises the following: (a) configuring a duct to have an effective outer wall, an effective inner wall, a cross-sectional shape, a first cross-sectional area and an exit area, the first cross-sectional area and the exit area being different in size; (b) generating a first flow at the first cross-sectional area, the first flow having a total pressure and a speed equal to or greater than a local speed of sound; and (c) generating a positive streamwise pressure gradient in a second flow in proximity of the exit area. The second flow results from the first flow. Fluid mixing is enhanced downstream from the duct exit area.

  20. 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.

  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. PMID:27032791

  2. The evolution of mantle mixing.

    PubMed

    Allègre, Claude J

    2002-11-15

    We present a geochemical overview of the canonic model that suggests a two-layer mantle for most of the Earth's history. A change in the Rayleigh number may have modified the convection and now allows the subduction of oceanic plates into the lower mantle, which was not the case in the past. The measurement of stirring time in the source of mid-ocean-ridge basalt, together with Xe- and Pb-isotopic ratios in the mid-ocean-ridge-basalt source, suggests that the upper mantle is separated into two domains, one above the 400 km discontinuity (asthenosphere) with rapid mixing and short residence time, and another between the 400 and 670 km discontinuities with sluggish mixing and a residence time of ca. 1.5 x 10(9) yr. PMID:12460474

  3. DNA Methylation in Osteoarthritis

    PubMed Central

    den Hollander, Wouter; Meulenbelt, Ingrid

    2015-01-01

    Osteoarthritis (OA) is a prevalent disease of articular joints and primarily characterized by degradation and calcification of articular cartilage. Presently, no effective treatment other than pain relief exists and patients ultimately need to undergo replacement surgery of the affected joint. During disease progression articular chondrocytes, the single cell type present in articular cartilage, show altered transcriptional profiles and undergo phenotypic changes that resemble the terminal differentiation route apparent in growth plate chondrocytes. Hence, given its prominent function in both regulating gene expression and maintaining cellular phenotypes, DNA methylation of CpG dinucleotides is intensively studied in the context of OA. An increasing number of studies have been published that employed a targeted approach on genes known to play a role in OA pathophysiology. As of such, it has become clear that OA responsive DNA methylation changes seem to mediate disease associated aberrant gene expression. Furthermore, established OA susceptibility alleles such as GDF5 and DIO2 appear to confer OA risk via DNA methylation and respective pathophysiological expression changes. In more recent years, genome wide profiling of DNA methylation in OA affected articular cartilage has emerged as a powerful tool to address the epigenetic changes in their entirety, which has resulted in the identification of putative patient subgroups as well as generic OA associated pathways. PMID:27019616

  4. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor); Breaker, Ronald R. (Inventor)

    1998-01-01

    The present invention discloses deoxyribonucleic acid enzymes--catalytic or enzymatic DNA molecules--capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

  5. TRANSFECTION WITH BACULOVIRUS DNA

    EPA Science Inventory

    Purified DNA from the nuclear polyhedrosis viruses of Autographa californica (AcM NPV) and Rachiplusia ou (RoM NPV) were found to be infectious in TN-368 cells employing the calcium phosphate precipitation technique (F.L. Graham and A.J. van der Eb, Virology, 52, 456-467, 1973). ...

  6. DNA Replication Origins

    PubMed Central

    Leonard, Alan C.; Méchali, Marcel

    2013-01-01

    The onset of genomic DNA synthesis requires precise interactions of specialized initiator proteins with DNA at sites where the replication machinery can be loaded. These sites, defined as replication origins, are found at a few unique locations in all of the prokaryotic chromosomes examined so far. However, replication origins are dispersed among tens of thousands of loci in metazoan chromosomes, thereby raising questions regarding the role of specific nucleotide sequences and chromatin environment in origin selection and the mechanisms used by initiators to recognize replication origins. Close examination of bacterial and archaeal replication origins reveals an array of DNA sequence motifs that position individual initiator protein molecules and promote initiator oligomerization on origin DNA. Conversely, the need for specific recognition sequences in eukaryotic replication origins is relaxed. In fact, the primary rule for origin selection appears to be flexibility, a feature that is modulated either by structural elements or by epigenetic mechanisms at least partly linked to the organization of the genome for gene expression. PMID:23838439

  7. DNA Methylation in Osteoarthritis.

    PubMed

    den Hollander, Wouter; Meulenbelt, Ingrid

    2015-12-01

    Osteoarthritis (OA) is a prevalent disease of articular joints and primarily characterized by degradation and calcification of articular cartilage. Presently, no effective treatment other than pain relief exists and patients ultimately need to undergo replacement surgery of the affected joint. During disease progression articular chondrocytes, the single cell type present in articular cartilage, show altered transcriptional profiles and undergo phenotypic changes that resemble the terminal differentiation route apparent in growth plate chondrocytes. Hence, given its prominent function in both regulating gene expression and maintaining cellular phenotypes, DNA methylation of CpG dinucleotides is intensively studied in the context of OA. An increasing number of studies have been published that employed a targeted approach on genes known to play a role in OA pathophysiology. As of such, it has become clear that OA responsive DNA methylation changes seem to mediate disease associated aberrant gene expression. Furthermore, established OA susceptibility alleles such as GDF5 and DIO2 appear to confer OA risk via DNA methylation and respective pathophysiological expression changes. In more recent years, genome wide profiling of DNA methylation in OA affected articular cartilage has emerged as a powerful tool to address the epigenetic changes in their entirety, which has resulted in the identification of putative patient subgroups as well as generic OA associated pathways. PMID:27019616

  8. DNA-coated microcrystals.

    PubMed

    Kreiner, Michaela; Fuglevand, Geeta; Moore, Barry D; Parker, Marie-Claire

    2005-06-01

    Coprecipitation leads to self-assembly of bioactive DNA on the surface of salt, sugar or amino-acid crystals and provides a rapid inexpensive immobilization method suitable for preparing dry-powder formulations of nucleic acids, useful for storage, imaging and drug delivery. PMID:15917916

  9. Nutrients and DNA Methylation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Epigenetics is a new mechanism responsible for development, aging, and disease process such as cancer development. One major epigenetic phenomenon is DNA methylation, which attributes to gene expression and integrity. Deepening the knowledge on one-carbon metabolism is very important to understandin...

  10. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  11. Field Deployable DNA analyzer

    SciTech Connect

    Wheeler, E; Christian, A; Marion, J; Sorensen, K; Arroyo, E; Vrankovich, G; Hara, C; Nguyen, C

    2005-02-09

    This report details the feasibility of a field deployable DNA analyzer. Steps for swabbing cells from surfaces and extracting DNA in an automatable way are presented. Since enzymatic amplification reactions are highly sensitive to environmental contamination, sample preparation is a crucial step to make an autonomous deployable instrument. We perform sample clean up and concentration in a flow through packed bed. For small initial samples, whole genome amplification is performed in the packed bed resulting in enough product for subsequent PCR amplification. In addition to DNA, which can be used to identify a subject, protein is also left behind, the analysis of which can be used to determine exposure to certain substances, such as radionuclides. Our preparative step for DNA analysis left behind the protein complement as a waste stream; we determined to learn if the proteins themselves could be analyzed in a fieldable device. We successfully developed a two-step lateral flow assay for protein analysis and demonstrate a proof of principle assay.

  12. DNA tagged microparticles

    DOEpatents

    Farquar, George R.; Leif, Roald N.; Wheeler, Elizabeth

    2016-03-22

    In one embodiment, a product includes a plurality of particles, each particle including: a carrier that includes a non-toxic material; and at least one DNA barcode coupled to the carrier, where the particles each have a diameter in a range from about 1 nanometer to about 100 microns.

  13. Making environmental DNA count.

    PubMed

    Kelly, Ryan P

    2016-01-01

    The arc of reception for a new technology or method--like the reception of new information itself--can pass through predictable stages, with audiences' responses evolving from 'I don't believe it', through 'well, maybe' to 'yes, everyone knows that' to, finally, 'old news'. The idea that one can sample a volume of water, sequence DNA out of it, and report what species are living nearby has experienced roughly this series of responses among biologists, beginning with the microbial biologists who developed genetic techniques to reveal the unseen microbiome. 'Macrobial' biologists and ecologists--those accustomed to dealing with species they can see and count--have been slower to adopt such molecular survey techniques, in part because of the uncertain relationship between the number of recovered DNA sequences and the abundance of whole organisms in the sampled environment. In this issue of Molecular Ecology Resources, Evans et al. (2015) quantify this relationship for a suite of nine vertebrate species consisting of eight fish and one amphibian. Having detected all of the species present with a molecular toolbox of six primer sets, they consistently find DNA abundances are associated with species' biomasses. The strength and slope of this association vary for each species and each primer set--further evidence that there is no universal parameter linking recovered DNA to species abundance--but Evans and colleagues take a significant step towards being able to answer the next question audiences tend to ask: 'Yes, but how many are there?' PMID:26768195

  14. Melting behavior and different bound states in three-stranded DNA models.

    PubMed

    Maji, Jaya; Bhattacharjee, Somendra M; Seno, Flavio; Trovato, Antonio

    2014-01-01

    Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and Scheraga models). Within this framework, the existence of a three-stranded DNA bound state in conditions where a duplex DNA would be in the denaturated state was recently predicted from a study of three directed polymer models on simplified hierarchical lattices (d>2) and in 1+1 dimensions. Such a phenomenon which is similar to the Efimov effect in nuclear physics was named Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a Sierpinski gasket of dimensions d<2 by assigning extra weight factors to fork openings and closings, to induce a two-strand DNA melting. In such a context we can find again the existence of the Efimov-DNA-like state but quite surprisingly we discover also the presence of a different phase, to be called a mixed state, where the strands are pair-wise bound but without three chain contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the mixed phase is a thermodynamic phase. PMID:24580186

  15. Canine Mammary Mixed Tumours: A Review

    PubMed Central

    Dantas Cassali, Geovanni; Cavalheiro Bertagnolli, Angélica; Ferreira, Enio; Araújo Damasceno, Karine; de Oliveira Gamba, Conrado; Bonolo de Campos, Cecília

    2012-01-01

    Mammary mixed tumours are the most frequent neoplasias in female dogs. In humans, mixed tumours are frequently found in the salivary glands and are known as pleomorphic adenomas. In addition to their histomorphologic similarities, mixed tumours and pleomorphic adenomas have the potential to become malignant and give rise to carcinomas in mixed tumours and carcinomas ex-pleomorphic adenoma, respectively. The factors associated with malignant transformation are still poorly known in the case of canine mixed tumours. However, this form of neoplasia tends to be associated with a better prognosis than other malignant histological types. This paper discusses the main features associated with female canine mammary mixed tumours. PMID:23193497

  16. Flavor mixing and quark decay

    NASA Astrophysics Data System (ADS)

    Chu Wang, Ling-Lie

    1981-01-01

    Since this is an experimental conference I shall begin my talk with that spirit. We can view that the subject of my talk as a result of ''the ORY Collaboration'' with more than fifty theorists involved. The topics covered are the results of four task forces: I. The mixing Matrix Task Force, II.. The D-decay Task Force, III. the Boredom-Escaping Group and IV. the Far-and-Beyond Group.

  17. Domain swapping reveals that the C- and N-terminal domains of DnaG and DnaB, respectively, are functional homologues.

    PubMed

    Chintakayala, Kiran; Larson, Marilynn A; Grainger, William H; Scott, David J; Griep, Mark A; Hinrichs, Steven H; Soultanas, Panos

    2007-03-01

    The bacterial primase (DnaG)-helicase (DnaB) interaction is mediated by the C-terminal domain of DnaG (p16) and a linker that joins the N- and C-terminal domains (p17 and p33 respectively) of DnaB. The crystal and nuclear magnetic resonance structures of p16 from Escherichia coli and Bacillus stearothermophilus DnaG proteins revealed a unique structural homology with p17, despite the lack of amino acid sequence similarity. The functional significance of this is not clear. Here, we have employed a 'domain swapping' approach to replace p17 with its structural homologue p16 to create chimeras. p33 alone hydrolyses ATP but exhibits no helicase activity. Fusing p16 (p16-p33) or DnaG (G-p33) to the N-terminus of p33 produced chimeras with partially restored helicase activities. Neither chimera interacted with DnaG. The p16-p33 chimera formed hexamers while G-p33 assembled into tetramers. Furthermore, G-p33 and DnaB formed mixed oligomers with ATPase activity better than that of the DnaB/DnaG complex and helicase activity better than the sum of the individual DnaB and G-p33 activities but worse than that of the DnaB/DnaG complex. Our combined data provide direct evidence that p16 and p17 are not only structural but also functional homologues, albeit their amino acid composition differences are likely to influence their precise roles. PMID:17367384

  18. Emerging roles of DNA-PK besides DNA repair.

    PubMed

    Kong, Xianming; Shen, Ying; Jiang, Na; Fei, Xin; Mi, Jun

    2011-08-01

    The DNA-dependent protein kinase (DNA-PK) is a DNA-activated serine/threonine protein kinase, and abundantly expressed in almost all mammalian cells. The roles of DNA-PK in DNA-damage repair pathways, including non-homologous end-joining (NHEJ) repair and homologous recombinant (HR) repair, have been studied intensively. However, the high levels of DNA-PK in human cells are somewhat paradoxical in that it does not impart any increased ability to repair DNA damage. If DNA-PK essentially exceeds the demand for DNA damage repair, why do human cells universally express such high levels of this huge complex? DNA-PK has been recently reported to be involved in metabolic gene regulation in response to feeding/insulin stimulation; our studies have also suggested a role of DNA-PK in the regulation of the homeostasis of cell proliferation. These novel findings expand our horizons about the importance of DNA-PK. PMID:21514376

  19. Borrowing nuclear DNA helicases to protect mitochondrial DNA.

    PubMed

    Ding, Lin; Liu, Yilun

    2015-01-01

    In normal cells, mitochondria are the primary organelles that generate energy, which is critical for cellular metabolism. Mitochondrial dysfunction, caused by mitochondrial DNA (mtDNA) mutations or an abnormal mtDNA copy number, is linked to a range of human diseases, including Alzheimer's disease, premature aging‎ and cancer. mtDNA resides in the mitochondrial lumen, and its duplication requires the mtDNA replicative helicase, Twinkle. In addition to Twinkle, many DNA helicases, which are encoded by the nuclear genome and are crucial for nuclear genome integrity, are transported into the mitochondrion to also function in mtDNA replication and repair. To date, these helicases include RecQ-like helicase 4 (RECQ4), petite integration frequency 1 (PIF1), DNA replication helicase/nuclease 2 (DNA2) and suppressor of var1 3-like protein 1 (SUV3). Although the nuclear functions of some of these DNA helicases have been extensively studied, the regulation of their mitochondrial transport and the mechanisms by which they contribute to mtDNA synthesis and maintenance remain largely unknown. In this review, we attempt to summarize recent research progress on the role of mammalian DNA helicases in mitochondrial genome maintenance and the effects on mitochondria-associated diseases. PMID:25984607

  20. 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.