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Sample records for multiple dna dyes

  1. Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature

    DEFF Research Database (Denmark)

    Guðnason, Haukur; Dufva, Hans Martin; Bang, Dang Duong

    2007-01-01

    investigate 15 different intercalating DNA dyes for their inhibitory effects on PCR, effects on DNA melting temperature and possible preferential binding to GC-rich sequences. Our results demonstrated that in contrast to the results of SYBR Green I, two intercalating dyes SYTO-13 and SYTO-82 do not inhibit......The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applications utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include...... the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve analysis. Although a few alternative dyes without some of these limitations have been recently proposed, no large-scale investigation into the properties of intercalating dyes has been performed. In this study, we...

  2. Part-per-trillion level detection of estradiol by competitive fluorescence immunoassay using DNA/dye conjugate as antibody multiple labels.

    Science.gov (United States)

    Zhu, Shengchao; Zhang, Qin; Guo, Liang-Hong

    2008-08-22

    Fluorescent organic dyes are currently the standard signal-generating labels used in microarray quantification. However, new labeling strategies are needed to meet the demand for high sensitivity in the detection of low-abundance proteins and small molecules. In this report, a long-chain DNA/dye conjugate was used to attach multiple fluorescence labels on antibodies to improve signal intensity and immunoassay sensitivity. Compared with the 30 base-pair (bp) oligonucleotide used in our previous work [Q. Zhang, L.-H. Guo, Bioconjugate Chem. 18 (2007) 1668-1672], conjugation of a 219 bp DNA in solution with a fluorescent DNA binder SYBR Green I resulted in more than sixfold increase in signal intensity, consistent with the increase in bp number. In a direct immunoassay for the detection of goat anti-mouse IgG in a mouse IgG-coated 96-well plate, the long DNA conjugate label also produced higher fluorescence than the short one, accompanied by about 15-fold improvement in the detection limit. To demonstrate its advantage in real applications, the DNA/dye conjugate was employed in the competitive immunoassay of 17beta-estradiol, a clinically and environmentally important analyte. The biotin-terminated DNA was attached to biotinylated anti-estradiol antibody through the biotin/streptavidin/biotin bridge after the immuno-reaction was completed, followed by conjugation with SYBR Green I. The limit of detection for 17beta-estradiol is 1.9 pg mL(-1), which is 200-fold lower than the assay using fluorescein-labeled antibodies. The new multiple labeling strategy uses readily available reagents, and is also compatible with current biochip platform. It has great potential in the sensitive detection of protein and antibody microarrays.

  3. Incorporating Multiple Energy Relay Dyes in Liquid Dye-Sensitized Solar Cells

    KAUST Repository

    Yum, Jun-Ho; Hardin, Brian E.; Hoke, Eric T.; Baranoff, Etienne; Zakeeruddin, Shaik M.; Nazeeruddin, Mohammad K.; Torres, Tomas; McGehee, Michael D.; Grä tzel, Michael

    2011-01-01

    Panchromatic response is essential to increase the light-harvesting efficiency in solar conversion systems. Herein we show increased light harvesting from using multiple energy relay dyes inside dye-sensitized solar cells. Additional photoresponse

  4. Incorporating Multiple Energy Relay Dyes in Liquid Dye-Sensitized Solar Cells

    KAUST Repository

    Yum, Jun-Ho

    2011-01-05

    Panchromatic response is essential to increase the light-harvesting efficiency in solar conversion systems. Herein we show increased light harvesting from using multiple energy relay dyes inside dye-sensitized solar cells. Additional photoresponse from 400-590 nm matching the optical window of the zinc phthalocyanine sensitizer was observed due to Förster resonance energy transfer (FRET) from the two energy relay dyes to the sensitizing dye. The complementary absorption spectra of the energy relay dyes and high excitation transfer efficiencies result in a 35% increase in photovoltaic performance. © 2011 Wiley-VCH Verlag GmbH& Co. KGaA.

  5. Photodegradation in multiple-dye luminescent solar concentrators

    International Nuclear Information System (INIS)

    Mooney, Alex M.; Warner, Kathryn E.; Fontecchio, Paul J.; Zhang, Yu-Zhong; Wittmershaus, Bruce P.

    2013-01-01

    Combining multiple organic dyes to form a fluorescence resonance energy transfer (FRET) network is a useful strategy for extending the spectral range of sunlight absorbed by a luminescent solar concentrator (LSC). Excitation transfer out of the higher energy level dyes in the transfer series competes effectively with their photodegradation rates. Improvements in photostability up to a factor of 18 are observed for the first dye in the FRET series. FRET networks are shown to be a viable means of decreasing the rate of photodegradation of organic dyes used in LSCs. This comes at the expense of the final dye in the network; the depository of most of the excitations created by absorbing sunlight. The photostability and performance of an efficient FRET LSC rest heavily on the photostability and fluorescence quantum yield of the final dye. -- Highlights: • Photodegradation kinetics of multiple-dye FRET LSCs are reported. • The FRET network decreased the first dye's photodegradation rate by a factor of 18. • The final dye in the FRET LSC protects other dyes at its own expense. • The final dye must have excellent photostability and fluorescence quantum yield

  6. Extension lifetime for dye-sensitized solar cells through multiple dye adsorption/desorption process

    Science.gov (United States)

    Chiang, Yi-Fang; Chen, Ruei-Tang; Shen, Po-Shen; Chen, Peter; Guo, Tzung-Fang

    2013-03-01

    In this study, we propose a novel concept of extending the lifetime of dye-sensitized solar cells (DSCs) and reducing the costs of re-conditioning DSCs by recycling the FTO/TiO2 substrates. The photovoltaic performances of DSCs using substrates with various cycles of dye uptake and rinse off history are tested. The results show that dye adsorption and Voc are significantly increased under multiple dye adsorption/desorption process and resulted in the improvement of power conversion efficiency. Moreover, the dyeing kinetics is faster after multiple recycling processes, which is favorable for the industrial application. With surface analysis and charge transport characteristics, we also demonstrate the optimal functionality of TiO2/dye interface for the improved Voc and efficiency. The results confirm that the improved performances are due to increased dye loading and dense packing of dye molecules. Our results are beneficial for the understanding on the extension of DSCs lifetime after long-term operation in the application of DSC modules. This approach may also be applied in the replacement of newly synthesized photosensitizes to the active cells.

  7. Screening of freshwater fungi for decolorizing multiple synthetic dyes.

    Science.gov (United States)

    Yang, Panpan; Shi, Wenxiao; Wang, Hongkai; Liu, Hongmei

    The biodegradation of synthetic dyes by fungi is emerging as an effective and promising approach. In the present study, freshwater fungal strains isolated from submerged woods were screened for the decolorization of 7 synthetic dyes. Subsequently, 13 isolates with high decolorization capability were assessed in a liquid system; they belonged to 9 different fungal species. Several strains exhibited a highly effective decolorization of multiple types of dyes. New absorbance peaks appeared after the treatment with 3 fungal strains, which suggests that a biotransformation process occurred through fungal biodegradation. These results showed the unexploited and valuable capability of freshwater fungi for the treatment of dye-containing effluents. The ability of certain fungi to decolorize dyes is reported here for the first time. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  8. Investigation of hair dye deposition, hair color loss, and hair damage during multiple oxidative dyeing and shampooing cycles.

    Science.gov (United States)

    Zhang, Guojin; McMullen, Roger L; Kulcsar, Lidia

    2016-01-01

    Color fastness is a major concern for consumers and manufacturers of oxidative hair dye products. Hair dye loss results from multiple wash cycles in which the hair dye is dissolved by water and leaches from the hair shaft. In this study, we carried out a series of measurements to help us better understand the kinetics of the leaching process and pathways associated with its escape from the fiber. Hair dye leaching kinetics was measured by suspending hair in a dissolution apparatus and monitoring the dye concentration in solution (leached dye) with an ultraviolet-visible spectrophotometer. The physical state of dye deposited in hair fibers was evaluated by a reflectance light microscopy technique, based on image stacking, allowing enhanced depth of field imaging. The dye distribution within the fiber was monitored by infrared spectroscopic imaging of hair fiber cross sections. Damage to the ultrafine structure of the hair cuticle (surface, endocuticle, and cell membrane complex) and cortex (cell membrane complex) was determined in hair cross sections and on the hair fiber surface with atomic force microscopy. Using differential scanning calorimetry, we investigated how consecutive coloring and leaching processes affect the internal proteins of hair. Further, to probe the surface properties of hair we utilized contact angle measurements. This study was conducted on both pigmented and nonpigmented hair to gain insight into the influence of melanin on the hair dye deposition and leaching processes. Both types of hair were colored utilizing a commercial oxidative hair dye product based on pyrazole chemistry.

  9. Preparation of fluorescent-dye-labeled cDNA from RNA for microarray hybridization.

    Science.gov (United States)

    Ares, Manuel

    2014-01-01

    This protocol describes how to prepare fluorescently labeled cDNA for hybridization to microarrays. It consists of two steps: first, a mixture of anchored oligo(dT) and random hexamers is used to prime amine-modified cDNA synthesis by reverse transcriptase using a modified deoxynucleotide with a reactive amine group (aminoallyl-dUTP) and an RNA sample as a template. Second, the cDNA is purified and exchanged into bicarbonate buffer so that the amine groups in the cDNA react with the dye N-hydroxysuccinimide (NHS) esters, covalently joining the dye to the cDNA. The dye-coupled cDNA is purified again, and the amount of dye incorporated per microgram of cDNA is determined.

  10. Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions.

    Science.gov (United States)

    Nakayama, Yuki; Yamaguchi, Hiromi; Einaga, Naoki; Esumi, Mariko

    2016-01-01

    The Qubit fluorometer is a DNA quantification device based on the fluorescence intensity of fluorescent dye binding to double-stranded DNA (dsDNA). Qubit is generally considered useful for checking DNA quality before next-generation sequencing because it measures intact dsDNA. To examine the most accurate and suitable methods for quantifying DNA for quality assessment, we compared three quantification methods: NanoDrop, which measures UV absorbance; Qubit; and quantitative PCR (qPCR), which measures the abundance of a target gene. For the comparison, we used three types of DNA: 1) DNA extracted from fresh frozen liver tissues (Frozen-DNA); 2) DNA extracted from formalin-fixed, paraffin-embedded liver tissues comparable to those used for Frozen-DNA (FFPE-DNA); and 3) DNA extracted from the remaining fractions after RNA extraction with Trizol reagent (Trizol-DNA). These DNAs were serially diluted with distilled water and measured using three quantification methods. For Frozen-DNA, the Qubit values were not proportional to the dilution ratio, in contrast with the NanoDrop and qPCR values. This non-proportional decrease in Qubit values was dependent on a lower salt concentration, and over 1 mM NaCl in the DNA solution was required for the Qubit measurement. For FFPE-DNA, the Qubit values were proportional to the dilution ratio and were lower than the NanoDrop values. However, electrophoresis revealed that qPCR reflected the degree of DNA fragmentation more accurately than Qubit. Thus, qPCR is superior to Qubit for checking the quality of FFPE-DNA. For Trizol-DNA, the Qubit values were proportional to the dilution ratio and were consistently lower than the NanoDrop values, similar to FFPE-DNA. However, the qPCR values were higher than the NanoDrop values. Electrophoresis with SYBR Green I and single-stranded DNA (ssDNA) quantification demonstrated that Trizol-DNA consisted mostly of non-fragmented ssDNA. Therefore, Qubit is not always the most accurate method for

  11. S - and N-alkylating agents diminish the fluorescence of fluorescent dye-stained DNA.

    Science.gov (United States)

    Giesche, Robert; John, Harald; Kehe, Kai; Schmidt, Annette; Popp, Tanja; Balzuweit, Frank; Thiermann, Horst; Gudermann, Thomas; Steinritz, Dirk

    2017-01-25

    Sulfur mustard (SM), a chemical warfare agent, causes DNA alkylation, which is believed to be the main cause of its toxicity. SM DNA adducts are commonly used to verify exposure to this vesicant. However, the required analytical state-of-the-art mass-spectrometry methods are complex, use delicate instruments, are not mobile, and require laboratory infrastructure that is most likely not available in conflict zones. Attempts have thus been made to develop rapid detection methods that can be used in the field. The analysis of SM DNA adducts (HETE-G) by immunodetection is a convenient and suitable method. For a diagnostic assessment, HETE-G levels must be determined in relation to the total DNA in the sample. Total DNA can be easily visualized by the use of fluorescent DNA dyes. This study examines whether SM and related compounds affect total DNA staining, an issue that has not been investigated before. After pure DNA was extracted from human keratinocytes (HaCaT cells), DNA was exposed to different S- and N-alkylating agents. Our experiments revealed a significant, dose-dependent decrease in the fluorescence signal of fluorescent dye-stained DNA after exposure to alkylating agents. After mass spectrometry and additional fluorescence measurements ruled out covalent modifications of ethidium bromide (EthBr) by SM, we assumed that DNA crosslinks caused DNA condensation and thereby impaired access of the fluorescent dyes to the DNA. DNA digestion by restriction enzymes restored fluorescence, a fact that strengthened our hypothesis. However, monofunctional agents, which are unable to crosslink DNA, also decreased the fluorescence signal. In subsequent experiments, we demonstrated that protons produced during DNA alkylation caused a pH decrease that was found responsible for the reduction in fluorescence. The use of an appropriate buffer system eliminated the adverse effect of alkylating agents on DNA staining with fluorescent dyes. An appropriate buffer system is thus

  12. Two-photon fluorescence and fluorescence imaging of two styryl heterocyclic dyes combined with DNA.

    Science.gov (United States)

    Gao, Chao; Liu, Shu-yao; Zhang, Xian; Liu, Ying-kai; Qiao, Cong-de; Liu, Zhao-e

    2016-03-05

    Two new styryl heterocyclic two-photon (TP) materials, 4-[4-(N-methyl)styrene]-imidazo [4,5-f][1,10] phenanthroline-benzene iodated salt (probe-1) and 4,4-[4-(N-methyl)styrene]-benzene iodated salt (probe-2) were successfully synthesized and studied as potential fluorescent probes of DNA detection. The linear and nonlinear photophysical properties of two compounds in different solvents were investigated. The absorption, one- and two-photon fluorescent spectra of the free dye and dye-DNA complex were also examined to evaluate their photophysical properties. The binding constants of dye-DNA were obtained according to Scatchard equation with good values. The results showed that two probes could be used as fluorescent DNA probes by two-photon excitation, and TP fluorescent properties of probe-1 are superior to that of probe-2. The fluorescent method date indicated that the mechanisms of dye-DNA complex interaction may be groove binding for probe-1 and electrostatic interaction for probe-2, respectively. The MTT assay experiments showed two probes are low toxicity. Moreover, the TP fluorescence imaging of DNA detection in living cells at 800 nm indicated that the ability to locate in cell nuclei of probe-1 is better than that of probe-2. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model.

    Science.gov (United States)

    Moreira, Bernardo G; You, Yong; Owczarzy, Richard

    2015-03-01

    Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5' end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2 kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine-purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications. Copyright © 2015. Published by Elsevier B.V.

  14. DNA photocleavage by DNA and DNA-LNA amino acid-dye conjugates

    Czech Academy of Sciences Publication Activity Database

    Biton, A.; Ezra, A.; Kašpárková, Jana; Brabec, Viktor; Yavin, E.

    2010-01-01

    Roč. 21, č. 4 (2010), s. 616-621 ISSN 1043-1802 R&D Projects: GA AV ČR(CZ) IAA400040803 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA * photocleavage * triplex forming oligonucleotides Subject RIV: BO - Biophysics Impact factor: 5.002, year: 2010

  15. Protein search for multiple targets on DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lange, Martin [Johannes Gutenberg University, Mainz 55122 (Germany); Department of Chemistry, Rice University, Houston, Texas 77005 (United States); Kochugaeva, Maria [Department of Chemistry, Rice University, Houston, Texas 77005 (United States); Kolomeisky, Anatoly B., E-mail: tolya@rice.edu [Department of Chemistry, Rice University, Houston, Texas 77005 (United States); Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005 (United States)

    2015-09-14

    Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic approach that takes into account most relevant physical-chemical processes and leads to fully analytical description of all dynamic properties. Specifically, systems with two and three targets have been explicitly investigated. It is found that multiple targets in most cases accelerate the search in comparison with a single target situation. However, the acceleration is not always proportional to the number of targets. Surprisingly, there are even situations when it takes longer to find one of the multiple targets in comparison with the single target. It depends on the spatial position of the targets, distances between them, average scanning lengths of protein molecules on DNA, and the total DNA lengths. Physical-chemical explanations of observed results are presented. Our predictions are compared with experimental observations as well as with results from a continuum theory for the protein search. Extensive Monte Carlo computer simulations fully support our theoretical calculations.

  16. Effects on DNA repair in human lymphocytes exposed to the food dye tartrazine yellow.

    Science.gov (United States)

    Soares, Bruno Moreira; Araújo, Taíssa Maíra Thomaz; Ramos, Jorge Amando Batista; Pinto, Laine Celestino; Khayat, Bruna Meireles; De Oliveira Bahia, Marcelo; Montenegro, Raquel Carvalho; Burbano, Rommel Mario Rodríguez; Khayat, André Salim

    2015-03-01

    Tartrazine is a food additive that belongs to a class of artificial dyes and contains an azo group. Studies about its genotoxic, cytotoxic and mutagenic effects are controversial and, in some cases, unsatisfactory. This work evaluated the potential in vitro cytotoxicity, genotoxicity and effects on DNA repair of human lymphocytes exposed to the dye. We assessed the cytotoxicity of tartrazine by 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide test and the response of DNA repair through comet assay (alkaline version). We used different concentrations of the dye, ranging from 0.25-64.0 mM. The results demonstrated that tartrazine has no cytotoxic effects. However, this dye had a significant genotoxic effect at all concentrations tested. Although most of the damage was amenable to repair, some damage remained higher than positive control after 24 h of repair. These data demonstrate that tartrazine may be harmful to health and its prolonged use could trigger carcinogenesis. Copyright© 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  17. Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation.

    Science.gov (United States)

    Dixit, Aparna Banerjee; Ray, Krishanu; Black, Lindsay W

    2012-12-11

    Viral genome packaging into capsids is powered by high-force-generating motor proteins. In the presence of all packaging components, ATP-powered translocation in vitro expels all detectable tightly bound YOYO-1 dye from packaged short dsDNA substrates and removes all aminoacridine dye from packaged genomic DNA in vivo. In contrast, in the absence of packaging, the purified T4 packaging ATPase alone can only remove up to ∼1/3 of DNA-bound intercalating YOYO-1 dye molecules in the presence of ATP or ATP-γ-S. In sufficient concentration, intercalating dyes arrest packaging, but rare terminase mutations confer resistance. These distant mutations are highly interdependent in acquiring function and resistance and likely mark motor contact points with the translocating DNA. In stalled Y-DNAs, FRET has shown a decrease in distance from the phage T4 terminase C terminus to portal consistent with a linear motor, and in the Y-stem DNA compression between closely positioned dye pairs. Taken together with prior FRET studies of conformational changes in stalled Y-DNAs, removal of intercalating compounds by the packaging motor demonstrates conformational change in DNA during normal translocation at low packaging resistance and supports a proposed linear "DNA crunching" or torsional compression motor mechanism involving a transient grip-and-release structural change in B form DNA.

  18. Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe

    Directory of Open Access Journals (Sweden)

    Dominika Żurek-Biesiada

    2016-06-01

    Full Text Available Single Molecule Localization Microscopy (SMLM is a recently emerged optical imaging method that was shown to achieve a resolution in the order of tens of nanometers in intact cells. Novel high resolution imaging methods might be crucial for understanding of how the chromatin, a complex of DNA and proteins, is arranged in the eukaryotic cell nucleus. Such an approach utilizing switching of a fluorescent, DNA-binding dye Vybrant® DyeCycle™ Violet has been previously demonstrated by us (Żurek-Biesiada et al., 2015 [1]. Here we provide quantitative information on the influence of the chemical environment on the behavior of the dye, discuss the variability in the DNA-associated signal density, and demonstrate direct proof of enhanced structural resolution. Furthermore, we compare different visualization approaches. Finally, we describe various opportunities of multicolor DNA/SMLM imaging in eukaryotic cell nuclei.

  19. Toxicity, mutagenicity and transport in Saccharomyces cerevisiae of three popular DNA intercalating fluorescent dyes.

    Science.gov (United States)

    Sayas, Enric; García-López, Federico; Serrano, Ramón

    2015-09-01

    We have compared the toxicity, mutagenicity and transport in Saccharomyces cerevisiae of three DNA-intercalating fluorescent dyes widely used to stain DNA in gels. Safety data about ethidium bromide (EtBr) are contradictory, and two compounds of undisclosed structure (Redsafe and Gelred) have been proposed as safe alternatives. Our results indicate that all three compounds inhibit yeast growth, with Gelred being the most inhibitory and also the only one causing cell death. EtBr and Gelred, but not Redsafe, induce massive formation of petite (non-respiratory) mutants, but only EtBr induces massive loss of mitochondrial DNA. All three compounds increase reversion of a chromosomal point mutation (lys2-801(amber) ), with Gelred being the most mutagenic and Redsafe the least. These dyes are all cationic and are probably taken by cells through non-selective cation channels. We could measure the glucose-energized transport of EtBr and Gelred inside the cells, while uptake of Redsafe was below our detection limit. We conclude that although all three compounds are toxic and mutagenic in the yeast system, Redsafe is the safest for yeast, probably because of very limited uptake by these cells. Copyright © 2015 John Wiley & Sons, Ltd.

  20. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  1. Novel synthetic approach to asymmetric monocationic trimethine cyanine dyes derived from N-ethyl quinolinum moiety. Combined fluorescent and ICD probes for AT-DNA labelling

    Energy Technology Data Exchange (ETDEWEB)

    Kurutos, Atanas [Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry, University of Sofia, 1164 Sofia (Bulgaria); Crnolatac, Ivo; Orehovec, Iva [Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb (Croatia); Gadjev, Nikolai [Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry, University of Sofia, 1164 Sofia (Bulgaria); Piantanida, Ivo, E-mail: pianta@irb.hr [Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb (Croatia); Deligeorgiev, Todor, E-mail: ohtak@chem.uni-sofia.bg [Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry, University of Sofia, 1164 Sofia (Bulgaria)

    2016-06-15

    Two asymmetric monocationic trimethine cyanine dyes were obtained via condensation reaction between 2-methylbenzothialolium salts containing various (aliphatic and benzyl) substituents on the nitrogen atom of the benzothiazolic chromophore, and 1-ethyl−4-(2-(phenylamine)vinyl)quinolin−1-ium iodide, by a novel improved method at room temperature under mild conditions. Both compounds bind non-covalently to double stranded DNA and RNA by micromolar affinity, but give highly selective fluorescent response>650 nm for only AT-DNA sequences at excess of DNA over dye, combined with equally AT-DNA selective ICD response at dye/DNA crowded conditions (r{sub [dye]/[AT-DNA]}>0.2)-namely ICD bands (attributed to dye-dimer formation) allow determination of AT-DNA at submicromolar concentrations. Selectivity was attributed to particular steric properties of AT-DNA minor groove in respect to other studied ds-DNA/RNA. Comparison of aliphatic- and benzyl- dye showed that only aliphatic- derivative revealed ICD band upon binding to AU-RNA major groove and short AT-sequences in mixed sequence (ct-)DNA.

  2. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Myungkoo [Iowa State Univ., Ames, IA (United States)

    1995-12-06

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ~25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G2 or G3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N2-dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N2-dG.

  3. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    International Nuclear Information System (INIS)

    Suh, Myungkoo.

    1995-01-01

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ∼ 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G 2 or G 3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N 2 -dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N 2 -dG

  4. A performance study on three qPCR quantification kits and their compatibilities with the 6-dye DNA profiling systems.

    Science.gov (United States)

    Lin, Sze-Wah; Li, Christina; Ip, Stephen C Y

    2018-03-01

    DNA quantification plays an integral role in forensic DNA profiling. Not only does it estimate the total amount of amplifiable human autosomal and male DNA to ensure optimal amplification of target DNA for subsequent analysis, but also assesses the extraction efficiency and purity of the DNA extract. Latest DNA quantification systems even offer an estimate for the degree of DNA degradation in a sample. Here, we report the performance of three new generation qPCR kits, namely Investigator ® Quantiplex HYres Kit from QIAGEN, Quantifiler ® Trio DNA Quantification Kit from Applied Biosystems™, and PowerQuant ® System from Promega, and their compatibilities with three 6-dye DNA profiling systems. Our results have demonstrated that all three kits generate standard curves with satisfactory consistency and reproducibility, and are capable of screening out traces of male DNA in the presence of 30-fold excess of female DNA. They also exhibit a higher tolerance to PCR inhibition than Quantifiler ® Human DNA Quantification Kit from Applied Biosystems™ in autosomal DNA quantification. PowerQuant ® , as compared to Quantiplex HYres and Quantifiler ® Trio, shows a better precision for both autosomal and male DNA quantifications. Quantifiler ® Trio and PowerQuant ® in contrast to Quantiplex HYres offer better correlations with lower discrepancies between autosomal and male DNA quantification, and their additional degradation index features provide a detection platform for inhibited and/or degraded DNA template. Regarding the compatibility between these quantification and profiling systems: (1) both Quantifiler ® Trio and PowerQuant ® work well with GlobalFiler and Fusion 6C, allowing a fairly accurate prediction of their DNA typing results based on the quantification values; (2) Quantiplex HYres offers a fairly reliable IPC system for detecting any potential inhibitions on Investigator 24plex, whereas Quantifiler ® Trio and PowerQuant ® suit better for Global

  5. CSA: An efficient algorithm to improve circular DNA multiple alignment

    Directory of Open Access Journals (Sweden)

    Pereira Luísa

    2009-07-01

    Full Text Available Abstract Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. Results In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes. To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. Conclusion The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment

  6. Material Selection for Dye Sensitized Solar Cells Using Multiple Attribute Decision Making Approach

    Directory of Open Access Journals (Sweden)

    Sarita Baghel

    2014-01-01

    Full Text Available Dye sensitized solar cells (DSCs provide a potential alternative to conventional p-n junction photovoltaic devices. The semiconductor thin film plays a crucial role in the working of DSC. This paper aims at formulating a process for the selection of optimum semiconductor material for nanostructured thin film using multiple attribute decision making (MADM approach. Various possible available semiconducting materials and their properties like band gap, cost, mobility, rate of electron injection, and static dielectric constant are considered and MADM technique is applied to select the best suited material. It was found that, out of all possible candidates, titanium dioxide (TiO2 is the best semiconductor material for application in DSC. It was observed that the proposed results are in good agreement with the experimental findings.

  7. Enhancing the Sensitivity of DNA Microarray Using Dye-Doped Silica Nanoparticles: Detection of Human Papilloma Virus

    Science.gov (United States)

    Enrichi, F.; Riccò, R.; Meneghello, A.; Pierobon, R.; Canton, G.; Cretaio, E.

    2010-10-01

    DNA microarray is a high-throughput technology used for detection and quantification of nucleic acid molecules and others of biological interest. The analysis is based on the specific hybridization between probe sequences deposited in array and a target ss-DNA amplified by PCR and functionalized by a fluorescent dye. Organic labels have well known disadvantages like photobleaching and low signal intensities, which put a limitation to the lower amount of DNA material that can be detected. Therefore for trace analysis the development of more efficient biomarkers is required. With this aim we present in this paper the synthesis and application of alternative hybrid nanosystems obtained by incorporating standard fluorescent molecules into monodisperse silica nanoparticles. Efficient application to the detection of Human Papilloma Virus is demonstrated. This virus is associated to the formation of cervical cancer, a leading cause of death by cancer for women worldwide. It is shown that the use of the novel biomarkers increases the optical signal of about one order of magnitude with respect to the free dyes or quantum dots in conventional instruments. This is due to the high number of molecules that can be accommodated into each nanoparticle, to the reduced photobleaching and to the improved environmental protection of the dyes when encapsulated in the silica matrix. The cheap and easy synthesis of these luminescent particles, the stability in water, the surface functionalizability and bio-compatibility make them very promising for present and future bio-labeling and bio-imaging applications.

  8. Photoelectrode Fabrication of Dye-Sensitized Nanosolar Cells Using Multiple Spray Coating Technique

    Directory of Open Access Journals (Sweden)

    Chien-Chih Chen

    2013-01-01

    Full Text Available This paper presents a spray coating technique for fabricating nanoporous film of photoelectrode in dye-sensitized nanosolar cells (DSSCs. Spray coating can quickly fabricate nanoporous film of the photoelectrode with lower cost, which can further help the DSSCs to be commercialized in the future. This paper analyzed photoelectric conversion efficiency of the DSSCs using spray coated photoelectrode in comparison with the photoelectrode made with the doctor blade method. Spray coating can easily control transmittance of the photoelectrode through the multiple spray coating process. This work mainly used a dispersant with help of ultrasonic oscillation to prepare the required nano-TiO2 solution and then sprayed it on the ITO glasses. In this work, a motor-operated conveyor belt was built to transport the ITO glasses automatically for multiple spray coating and drying alternately. Experiments used transmittance of the photoelectrode as a fabrication parameter to analyze photoelectric conversion efficiency of the DSSCs. The influencing factors of the photoelectrode transmittance during fabrication are the spray flow rate, the spray distance, and the moving speed of the conveyor belt. The results show that DSSC with the photoelectrode transmittance of ca. 68.0 ± 1.5% and coated by the spray coating technique has the best photoelectric conversion efficiency in this work.

  9. MtDNA T4216C variation in multiple sclerosis

    DEFF Research Database (Denmark)

    Andalib, Sasan; Emamhadi, Mohammadreza; Yousefzadeh-Chabok, Shahrokh

    2016-01-01

    MtDNA T4216C variation has frequently been investigated in Multiple Sclerosis (MS) patients; nonetheless, controversy has existed about the evidence of association of this variation with susceptibility to MS. The present systematic review and meta-analysis converge the results of the preceding pu...

  10. A multiplex microplatform for the detection of multiple DNA methylation events using gold-DNA affinity.

    Science.gov (United States)

    Sina, Abu Ali Ibn; Foster, Matthew Thomas; Korbie, Darren; Carrascosa, Laura G; Shiddiky, Muhammad J A; Gao, Jing; Dey, Shuvashis; Trau, Matt

    2017-10-07

    We report a new multiplexed strategy for the electrochemical detection of regional DNA methylation across multiple regions. Using the sequence dependent affinity of bisulfite treated DNA towards gold surfaces, the method integrates the high sensitivity of a micro-fabricated multiplex device comprising a microarray of gold electrodes, with the powerful multiplexing capability of multiplex-PCR. The synergy of this combination enables the monitoring of the methylation changes across several genomic regions simultaneously from as low as 500 pg μl -1 of DNA with no sequencing requirement.

  11. Structures of an Apo and a Binary Complex of an Evolved Archeal B Family DNA Polymerase Capable of Synthesising Highly Cy-Dye Labelled DNA

    Science.gov (United States)

    Wynne, Samantha A.; Pinheiro, Vitor B.; Holliger, Philipp; Leslie, Andrew G. W.

    2013-01-01

    Thermophilic DNA polymerases of the polB family are of great importance in biotechnological applications including high-fidelity PCR. Of particular interest is the relative promiscuity of engineered versions of the exo- form of polymerases from the Thermo- and Pyrococcales families towards non-canonical substrates, which enables key advances in Next-generation sequencing. Despite this there is a paucity of structural information to guide further engineering of this group of polymerases. Here we report two structures, of the apo form and of a binary complex of a previously described variant (E10) of Pyrococcus furiosus (Pfu) polymerase with an ability to fully replace dCTP with Cyanine dye-labeled dCTP (Cy3-dCTP or Cy5-dCTP) in PCR and synthesise highly fluorescent “CyDNA” densely decorated with cyanine dye heterocycles. The apo form of Pfu-E10 closely matches reported apo form structures of wild-type Pfu. In contrast, the binary complex (in the replicative state with a duplex DNA oligonucleotide) reveals a closing movement of the thumb domain, increasing the contact surface with the nascent DNA duplex strand. Modelling based on the binary complex suggests how bulky fluorophores may be accommodated during processive synthesis and has aided the identification of residues important for the synthesis of unnatural nucleic acid polymers. PMID:23940661

  12. Optically controlled multiple switching operations of DNA biopolymer devices

    International Nuclear Information System (INIS)

    Hung, Chao-You; Tu, Waan-Ting; Lin, Yi-Tzu; Fruk, Ljiljana; Hung, Yu-Chueh

    2015-01-01

    We present optically tunable operations of deoxyribonucleic acid (DNA) biopolymer devices, where a single high-resistance state, write-once read-many-times memory state, write-read-erase memory state, and single low-resistance state can be achieved by controlling UV irradiation time. The device is a simple sandwich structure with a spin-coated DNA biopolymer layer sandwiched by two electrodes. Upon irradiation, the electrical properties of the device are adjusted owing to a phototriggered synthesis of silver nanoparticles in DNA biopolymer, giving rise to multiple switching scenarios. This technique, distinct from the strategy of doping of pre-formed nanoparticles, enables a post-film fabrication process for achieving optically controlled memory device operations, which provides a more versatile platform to fabricate organic memory and optoelectronic devices

  13. Optically controlled multiple switching operations of DNA biopolymer devices

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Chao-You; Tu, Waan-Ting; Lin, Yi-Tzu [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Fruk, Ljiljana [Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA (United Kingdom); Hung, Yu-Chueh, E-mail: ychung@ee.nthu.edu.tw [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

    2015-12-21

    We present optically tunable operations of deoxyribonucleic acid (DNA) biopolymer devices, where a single high-resistance state, write-once read-many-times memory state, write-read-erase memory state, and single low-resistance state can be achieved by controlling UV irradiation time. The device is a simple sandwich structure with a spin-coated DNA biopolymer layer sandwiched by two electrodes. Upon irradiation, the electrical properties of the device are adjusted owing to a phototriggered synthesis of silver nanoparticles in DNA biopolymer, giving rise to multiple switching scenarios. This technique, distinct from the strategy of doping of pre-formed nanoparticles, enables a post-film fabrication process for achieving optically controlled memory device operations, which provides a more versatile platform to fabricate organic memory and optoelectronic devices.

  14. Hoechst 33258 dye generates DNA-protein cross-links during ultraviolet light-induced photolysis of bromodeoxyuridine in replicated and repaired DNA

    Energy Technology Data Exchange (ETDEWEB)

    Guo Xicang; Morgan, W.F.; Cleaver, J.E.

    1986-08-01

    Substitution of bromodeoxyuridine for thymidine in the DNA of mammalian cells sensitizes them to a range of wavelengths of ultraviolet light. Cells are also sensitized to photochemical reactions involving dyes such as Hoechst 33258, which is used to produce differential staining of chromatids according to their bromodeoxyuridine content. Irradiation with 313 nm light of human and hamster cells containing bromodeoxyuridine in their DNA produced single-strand breaks but no DNA-protein cross-links. Irradiation with 360 nm light in the presence of Hoechst 33258 produced extensive DNA-protein cross-linkage as well as single-strand breaks. These cross-links were observed in DNA containing bromodeoxyuridine incorporated by either semiconservative or repair replication. When the protein was removed with proteinase K, bromodeoxyuridine in repair patches after irradiation by doses of ultraviolet (254 nm) light as low as 0.26 J/m/sup 2/ could readily be detected. Hoechst 33258-mediated photolysis, therefore, provides a sensitive new technique for measuring repair replication after ultraviolet light irradiation.

  15. Complexes of DNA with fluorescent dyes are effective reagents for detection of autoimmune antibodies

    DEFF Research Database (Denmark)

    Domljanovic, Ivana; Carstens, Annika; Okholm, Anders

    2017-01-01

    as targets for these antibodies. This is done in a simple, rapid and specific immunofluorescence assay. Specifically, employing 3D nanostructures (DNA origami), we present a new approach in the detection and study of human antibodies to DNA. We demonstrate the detection of anti-DNA antibodies...

  16. Capillary electrophoresis of Big-Dye terminator sequencing reactions for human mtDNA Control Region haplotyping in the identification of human remains.

    Science.gov (United States)

    Montesino, Marta; Prieto, Lourdes

    2012-01-01

    Cycle sequencing reaction with Big-Dye terminators provides the methodology to analyze mtDNA Control Region amplicons by means of capillary electrophoresis. DNA sequencing with ddNTPs or terminators was developed by (1). The progressive automation of the method by combining the use of fluorescent-dye terminators with cycle sequencing has made it possible to increase the sensibility and efficiency of the method and hence has allowed its introduction into the forensic field. PCR-generated mitochondrial DNA products are the templates for sequencing reactions. Different set of primers can be used to generate amplicons with different sizes according to the quality and quantity of the DNA extract providing sequence data for different ranges inside the Control Region.

  17. Competitive annealing of multiple DNA origami: formation of chimeric origami

    International Nuclear Information System (INIS)

    Majikes, Jacob M; Nash, Jessica A; LaBean, Thomas H

    2016-01-01

    Scaffolded DNA origami are a robust tool for building discrete nanoscale objects at high yield. This strategy ensures, in the design process, that the desired nanostructure is the minimum free energy state for the designed set of DNA sequences. Despite aiming for the minimum free energy structure, the folding process which leads to that conformation is difficult to characterize, although it has been the subject of much research. In order to shed light on the molecular folding pathways, this study intentionally frustrates the folding process of these systems by simultaneously annealing the staple pools for multiple target or parent origami structures, forcing competition. A surprising result of these competitive, simultaneous anneals is the formation of chimeric DNA origami which inherit structural regions from both parent origami. By comparing the regions inherited from the parent origami, relative stability of substructures were compared. This allowed examination of the folding process with typical characterization techniques and materials. Anneal curves were then used as a means to rapidly generate a phase diagram of anticipated behavior as a function of staple excess and parent staple ratio. This initial study shows that competitive anneals provide an exciting way to create diverse new nanostructures and may be used to examine the relative stability of various structural motifs. (paper)

  18. Epigenetic changes in neurology: DNA methylation in multiple sclerosis.

    Science.gov (United States)

    Iridoy Zulet, M; Pulido Fontes, L; Ayuso Blanco, T; Lacruz Bescos, F; Mendioroz Iriarte, M

    2017-09-01

    Epigenetics is defined as the study of the mechanisms that regulate gene expression without altering the underlying DNA sequence. The best known is DNA methylation. Multiple Sclerosis (MS) is a disease with no entirely known etiology, in which it is stated that the involvement of environmental factors on people with a genetic predisposition, may be key to the development of the disease. It is at this intersection between genetic predisposition and environmental factors where DNA methylation may play a pathogenic role. A literature review of the effects of environmental risk factors for the development of MS can have on the different epigenetic mechanisms as well as the implication that such changes have on the development of the disease. Knowledge of epigenetic modifications involved in the pathogenesis of MS, opens a new avenue of research for identification of potential biomarkers, as well as finding new therapeutic targets. Copyright © 2015 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

  19. Multiple approaches towards decolorization and reuse of a textile dye (VB-B) by a marine bacterium Shewanella decolorationis

    Digital Repository Service at National Institute of Oceanography (India)

    SatheeshBabu, S.; Mohandass, C.; VijayRaj, A.S.; Rajasabapathy, R.; Dhale, M.A.

    stream_size 41279 stream_content_type text/plain stream_name Water_Air_Soil_Pollut_224_1500a.pdf.txt stream_source_info Water_Air_Soil_Pollut_224_1500a.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8...     1    Author version: Water Air Soil Pollut., vol.224(4); 2013; 1500 Multiple approaches towards decolorization and reuse of a textile dye (VB-B) by a marine bacterium Shewanella decolorationis S. Satheesh Babu, C.Mohandass*, A.S.Vijay Raj, R...

  20. Multiple conformational states of DnaA protein regulate its interaction with DnaA boxes in the initiation of DNA replication.

    Science.gov (United States)

    Patel, Meera J; Bhatia, Lavesh; Yilmaz, Gulden; Biswas-Fiss, Esther E; Biswas, Subhasis B

    2017-09-01

    DnaA protein is the initiator of genomic DNA replication in prokaryotes. It binds to specific DNA sequences in the origin of DNA replication and unwinds small AT-rich sequences downstream for the assembly of the replisome. The mechanism of activation of DnaA that enables it to bind and organize the origin DNA and leads to replication initiation remains unclear. In this study, we have developed double-labeled fluorescent DnaA probes to analyze conformational states of DnaA protein upon binding DNA, nucleotide, and Soj sporulation protein using Fluorescence Resonance Energy Transfer (FRET). Our studies demonstrate that DnaA protein undergoes large conformational changes upon binding to substrates and there are multiple distinct conformational states that enable it to initiate DNA replication. DnaA protein adopted a relaxed conformation by expanding ~15Å upon binding ATP and DNA to form the ATP·DnaA·DNA complex. Hydrolysis of bound ATP to ADP led to a contraction of DnaA within the complex. The relaxed conformation of DnaA is likely required for the formation of the multi-protein ATP·DnaA·DNA complex. In the initiation of sporulation, Soj binding to DnaA prevented relaxation of its conformation. Soj·ADP appeared to block the activation of DnaA, suggesting a mechanism for Soj·ADP in switching initiation of DNA replication to sporulation. Our studies demonstrate that multiple conformational states of DnaA protein regulate its binding to DNA in the initiation of DNA replication. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

  2. Quantification of dsDNA using the Hitachi F-7000 Fluorescence Spectrophotometer and PicoGreen dye.

    Science.gov (United States)

    Moreno, Luis A; Cox, Kendra L

    2010-11-05

    Quantification of DNA, especially in small concentrations, is an important task with a wide range of biological applications including standard molecular biology assays such as synthesis and purification of DNA, diagnostic applications such as quantification of DNA amplification products, and detection of DNA molecules in drug preparations. During this video we will demonstrate the capability of the Hitachi F-7000 Fluorescence Spectrophotometer equipped with a Micro Plate Reader accessory to perform dsDNA quantification using Molecular Probes Quant-it PicoGreen dye reagent kit. The F-7000 Fluorescence Spectrophotometer offers high sensitivity and high speed measurements. It is a highly flexible system capable of measuring fluorescence, luminescence, and phosphorescence. Several measuring modes are available, including wavelength scan, time scan, photometry and 3-D scan measurement. The spectrophotometer has sensitivity in the range of 50 picomoles of fluorescein when using a 300 μL sample volume in the microplate, and is capable of measuring scan speeds of 60,000 nm/minute. It also has a wide dynamic range of up to 5 orders of magnitude which allows for the use of calibration curves over a wide range of concentrations. The optical system uses all reflective optics for maximum energy and sensitivity. The standard wavelength range is 200 to 750 nm, and can be extended to 900 nm when using one of the optional near infrared photomultipliers. The system allows optional temperature control for the plate reader from 5 to 60 degrees Celsius using an optional external temperature controlled liquid circulator. The microplate reader allows for the use of 96 well microplates, and the measuring speed for 96 wells is less than 60 seconds when using the kinetics mode. Software controls for the F-7000 and Microplate Reader are also highly flexible. Samples may be set in either column or row formats, and any combination of wells may be chosen for sample measurements. This allows

  3. Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

    Energy Technology Data Exchange (ETDEWEB)

    Żurek-Biesiada, Dominika [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Szczurek, Aleksander T. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Prakash, Kirti [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Mohana, Giriram K. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Lee, Hyun-Keun [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Roignant, Jean-Yves [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Birk, Udo J. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Dobrucki, Jurek W., E-mail: jerzy.dobrucki@uj.edu.pl [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Cremer, Christoph, E-mail: c.cremer@imb-mainz.de [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany)

    2016-05-01

    Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.

  4. Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance

    Directory of Open Access Journals (Sweden)

    Haque Kashif A

    2005-09-01

    Full Text Available Abstract Background Whole genome amplification (WGA promises to eliminate practical molecular genetic analysis limitations associated with genomic DNA (gDNA quantity. We evaluated the performance of multiple displacement amplification (MDA WGA using gDNA extracted from lymphoblastoid cell lines (N = 27 with a range of starting gDNA input of 1–200 ng into the WGA reaction. Yield and composition analysis of whole genome amplified DNA (wgaDNA was performed using three DNA quantification methods (OD, PicoGreen® and RT-PCR. Two panels of N = 15 STR (using the AmpFlSTR® Identifiler® panel and N = 49 SNP (TaqMan® genotyping assays were performed on each gDNA and wgaDNA sample in duplicate. gDNA and wgaDNA masses of 1, 4 and 20 ng were used in the SNP assays to evaluate the effects of DNA mass on SNP genotyping assay performance. A total of N = 6,880 STR and N = 56,448 SNP genotype attempts provided adequate power to detect differences in STR and SNP genotyping performance between gDNA and wgaDNA, and among wgaDNA produced from a range of gDNA templates inputs. Results The proportion of double-stranded wgaDNA and human-specific PCR amplifiable wgaDNA increased with increased gDNA input into the WGA reaction. Increased amounts of gDNA input into the WGA reaction improved wgaDNA genotyping performance. Genotype completion or genotype concordance rates of wgaDNA produced from all gDNA input levels were observed to be reduced compared to gDNA, although the reduction was not always statistically significant. Reduced wgaDNA genotyping performance was primarily due to the increased variance of allelic amplification, resulting in loss of heterozygosity or increased undetermined genotypes. MDA WGA produces wgaDNA from no template control samples; such samples exhibited substantial false-positive genotyping rates. Conclusion The amount of gDNA input into the MDA WGA reaction is a critical determinant of genotyping performance of wgaDNA. At least 10 ng of

  5. Sensitive optical bio-sensing of p-type WSe2 hybridized with fluorescent dye attached DNA by doping and de-doping effects

    Science.gov (United States)

    Han, Kyu Hyun; Kim, Jun Young; Jo, Seong Gi; Seo, Changwon; Kim, Jeongyong; Joo, Jinsoo

    2017-10-01

    Layered transition metal dichalcogenides, such as MoS2, WSe2 and WS2, are exciting two-dimensional (2D) materials because they possess tunable optical and electrical properties that depend on the number of layers. In this study, the nanoscale photoluminescence (PL) characteristics of the p-type WSe2 monolayer, and WSe2 layers hybridized with the fluorescent dye Cy3 attached to probe-DNA (Cy3/p-DNA), have been investigated as a function of the concentration of Cy3/DNA by using high-resolution laser confocal microscopy. With increasing concentration of Cy3/p-DNA, the measured PL intensity decreases and its peak is red-shifted, suggesting that the WSe2 layer has been p-type doped with Cy3/p-DNA. Then, the PL intensity of the WSe2/Cy3/p-DNA hybrid system increases and the peak is blue-shifted through hybridization with relatively small amounts of target-DNA (t-DNA) (50-100 nM). This effect originates from charge and energy transfer from the Cy3/DNA to the WSe2. For t-DNA detection, our systems using p-type WSe2 have the merit in terms of the increase of PL intensity. The p-type WSe2 monolayers can be a promising nanoscale 2D material for sensitive optical bio-sensing based on the doping and de-doping responses to biomaterials.

  6. Common DNA methylation alterations in multiple brain regions in autism.

    Science.gov (United States)

    Ladd-Acosta, C; Hansen, K D; Briem, E; Fallin, M D; Kaufmann, W E; Feinberg, A P

    2014-08-01

    Autism spectrum disorders (ASD) are increasingly common neurodevelopmental disorders defined clinically by a triad of features including impairment in social interaction, impairment in communication in social situations and restricted and repetitive patterns of behavior and interests, with considerable phenotypic heterogeneity among individuals. Although heritability estimates for ASD are high, conventional genetic-based efforts to identify genes involved in ASD have yielded only few reproducible candidate genes that account for only a small proportion of ASDs. There is mounting evidence to suggest environmental and epigenetic factors play a stronger role in the etiology of ASD than previously thought. To begin to understand the contribution of epigenetics to ASD, we have examined DNA methylation (DNAm) in a pilot study of postmortem brain tissue from 19 autism cases and 21 unrelated controls, among three brain regions including dorsolateral prefrontal cortex, temporal cortex and cerebellum. We measured over 485,000 CpG loci across a diverse set of functionally relevant genomic regions using the Infinium HumanMethylation450 BeadChip and identified four genome-wide significant differentially methylated regions (DMRs) using a bump hunting approach and a permutation-based multiple testing correction method. We replicated 3/4 DMRs identified in our genome-wide screen in a different set of samples and across different brain regions. The DMRs identified in this study represent suggestive evidence for commonly altered methylation sites in ASD and provide several promising new candidate genes.

  7. Prevalence and multiplicity of cutaneous beta papilloma viruses in plucked hairs depend on cellular DNA input.

    Science.gov (United States)

    Weissenborn, S J; Neale, R; de Koning, M N C; Waterboer, T; Abeni, D; Bouwes Bavinck, J N; Wieland, U; Pfister, H J

    2009-11-01

    In view of the low loads of beta human papillomaviruses in skin samples, amounts of cellular DNA used in qualitative PCR may become limiting for virus detection and introduce variations in prevalence and multiplicity. This issue was explored within the context of a multicentre study and increasing prevalence and multiplicity was found with increasing input amounts of cellular DNA extracted from hair bulbs. To improve the quality and comparability between different epidemiologic studies ideally equal amounts of cellular DNA should be employed. When cellular DNA input varies this should be clearly taken into account in assessing viral prevalence and multiplicity.

  8. Precise Sequential DNA Ligation on A Solid Substrate: Solid-Based Rapid Sequential Ligation of Multiple DNA Molecules

    Science.gov (United States)

    Takita, Eiji; Kohda, Katsunori; Tomatsu, Hajime; Hanano, Shigeru; Moriya, Kanami; Hosouchi, Tsutomu; Sakurai, Nozomu; Suzuki, Hideyuki; Shinmyo, Atsuhiko; Shibata, Daisuke

    2013-01-01

    Ligation, the joining of DNA fragments, is a fundamental procedure in molecular cloning and is indispensable to the production of genetically modified organisms that can be used for basic research, the applied biosciences, or both. Given that many genes cooperate in various pathways, incorporating multiple gene cassettes in tandem in a transgenic DNA construct for the purpose of genetic modification is often necessary when generating organisms that produce multiple foreign gene products. Here, we describe a novel method, designated PRESSO (precise sequential DNA ligation on a solid substrate), for the tandem ligation of multiple DNA fragments. We amplified donor DNA fragments with non-palindromic ends, and ligated the fragment to acceptor DNA fragments on solid beads. After the final donor DNA fragments, which included vector sequences, were joined to the construct that contained the array of fragments, the ligation product (the construct) was thereby released from the beads via digestion with a rare-cut meganuclease; the freed linear construct was circularized via an intra-molecular ligation. PRESSO allowed us to rapidly and efficiently join multiple genes in an optimized order and orientation. This method can overcome many technical challenges in functional genomics during the post-sequencing generation. PMID:23897972

  9. In-gel multiple displacement amplification of long DNA fragments diluted to the single molecule level.

    Science.gov (United States)

    Michikawa, Yuichi; Sugahara, Keisuke; Suga, Tomo; Ohtsuka, Yoshimi; Ishikawa, Kenichi; Ishikawa, Atsuko; Shiomi, Naoko; Shiomi, Tadahiro; Iwakawa, Mayumi; Imai, Takashi

    2008-12-15

    The isolation and multiple genotyping of long individual DNA fragments are needed to obtain haplotype information for diploid organisms. Limiting dilution of sample DNA followed by multiple displacement amplification is a useful technique but is restricted to short (reaction (PCR)-ready form. The haplotypes of seven SNPs spanning 240 kb of the DNA surrounding the human ATM gene region on chromosome 11 were determined for 10 individuals, demonstrating the feasibility of this new method.

  10. Interfacing click chemistry with automated oligonucleotide synthesis for the preparation of fluorescent DNA probes containing internal xanthene and cyanine dyes

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Wengel, Jesper

    2013-01-01

    Double-labeled oligonucleotide probes containing fluorophores interacting by energy-transfer mechanisms are essential for modern bioanalysis, molecular diagnostics, and in vivo imaging techniques. Although bright xanthene and cyanine dyes are gaining increased prominence within these fields, little...

  11. Analysis of multiple single nucleotide polymorphisms (SNP) on DNA traces from plasma and dried blood samples

    NARCIS (Netherlands)

    Catsburg, Arnold; van der Zwet, Wil C.; Morre, Servaas A.; Ouburg, Sander; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

    2007-01-01

    Reliable analysis of single nucleotide polymorphisms (SNPs) in DNA derived from samples containing low numbers of cells or from suboptimal sources can be difficult. A new procedure to characterize multiple SNPs in traces of DNA from plasma and old dried blood samples was developed. Six SNPs in the

  12. Inactivating UBE2M impacts the DNA damage response and genome integrity involving multiple cullin ligases.

    Directory of Open Access Journals (Sweden)

    Scott Cukras

    Full Text Available Protein neddylation is involved in a wide variety of cellular processes. Here we show that the DNA damage response is perturbed in cells inactivated with an E2 Nedd8 conjugating enzyme UBE2M, measured by RAD51 foci formation kinetics and cell based DNA repair assays. UBE2M knockdown increases DNA breakages and cellular sensitivity to DNA damaging agents, further suggesting heightened genomic instability and defective DNA repair activity. Investigating the downstream Cullin targets of UBE2M revealed that silencing of Cullin 1, 2, and 4 ligases incurred significant DNA damage. In particular, UBE2M knockdown, or defective neddylation of Cullin 2, leads to a blockade in the G1 to S progression and is associated with delayed S-phase dependent DNA damage response. Cullin 4 inactivation leads to an aberrantly high DNA damage response that is associated with increased DNA breakages and sensitivity of cells to DNA damaging agents, suggesting a DNA repair defect is associated. siRNA interrogation of key Cullin substrates show that CDT1, p21, and Claspin are involved in elevated DNA damage in the UBE2M knockdown cells. Therefore, UBE2M is required to maintain genome integrity by activating multiple Cullin ligases throughout the cell cycle.

  13. Inactivating UBE2M impacts the DNA damage response and genome integrity involving multiple cullin ligases.

    Science.gov (United States)

    Cukras, Scott; Morffy, Nicholas; Ohn, Takbum; Kee, Younghoon

    2014-01-01

    Protein neddylation is involved in a wide variety of cellular processes. Here we show that the DNA damage response is perturbed in cells inactivated with an E2 Nedd8 conjugating enzyme UBE2M, measured by RAD51 foci formation kinetics and cell based DNA repair assays. UBE2M knockdown increases DNA breakages and cellular sensitivity to DNA damaging agents, further suggesting heightened genomic instability and defective DNA repair activity. Investigating the downstream Cullin targets of UBE2M revealed that silencing of Cullin 1, 2, and 4 ligases incurred significant DNA damage. In particular, UBE2M knockdown, or defective neddylation of Cullin 2, leads to a blockade in the G1 to S progression and is associated with delayed S-phase dependent DNA damage response. Cullin 4 inactivation leads to an aberrantly high DNA damage response that is associated with increased DNA breakages and sensitivity of cells to DNA damaging agents, suggesting a DNA repair defect is associated. siRNA interrogation of key Cullin substrates show that CDT1, p21, and Claspin are involved in elevated DNA damage in the UBE2M knockdown cells. Therefore, UBE2M is required to maintain genome integrity by activating multiple Cullin ligases throughout the cell cycle.

  14. Detecting multiple DNA human profile from a mosquito blood meal.

    Science.gov (United States)

    Rabêlo, K C N; Albuquerque, C M R; Tavares, V B; Santos, S M; Souza, C A; Oliveira, T C; Moura, R R; Brandão, L A C; Crovella, S

    2016-08-26

    Criminal traces commonly found at crime scenes may present mixtures from two or more individuals. The scene of the crime is important for the collection of various types of traces in order to find the perpetrator of the crime. Thus, we propose that hematophagous mosquitoes found at crime scenes can be used to perform genetic testing of human blood and aid in suspect investigation. The aim of the study was to obtain a single Aedes aegypti mosquito profile from a human DNA mixture containing genetic materials of four individuals. We also determined the effect of blood acquisition time by setting time intervals of 24, 48, and 72 h after the blood meal. STR loci and amelogenin were analyzed, and the results showed that human DNA profiles could be obtained from hematophagous mosquitos at 24 h following the blood meal. It is possible that hematophagous mosquitoes can be used as biological remains at the scene of the crime, and can be used to detect human DNA profiles of up to four individuals.

  15. Scavenging Circulating Mitochondrial DNA as a Potential Therapeutic Option for Multiple Organ Dysfunction in Trauma Hemorrhage.

    Science.gov (United States)

    Aswani, Andrew; Manson, Joanna; Itagaki, Kiyoshi; Chiazza, Fausto; Collino, Massimo; Wupeng, Winston Liao; Chan, Tze Khee; Wong, W S Fred; Hauser, Carl J; Thiemermann, Chris; Brohi, Karim

    2018-01-01

    Trauma is a leading cause of death worldwide with 5.8 million deaths occurring yearly. Almost 40% of trauma deaths are due to bleeding and occur in the first few hours after injury. Of the remaining severely injured patients up to 25% develop a dysregulated immune response leading to multiple organ dysfunction syndrome (MODS). Despite improvements in trauma care, the morbidity and mortality of this condition remains very high. Massive traumatic injury can overwhelm endogenous homeostatic mechanisms even with prompt treatment. The underlying mechanisms driving MODS are also not fully elucidated. As a result, successful therapies for trauma-related MODS are lacking. Trauma causes tissue damage that releases a large number of endogenous damage-associated molecular patterns (DAMPs). Mitochondrial DAMPs released in trauma, such as mitochondrial DNA (mtDNA), could help to explain part of the immune response in trauma given the structural similarities between mitochondria and bacteria. MtDNA, like bacterial DNA, contains an abundance of highly stimulatory unmethylated CpG DNA motifs that signal through toll-like receptor-9 to produce inflammation. MtDNA has been shown to be highly damaging when injected into healthy animals causing acute organ injury to develop. Elevated circulating levels of mtDNA have been reported in trauma patients but an association with clinically meaningful outcomes has not been established in a large cohort. We aimed to determine whether mtDNA released after clinical trauma hemorrhage is sufficient for the development of MODS. Secondly, we aimed to determine the extent of mtDNA release with varying degrees of tissue injury and hemorrhagic shock in a clinically relevant rodent model. Our final aim was to determine whether neutralizing mtDNA with the nucleic acid scavenging polymer, hexadimethrine bromide (HDMBr), at a clinically relevant time point in vivo would reduce the severity of organ injury in this model. We have shown that the release of mtDNA

  16. Scavenging Circulating Mitochondrial DNA as a Potential Therapeutic Option for Multiple Organ Dysfunction in Trauma Hemorrhage

    Directory of Open Access Journals (Sweden)

    Andrew Aswani

    2018-05-01

    Full Text Available Trauma is a leading cause of death worldwide with 5.8 million deaths occurring yearly. Almost 40% of trauma deaths are due to bleeding and occur in the first few hours after injury. Of the remaining severely injured patients up to 25% develop a dysregulated immune response leading to multiple organ dysfunction syndrome (MODS. Despite improvements in trauma care, the morbidity and mortality of this condition remains very high. Massive traumatic injury can overwhelm endogenous homeostatic mechanisms even with prompt treatment. The underlying mechanisms driving MODS are also not fully elucidated. As a result, successful therapies for trauma-related MODS are lacking. Trauma causes tissue damage that releases a large number of endogenous damage-associated molecular patterns (DAMPs. Mitochondrial DAMPs released in trauma, such as mitochondrial DNA (mtDNA, could help to explain part of the immune response in trauma given the structural similarities between mitochondria and bacteria. MtDNA, like bacterial DNA, contains an abundance of highly stimulatory unmethylated CpG DNA motifs that signal through toll-like receptor-9 to produce inflammation. MtDNA has been shown to be highly damaging when injected into healthy animals causing acute organ injury to develop. Elevated circulating levels of mtDNA have been reported in trauma patients but an association with clinically meaningful outcomes has not been established in a large cohort. We aimed to determine whether mtDNA released after clinical trauma hemorrhage is sufficient for the development of MODS. Secondly, we aimed to determine the extent of mtDNA release with varying degrees of tissue injury and hemorrhagic shock in a clinically relevant rodent model. Our final aim was to determine whether neutralizing mtDNA with the nucleic acid scavenging polymer, hexadimethrine bromide (HDMBr, at a clinically relevant time point in vivo would reduce the severity of organ injury in this model. Conclusions: We have

  17. Model selection in Bayesian segmentation of multiple DNA alignments.

    Science.gov (United States)

    Oldmeadow, Christopher; Keith, Jonathan M

    2011-03-01

    The analysis of multiple sequence alignments is allowing researchers to glean valuable insights into evolution, as well as identify genomic regions that may be functional, or discover novel classes of functional elements. Understanding the distribution of conservation levels that constitutes the evolutionary landscape is crucial to distinguishing functional regions from non-functional. Recent evidence suggests that a binary classification of evolutionary rates is inappropriate for this purpose and finds only highly conserved functional elements. Given that the distribution of evolutionary rates is multi-modal, determining the number of modes is of paramount concern. Through simulation, we evaluate the performance of a number of information criterion approaches derived from MCMC simulations in determining the dimension of a model. We utilize a deviance information criterion (DIC) approximation that is more robust than the approximations from other information criteria, and show our information criteria approximations do not produce superfluous modes when estimating conservation distributions under a variety of circumstances. We analyse the distribution of conservation for a multiple alignment comprising four primate species and mouse, and repeat this on two additional multiple alignments of similar species. We find evidence of six distinct classes of evolutionary rates that appear to be robust to the species used. Source code and data are available at http://dl.dropbox.com/u/477240/changept.zip.

  18. Multiple regulatory systems coordinate DNA replication with cell growth in Bacillus subtilis.

    Directory of Open Access Journals (Sweden)

    Heath Murray

    2014-10-01

    Full Text Available In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth. Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades, however the mechanism(s that connects these cell cycle activities has eluded understanding. In order to help address this fundamental question we have investigated regulation of DNA replication in the model organism Bacillus subtilis. Contrary to the prevailing view we find that changes in DnaA protein level are not sufficient to account for nutrient-mediated growth rate control of DNA replication initiation, although this regulation does require both DnaA and the endogenous replication origin. We go on to report connections between DNA replication and several essential cellular activities required for rapid bacterial growth, including respiration, central carbon metabolism, fatty acid synthesis, phospholipid synthesis, and protein synthesis. Unexpectedly, the results indicate that multiple regulatory systems are involved in coordinating DNA replication with cell physiology, with some of the regulatory systems targeting oriC while others act in a oriC-independent manner. We propose that distinct regulatory systems are utilized to control DNA replication in response to diverse physiological and chemical changes.

  19. Multiple regulatory systems coordinate DNA replication with cell growth in Bacillus subtilis.

    Science.gov (United States)

    Murray, Heath; Koh, Alan

    2014-10-01

    In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth. Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades, however the mechanism(s) that connects these cell cycle activities has eluded understanding. In order to help address this fundamental question we have investigated regulation of DNA replication in the model organism Bacillus subtilis. Contrary to the prevailing view we find that changes in DnaA protein level are not sufficient to account for nutrient-mediated growth rate control of DNA replication initiation, although this regulation does require both DnaA and the endogenous replication origin. We go on to report connections between DNA replication and several essential cellular activities required for rapid bacterial growth, including respiration, central carbon metabolism, fatty acid synthesis, phospholipid synthesis, and protein synthesis. Unexpectedly, the results indicate that multiple regulatory systems are involved in coordinating DNA replication with cell physiology, with some of the regulatory systems targeting oriC while others act in a oriC-independent manner. We propose that distinct regulatory systems are utilized to control DNA replication in response to diverse physiological and chemical changes.

  20. Multiple Regulatory Systems Coordinate DNA Replication with Cell Growth in Bacillus subtilis

    Science.gov (United States)

    Murray, Heath; Koh, Alan

    2014-01-01

    In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth. Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades, however the mechanism(s) that connects these cell cycle activities has eluded understanding. In order to help address this fundamental question we have investigated regulation of DNA replication in the model organism Bacillus subtilis. Contrary to the prevailing view we find that changes in DnaA protein level are not sufficient to account for nutrient-mediated growth rate control of DNA replication initiation, although this regulation does require both DnaA and the endogenous replication origin. We go on to report connections between DNA replication and several essential cellular activities required for rapid bacterial growth, including respiration, central carbon metabolism, fatty acid synthesis, phospholipid synthesis, and protein synthesis. Unexpectedly, the results indicate that multiple regulatory systems are involved in coordinating DNA replication with cell physiology, with some of the regulatory systems targeting oriC while others act in a oriC-independent manner. We propose that distinct regulatory systems are utilized to control DNA replication in response to diverse physiological and chemical changes. PMID:25340815

  1. Multiple repair pathways mediate cellular tolerance to resveratrol-induced DNA damage.

    Science.gov (United States)

    Liu, Ying; Wu, Xiaohua; Hu, Xiaoqing; Chen, Ziyuan; Liu, Hao; Takeda, Shunichi; Qing, Yong

    2017-08-01

    Resveratrol (RSV) has been reported to exert health benefits for the prevention and treatment of many diseases, including cancer. The anticancer mechanisms of RSV seem to be complex and may be associated with genotoxic potential. To better understand the genotoxic mechanisms, we used wild-type (WT) and a panel of isogenic DNA-repair deficient DT40 cell lines to identify the DNA damage effects and molecular mechanisms of cellular tolerance to RSV. Our results showed that RSV induced significant formation of γ-H2AX foci and chromosome aberrations (CAs) in WT cells, suggesting direct DNA damage effects. Comparing the survival of WT with isogenic DNA-repair deficient DT40 cell lines demonstrated that single strand break repair (SSBR) deficient cell lines of Parp1 -/- , base excision repair (BER) deficient cell lines of Polβ -/- , homologous recombination (HR) mutants of Brca1 -/- and Brca2 -/- and translesion DNA synthesis (TLS) mutants of Rev3 -/- and Rad18 -/- were more sensitive to RSV. The sensitivities of cells were associated with enhanced DNA damage comparing the accumulation of γ-H2AX foci and number of CAs of isogenic DNA-repair deficient DT40 cell lines with WT cells. These results clearly demonstrated that RSV-induced DNA damage in DT40 cells, and multiple repair pathways including BER, SSBR, HR and TLS, play critical roles in response to RSV- induced genotoxicity. Copyright © 2017. Published by Elsevier Ltd.

  2. Multiple displacement amplification of whole genomic DNA from urediospores of Puccinia striiformis f. sp. tritici.

    Science.gov (United States)

    Zhang, R; Ma, Z H; Wu, B M

    2015-05-01

    Biotrophic fungi, such as Puccinia striiformis f. sp. tritici, because they cannot be cultured on nutrient media, to obtain adequate quantity of DNA for molecular genetic analysis, are usually propagated on living hosts, wheat plants in case of P. striiformis f. sp. tritici. The propagation process is time-, space- and labor-consuming and has been a bottleneck to molecular genetic analysis of this pathogen. In this study we evaluated multiple displacement amplification (MDA) of pathogen genomic DNA from urediospores as an alternative approach to traditional propagation of urediospores followed by DNA extraction. The quantities of pathogen genomic DNA in the products were further determined via real-time PCR with a pair of primers specific for the β-tubulin gene of P. striiformis f. sp. tritici. The amplified fragment length polymorphism (AFLP) fingerprints were also compared between the DNA products. The results demonstrated that adequate genomic DNA at fragment size larger than 23 Kb could be amplified from 20 to 30 urediospores via MDA method. The real-time PCR results suggested that although fresh urediospores collected from diseased leaves were the best, spores picked from diseased leaves stored for a prolonged period could also be used for amplification. AFLP fingerprints exhibited no significant differences between amplified DNA and DNA extracted with CTAB method, suggesting amplified DNA can represent the pathogen's genomic DNA very well. Therefore, MDA could be used to obtain genomic DNA from small precious samples (dozens of spores) for molecular genetic analysis of wheat stripe rust pathogen, and other fungi that are difficult to propagate.

  3. Laser Dyes

    Indian Academy of Sciences (India)

    amplification or generation of coherent light waves in the UV,. VIS, and near IR region. .... ciency in most flashlamp pumped dye lasers. It is used as reference dye .... have led to superior laser dyes with increased photostabilities. For instance ...

  4. Digital Droplet Multiple Displacement Amplification (ddMDA for Whole Genome Sequencing of Limited DNA Samples.

    Directory of Open Access Journals (Sweden)

    Minsoung Rhee

    Full Text Available Multiple displacement amplification (MDA is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet, ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

  5. Genetic analysis of yeast RPA1 reveals its multiple functions in DNA metabolism

    International Nuclear Information System (INIS)

    Umezu, K.; Sugawara, N.; Chen, C.; Haber, J.E.; Kolodner, R.D.

    1998-01-01

    Replication protein A (RPA) is a single-stranded DNA-binding protein identified as an essential factor for SV40 DNA replication in vitro. To understand the in vivo functions of RPA, we mutagenized the Saccharomyces cerevisiae RFA1 gene and identified 19 ultraviolet light (UV) irradiation- and methyl methane sulfonate (MMS)-sensitive mutants and 5 temperature-sensitive mutants. The UV- and MMS-sensitive mutants showed up to 10 4 to 10 5 times increased sensitivity to these agents. Some of the UV- and MMSsensitive mutants were killed by an HO-induced double-strand break atMAT. Physical analysis of recombination in one UV- and MMS-sensitive rfa1 mutant demonstrated that it was defective for mating type switching and single-strand annealing recombination. Two temperature-sensitive mutants were characterized in detail, and at the restrictive temperature were found to have an arrest phenotype and DNA content indicative of incomplete DNA replication. DNA sequence analysis indicated that most of the mutations altered amino acids that were conserved between yeast, human, and Xenopus RPA1. Taken together, we conclude that RPA1 has multiple roles in vivo and functions in DNA replication, repair, and recombination, like the single-stranded DNA-binding proteins of bacteria and phages. (author)

  6. How and why multiple MCMs are loaded at origins of DNA replication.

    Science.gov (United States)

    Das, Shankar P; Rhind, Nicholas

    2016-07-01

    Recent work suggests that DNA replication origins are regulated by the number of multiple mini-chromosome maintenance (MCM) complexes loaded. Origins are defined by the loading of MCM - the replicative helicase which initiates DNA replication and replication kinetics determined by origin's location and firing times. However, activation of MCM is heterogeneous; different origins firing at different times in different cells. Also, more MCMs are loaded in G1 than are used in S phase. These aspects of MCM biology are explained by the observation that multiple MCMs are loaded at origins. Having more MCMs at early origins makes them more likely to fire, effecting differences in origin efficiency that define replication timing. Nonetheless, multiple MCM loading raises new questions, such as how they are loaded, where these MCMs reside at origins, and how their presence affects replication timing. In this review, we address these questions and discuss future avenues of research. © 2016 WILEY Periodicals, Inc.

  7. Photoinduced dynamics of a cyanine dye: parallel pathways of non-radiative deactivation involving multiple excited-state twisted transients.

    Science.gov (United States)

    Upadhyayula, Srigokul; Nuñez, Vicente; Espinoza, Eli M; Larsen, Jillian M; Bao, Duoduo; Shi, Dewen; Mac, Jenny T; Anvari, Bahman; Vullev, Valentine I

    2015-04-01

    Cyanine dyes are broadly used for fluorescence imaging and other photonic applications. 3,3'-Diethylthiacyanine (THIA) is a cyanine dye composed of two identical aromatic heterocyclic moieties linked with a single methine, -CH 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 . The torsional degrees of freedom around the methine bonds provide routes for non-radiative decay, responsible for the inherently low fluorescence quantum yields. Using transient absorption spectroscopy, we determined that upon photoexcitation, the excited state relaxes along two parallel pathways producing three excited-state transients that undergo internal conversion to the ground state. The media viscosity impedes the molecular modes of ring rotation and preferentially affects one of the pathways of non-radiative decay, exerting a dominant effect on the emission

  8. DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.

    OpenAIRE

    Morgenstern, Burkhard

    2004-01-01

    DIALIGN is a widely used software tool for multiple DNA and protein sequence alignment. The program combines local and global alignment features and can therefore be applied to sequence data that cannot be correctly aligned by more traditional approaches. DIALIGN is available online through Bielefeld Bioinformatics Server (BiBiServ). The downloadable version of the program offers several new program features. To compare the output of different alignment programs, we developed the program AltA...

  9. An integrated multiple capillary array electrophoresis system for high-throughput DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Lu, X.

    1998-03-27

    A capillary array electrophoresis system was chosen to perform DNA sequencing because of several advantages such as rapid heat dissipation, multiplexing capabilities, gel matrix filling simplicity, and the mature nature of the associated manufacturing technologies. There are two major concerns for the multiple capillary systems. One concern is inter-capillary cross-talk, and the other concern is excitation and detection efficiency. Cross-talk is eliminated through proper optical coupling, good focusing and immersing capillary array into index matching fluid. A side-entry excitation scheme with orthogonal detection was established for large capillary array. Two 100 capillary array formats were used for DNA sequencing. One format is cylindrical capillary with 150 {micro}m o.d., 75 {micro}m i.d and the other format is square capillary with 300 {micro}m out edge and 75 {micro}m inner edge. This project is focused on the development of excitation and detection of DNA as well as performing DNA sequencing. The DNA injection schemes are discussed for the cases of single and bundled capillaries. An individual sampling device was designed. The base-calling was performed for a capillary from the capillary array with the accuracy of 98%.

  10. Visualization of DNA-containing structurs in various species of Chlorophyta, Rhodophyta and Cyanophyta using SYBR green I dye

    Czech Academy of Sciences Publication Activity Database

    Vítová, Milada; Hendrychová, Jana; Cepák, Vladislav; Zachleder, Vilém

    2005-01-01

    Roč. 50, č. 4 (2005), s. 333-340 ISSN 0015-5632 R&D Projects: GA ČR GA204/02/1438; GA ČR GA204/03/1113; GA AV ČR KJB5020305 Institutional research plan: CEZ:AV0Z5020903; CEZ:AV0Z60050516 Keywords : dna-containing * chlorophyta * rhodophyta Subject RIV: EE - Microbiology, Virology Impact factor: 0.918, year: 2005

  11. A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs

    Directory of Open Access Journals (Sweden)

    Gong Shiaochin

    2009-03-01

    Full Text Available Abstract Background Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. Results We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1 subclone genes of interest into BAC linking vectors, (2 insert desired reporter genes into respective genes and (3 link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. Conclusion The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

  12. A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs.

    Science.gov (United States)

    Maye, Peter; Stover, Mary Louise; Liu, Yaling; Rowe, David W; Gong, Shiaochin; Lichtler, Alexander C

    2009-03-13

    Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP) reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1) subclone genes of interest into BAC linking vectors, (2) insert desired reporter genes into respective genes and (3) link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

  13. Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil

    Science.gov (United States)

    Tay, Wee Tek; Walsh, Thomas K.; Downes, Sharon; Anderson, Craig; Jermiin, Lars S.; Wong, Thomas K. F.; Piper, Melissa C.; Chang, Ester Silva; Macedo, Isabella Barony; Czepak, Cecilia; Behere, Gajanan T.; Silvie, Pierre; Soria, Miguel F.; Frayssinet, Marie; Gordon, Karl H. J.

    2017-03-01

    The Old World bollworm Helicoverpa armigera is now established in Brazil but efforts to identify incursion origin(s) and pathway(s) have met with limited success due to the patchiness of available data. Using international agricultural/horticultural commodity trade data and mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and cytochrome b (Cyt b) gene markers, we inferred the origins and incursion pathways into Brazil. We detected 20 mtDNA haplotypes from six Brazilian states, eight of which were new to our 97 global COI-Cyt b haplotype database. Direct sequence matches indicated five Brazilian haplotypes had Asian, African, and European origins. We identified 45 parsimoniously informative sites and multiple substitutions per site within the concatenated (945 bp) nucleotide dataset, implying that probabilistic phylogenetic analysis methods are needed. High diversity and signatures of uniquely shared haplotypes with diverse localities combined with the trade data suggested multiple incursions and introduction origins in Brazil. Increasing agricultural/horticultural trade activities between the Old and New Worlds represents a significant biosecurity risk factor. Identifying pest origins will enable resistance profiling that reflects countries of origin to be included when developing a resistance management strategy, while identifying incursion pathways will improve biosecurity protocols and risk analysis at biosecurity hotspots including national ports.

  14. Simultaneous detection of multiple DNA targets by integrating dual-color graphene quantum dot nanoprobes and carbon nanotubes.

    Science.gov (United States)

    Qian, Zhaosheng; Shan, Xiaoyue; Chai, Lujing; Chen, Jianrong; Feng, Hui

    2014-12-01

    Simultaneous detection of multiple DNA targets was achieved based on a biocompatible graphene quantum dots (GQDs) and carbon nanotubes (CNTs) platform through spontaneous assembly between dual-color GQD-based probes and CNTs and subsequently self-recognition between DNA probes and targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Helix-coil transition of a four-way DNA junction observed by multiple fluorescence parameters.

    Science.gov (United States)

    Vámosi, György; Clegg, Robert M

    2008-10-16

    The thermal denaturation of immobile four-way DNA ("Holliday-") junctions with 17 base pair arms was studied via fluorescence spectroscopic measurements. Two arms of the molecule were labeled at the 5'-end with fluorescein and tetramethylrhodamine, respectively. Melting was monitored by the fluorescence intensity of the dyes, the fluorescence anisotropy of tetramethylrhodamine, and Forster resonance energy transfer (FRET) between fluorescein and rhodamine. To fit the thermal denaturation curves of the four-way junctions, two basic thermodynamic models were tested: (1) all-or-none transitions assuming a molecularity of one, two, or four and (2) a statistical "zipper" model. The all-or-none models correspond to reaction mechanisms assuming that the cooperative melting unit (that is, the structure changing from complete helix to complete coil) consists of (1) one arm, (2) two neighboring arms (which have one continuous strand common to the two arms), or (3) all four arms. In each case, the melting of the cooperative unit takes place in a single step. The tetramolecular reaction model (four-arm melting) yielded unrealistically low van't Hoff enthalpy and entropy values, whereas the monomolecular model (one-arm melting) resulted in a poor fit to the experimental data. The all-or-none bimolecular (two neighboring arm model) fit gave intermediate standard enthalpy change (Delta H) values between those expected for the melting of a duplex with a total length between the helix lengths of one and two arms (17 and 34 base pairs). Simulations according to the zipper model fit the experimental curves best when the length of the simulated duplex was assumed to be 34 base pairs, the length of a single strand. This suggests that the most important parameter determining the melting behavior of the molecule is the end-to-end distance of the strands (34 bases) rather than the length of the individual arms (17 base pairs) and that the equilibrium concentration of partially denatured

  16. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

    Science.gov (United States)

    Reshetnikov, Roman V; Sponer, Jiri; Rassokhina, Olga I; Kopylov, Alexei M; Tsvetkov, Philipp O; Makarov, Alexander A; Golovin, Andrey V

    2011-12-01

    A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. © The Author(s) 2011. Published by Oxford University Press.

  17. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

    Science.gov (United States)

    Reshetnikov, Roman V.; Sponer, Jiri; Rassokhina, Olga I.; Kopylov, Alexei M.; Tsvetkov, Philipp O.; Makarov, Alexander A.; Golovin, Andrey V.

    2011-01-01

    A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. PMID:21893589

  18. Sleep loss and acute drug abuse can induce DNA damage in multiple organs of mice.

    Science.gov (United States)

    Alvarenga, T A; Ribeiro, D A; Araujo, P; Hirotsu, C; Mazaro-Costa, R; Costa, J L; Battisti, M C; Tufik, S; Andersen, M L

    2011-09-01

    The purpose of the present study was to characterize the genetic damage induced by paradoxical sleep deprivation (PSD) in combination with cocaine or ecstasy (3,4-methylenedioxymethamphetamine; MDMA) in multiple organs of male mice using the single cell gel (comet) assay. C57BL/6J mice were submitted to PSD by the platform technique for 72 hours, followed by drug administration and evaluation of DNA damage in peripheral blood, liver and brain tissues. Cocaine was able to induce genetic damage in the blood, brain and liver cells of sleep-deprived mice at the majority of the doses evaluated. Ecstasy also induced increased DNA migration in peripheral blood cells for all concentrations tested. Analysis of damaged cells by the tail moment data suggests that ecstasy is a genotoxic chemical at the highest concentrations tested, inducing damage in liver or brain cells after sleep deprivation in mice. Taken together, our results suggest that cocaine and ecstasy/MDMA act as potent genotoxins in multiple organs of mice when associated with sleep loss.

  19. A quantum dot-aptamer beacon using a DNA intercalating dye as the FRET reporter: application to label-free thrombin detection.

    Science.gov (United States)

    Chi, Chun-Wei; Lao, Yeh-Hsing; Li, Yi-Shan; Chen, Lin-Chi

    2011-03-15

    A new quantum dot (QD)-aptamer (apt) beacon that acts by folding-induced dissociation of a DNA intercalating dye, BOBO-3(B), is demonstrated with label-free thrombin detection. The beacon, denoted as QD-apt:B, is constructed by (1) coupling of a single-stranded thrombin aptamer to Qdot 565 via EDC/Sulfo-NHS chemistry and (2) staining the duplex regions of the aptamer on QD with excess BOBO-3 before thrombin binding. When mixing a thrombin sample with QD-apt:B, BOBO-3 is competed away from the beacon due to target-induced aptamer folding, which then causes a decrease in QD fluorescence resonance energy transfer (FRET)-mediated BOBO-3 emission and achieves thrombin quantitation. In this work, the effects of Mg(2+), coupling time, and aptamer type on the beacon's performances are investigated and discussed thoroughly with various methods, including transmission electron microscopy (TEM), dynamic light scattering (DLS), and two-color differential gel electrophoresis. Using the best aptamer beacon (HTQ37), we attain highly specific and wide-range detection (from nM to μM) of thrombin in buffer, and the beacon can sense nM-range thrombin in 15% diluted serum. Compared to the reported QD aptamer assays, our method is advantageous from the aspect of using a simple sensory unit design without losing the detection sensitivity. Therefore, we consider the QD-apt:B beacon a potential alternative to immuno-reagents and an effective tool to study nucleic acid folding on QD as well. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes.

    Science.gov (United States)

    Lin, Xiaodong; Liu, Yaqing; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei; Wang, Shuo

    2018-02-21

    The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.

  1. DNA-dependent protein kinase in nonhomologous end joining: a lock with multiple keys?

    Science.gov (United States)

    Weterings, Eric; Chen, David J

    2007-10-22

    The DNA-dependent protein kinase (DNA-PK) is one of the central enzymes involved in DNA double-strand break (DSB) repair. It facilitates proper alignment of the two ends of the broken DNA molecule and coordinates access of other factors to the repair complex. We discuss the latest findings on DNA-PK phosphorylation and offer a working model for the regulation of DNA-PK during DSB repair.

  2. A Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments.

    Science.gov (United States)

    Gómez-Villegas, Miguel A; Salazar, Isabel; Sanz, Luis

    2014-02-01

    DNA microarray experiments require the use of multiple hypothesis testing procedures because thousands of hypotheses are simultaneously tested. We deal with this problem from a Bayesian decision theory perspective. We propose a decision criterion based on an estimation of the number of false null hypotheses (FNH), taking as an error measure the proportion of the posterior expected number of false positives with respect to the estimated number of true null hypotheses. The methodology is applied to a Gaussian model when testing bilateral hypotheses. The procedure is illustrated with both simulated and real data examples and the results are compared to those obtained by the Bayes rule when an additive loss function is considered for each joint action and the generalized loss 0-1 function for each individual action. Our procedure significantly reduced the percentage of false negatives whereas the percentage of false positives remains at an acceptable level.

  3. Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening

    Science.gov (United States)

    Machutta, Carl A.; Kollmann, Christopher S.; Lind, Kenneth E.; Bai, Xiaopeng; Chan, Pan F.; Huang, Jianzhong; Ballell, Lluis; Belyanskaya, Svetlana; Besra, Gurdyal S.; Barros-Aguirre, David; Bates, Robert H.; Centrella, Paolo A.; Chang, Sandy S.; Chai, Jing; Choudhry, Anthony E.; Coffin, Aaron; Davie, Christopher P.; Deng, Hongfeng; Deng, Jianghe; Ding, Yun; Dodson, Jason W.; Fosbenner, David T.; Gao, Enoch N.; Graham, Taylor L.; Graybill, Todd L.; Ingraham, Karen; Johnson, Walter P.; King, Bryan W.; Kwiatkowski, Christopher R.; Lelièvre, Joël; Li, Yue; Liu, Xiaorong; Lu, Quinn; Lehr, Ruth; Mendoza-Losana, Alfonso; Martin, John; McCloskey, Lynn; McCormick, Patti; O'Keefe, Heather P.; O'Keeffe, Thomas; Pao, Christina; Phelps, Christopher B.; Qi, Hongwei; Rafferty, Keith; Scavello, Genaro S.; Steiginga, Matt S.; Sundersingh, Flora S.; Sweitzer, Sharon M.; Szewczuk, Lawrence M.; Taylor, Amy; Toh, May Fern; Wang, Juan; Wang, Minghui; Wilkins, Devan J.; Xia, Bing; Yao, Gang; Zhang, Jean; Zhou, Jingye; Donahue, Christine P.; Messer, Jeffrey A.; Holmes, David; Arico-Muendel, Christopher C.; Pope, Andrew J.; Gross, Jeffrey W.; Evindar, Ghotas

    2017-07-01

    The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery.

  4. Binding of Multiple Rap1 Proteins Stimulates Chromosome Breakage Induction during DNA Replication.

    Directory of Open Access Journals (Sweden)

    Greicy H Goto

    2015-08-01

    Full Text Available Telomeres, the ends of linear eukaryotic chromosomes, have a specialized chromatin structure that provides a stable chromosomal terminus. In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomere length. Here we show that binding of multiple Rap1 proteins stimulates DNA double-stranded break (DSB induction at both telomeric and non-telomeric regions. Consistent with the role of DSB induction, Rap1 stimulates nearby recombination events in a dosage-dependent manner. Rap1 recruits Rif1 and Rif2 to telomeres, but neither Rif1 nor Rif2 is required for DSB induction. Rap1-mediated DSB induction involves replication fork progression but inactivation of checkpoint kinase Mec1 does not affect DSB induction. Rap1 tethering shortens artificially elongated telomeres in parallel with telomerase inhibition, and this telomere shortening does not require homologous recombination. These results suggest that Rap1 contributes to telomere homeostasis by promoting chromosome breakage.

  5. Multiple Determinations of Sperm DNA Fragmentation Show That Varicocelectomy Is Not Indicated for Infertile Patients with Subclinical Varicocele

    Directory of Open Access Journals (Sweden)

    Agustín García-Peiró

    2014-01-01

    Full Text Available Varicocele is one of the most common causes of low semen quality, which is reflected in high percentages of sperm cells with fragmented DNA. While varicocelectomy is usually performed to ameliorate a patient’s fertility, its impact on sperm DNA integrity in the case of subclinical varicocele is poorly documented. In this study, multiple DNA fragmentation analyses (TUNEL, SCD, and SCSA were performed on semen samples from sixty infertile patients with varicocele (15 clinical varicoceles, 19 clinical varicoceles after surgical treatment, 16 subclinical varicoceles, and 10 subclinical varicoceles after surgical treatment. TUNEL, SCD, and SCSA assays all showed substantial sperm DNA fragmentation levels that were comparable between subclinical and clinical varicocele patients. Importantly, varicocelectomy did improve sperm quality in patients with clinical varicocele; however, this was not the case in patients with subclinical varicocele. In summary, although infertile patients with clinical and subclinical varicocele have similar sperm DNA quality, varicocelectomy should only be advised for patients with clinical varicocele.

  6. Oxidative Stress Induced Lipid Peroxidation And DNA Adduct Formation In The Pathogenesis Of Multiple Myeloma And Lymphoma

    Directory of Open Access Journals (Sweden)

    Tandon, Ravi

    2013-02-01

    Full Text Available Objective: To access the oxidative stress status by quantification of byproducts generated during lipid peroxidation and DNA breakdown products generated during DNA damage in the blood serum of multiple myeloma and lymphoma patients.Material & Methods: Case control study comprised of 40 patients of multiple myeloma and 20 patients of lymphoma along with 20 age and sex-matched healthy subjects as controls. Levels of Malondialdehyde and 8-hydroxy-2-deoxy-Guanosine were measured to study the oxidative stress status in the study subjects.Results: The level of markers of DNA damage and lipid peroxidation were found to be raised significantly in the study subjects in comparison to healthy controls. The results indicate oxidative stress and DNA damage activity increase progressively with the progression of disease.Conclusion: Oxidative stress causes DNA damage and Lipid peroxidation which results in the formation of DNA adducts leading to mutations thereby indicate the role of oxidative stress in the pathogenesis of multiple myeloma and lymphoma.

  7. Targeting Ongoing DNA Damage in Multiple Myeloma: Effects of DNA Damage Response Inhibitors on Plasma Cell Survival

    Directory of Open Access Journals (Sweden)

    Ana Belén Herrero

    2017-05-01

    Full Text Available Human myeloma cell lines (HMCLs and a subset of myeloma patients with poor prognosis exhibit high levels of replication stress (RS, leading to DNA damage. In this study, we confirmed the presence of DNA double-strand breaks (DSBs in several HMCLs by measuring γH2AX and RAD51 foci and analyzed the effect of various inhibitors of the DNA damage response on MM cell survival. Inhibition of ataxia telangiectasia and Rad3-related protein (ATR, the main kinase mediating the response to RS, using the specific inhibitor VE-821 induced more cell death in HMCLs than in control lymphoblastoid cells and U266, an HMCL with a low level of DNA damage. The absence of ATR was partially compensated by ataxia telangiectasia-mutated protein (ATM, since chemical inhibition of both kinases using VE-821 and KU-55933 significantly increased the death of MM cells with DNA damage. We found that ATM and ATR are involved in DSB repair by homologous recombination (HR in MM. Inhibition of both kinases resulted in a stronger inhibition that may underlie cell death induction, since abolition of HR using two different inhibitors severely reduced survival of HMCLs that exhibit DNA damage. On the other hand, inhibition of the other route involved in DSB repair, non-homologous end joining (NHEJ, using the DNA-PK inhibitor NU7441, did not affect MM cell viability. Interestingly, we found that NHEJ inhibition did not increase cell death when HR was simultaneously inhibited with the RAD51 inhibitor B02, but it clearly increased the level of cell death when HR was inhibited with the MRE11 inhibitor mirin, which interferes with recombination before DNA resection takes place. Taken together, our results demonstrate for the first time that MM cells with ongoing DNA damage rely on an intact HR pathway, which thereby suggests therapeutic opportunities. We also show that inhibition of HR after the initial step of end resection might be more appropriate for inducing MM cell death, since it

  8. Multiple data sources improve DNA-based mark-recapture population estimates of grizzly bears.

    Science.gov (United States)

    Boulanger, John; Kendall, Katherine C; Stetz, Jeffrey B; Roon, David A; Waits, Lisette P; Paetkau, David

    2008-04-01

    A fundamental challenge to estimating population size with mark-recapture methods is heterogeneous capture probabilities and subsequent bias of population estimates. Confronting this problem usually requires substantial sampling effort that can be difficult to achieve for some species, such as carnivores. We developed a methodology that uses two data sources to deal with heterogeneity and applied this to DNA mark-recapture data from grizzly bears (Ursus arctos). We improved population estimates by incorporating additional DNA "captures" of grizzly bears obtained by collecting hair from unbaited bear rub trees concurrently with baited, grid-based, hair snag sampling. We consider a Lincoln-Petersen estimator with hair snag captures as the initial session and rub tree captures as the recapture session and develop an estimator in program MARK that treats hair snag and rub tree samples as successive sessions. Using empirical data from a large-scale project in the greater Glacier National Park, Montana, USA, area and simulation modeling we evaluate these methods and compare the results to hair-snag-only estimates. Empirical results indicate that, compared with hair-snag-only data, the joint hair-snag-rub-tree methods produce similar but more precise estimates if capture and recapture rates are reasonably high for both methods. Simulation results suggest that estimators are potentially affected by correlation of capture probabilities between sample types in the presence of heterogeneity. Overall, closed population Huggins-Pledger estimators showed the highest precision and were most robust to sparse data, heterogeneity, and capture probability correlation among sampling types. Results also indicate that these estimators can be used when a segment of the population has zero capture probability for one of the methods. We propose that this general methodology may be useful for other species in which mark-recapture data are available from multiple sources.

  9. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

    Science.gov (United States)

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence d...

  10. Nano-dyeing

    Directory of Open Access Journals (Sweden)

    Ning Cui-Juan

    2016-01-01

    Full Text Available Dyeing nanofibers is a frontier of both modern textile engineering and nanotechnology. This paper suggest a feasible method for dyeing nanofibers with a natural red (Roselle Calyx by bubble electrospinning. Reactive dye (Red S3B and acid dye (Red 2B were also used in the experiment for comparison. The dyeing process was finished during the spinning process.

  11. Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk.

    Science.gov (United States)

    Waller, Rosalie G; Darlington, Todd M; Wei, Xiaomu; Madsen, Michael J; Thomas, Alun; Curtin, Karen; Coon, Hilary; Rajamanickam, Venkatesh; Musinsky, Justin; Jayabalan, David; Atanackovic, Djordje; Rajkumar, S Vincent; Kumar, Shaji; Slager, Susan; Middha, Mridu; Galia, Perrine; Demangel, Delphine; Salama, Mohamed; Joseph, Vijai; McKay, James; Offit, Kenneth; Klein, Robert J; Lipkin, Steven M; Dumontet, Charles; Vachon, Celine M; Camp, Nicola J

    2018-02-01

    The high-risk pedigree (HRP) design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS) method in 11 extended, Utah, multiple myeloma (MM) HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM) cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu), a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val), a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.

  12. Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk.

    Directory of Open Access Journals (Sweden)

    Rosalie G Waller

    2018-02-01

    Full Text Available The high-risk pedigree (HRP design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS method in 11 extended, Utah, multiple myeloma (MM HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu, a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val, a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.

  13. Multiple DNA binding proteins contribute to timing of chromosome replication in E. coli

    DEFF Research Database (Denmark)

    Riber, Leise; Frimodt-Møller, Jakob; Charbon, Godefroid

    2016-01-01

    Chromosome replication in Escherichia coli is initiated from a single origin, oriC. Initiation involves a number of DNA binding proteins, but only DnaA is essential and specific for the initiation process. DnaA is an AAA+ protein that binds both ATP and ADP with similar high affinities. Dna...... replication is initiated, or the time window in which all origins present in a single cell are initiated, i.e. initiation synchrony, or both. Overall, these DNA binding proteins modulate the initiation frequency from oriC by: (i) binding directly to oriC to affect DnaA binding, (ii) altering the DNA topology...... in or around oriC, (iii) altering the nucleotide bound status of DnaA by interacting with non-coding chromosomal sequences, distant from oriC, that are important for DnaA activity. Thus, although DnaA is the key protein for initiation of replication, other DNA-binding proteins act not only on ori...

  14. Multiple and variable NHEJ-like genes are involved in resistance to DNA damage in Streptomyces ambofaciens

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    Grégory Hoff

    2016-11-01

    Full Text Available Non homologous end-joining (NHEJ is a double strand break (DSB repair pathway which does not require any homologous template and can ligate two DNA ends together. The basic bacterial NHEJ machinery involves two partners: the Ku protein, a DNA end binding protein for DSB recognition and the multifunctional LigD protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. In silico analyses performed in the 38 sequenced genomes of Streptomyces species revealed the existence of a large panel of NHEJ-like genes. Indeed, ku genes or ligD domain homologues are scattered throughout the genome in multiple copies and can be distinguished in two categories: the core NHEJ gene set constituted of conserved loci and the variable NHEJ gene set constituted of NHEJ-like genes present in only a part of the species. In Streptomyces ambofaciens ATCC 23877, not only the deletion of core genes but also that of variable genes led to an increased sensitivity to DNA damage induced by electron beam irradiation. Multiple mutants of ku, ligase or polymerase encoding genes showed an aggravated phenotype compared to single mutants. Biochemical assays revealed the ability of Ku-like proteins to protect and to stimulate ligation of DNA ends. RT-qPCR and GFP fusion experiments suggested that ku-like genes show a growth phase dependent expression profile consistent with their involvement in DNA repair during spores formation and/or germination.

  15. XRCC1 and PCNA are loading platforms with distinct kinetic properties and different capacities to respond to multiple DNA lesions

    Directory of Open Access Journals (Sweden)

    Leonhardt Heinrich

    2007-09-01

    Full Text Available Abstract Background Genome integrity is constantly challenged and requires the coordinated recruitment of multiple enzyme activities to ensure efficient repair of DNA lesions. We investigated the dynamics of XRCC1 and PCNA that act as molecular loading platforms and play a central role in this coordination. Results Local DNA damage was introduced by laser microirradation and the recruitment of fluorescent XRCC1 and PCNA fusion proteins was monitored by live cell microscopy. We found an immediate and fast recruitment of XRCC1 preceding the slow and continuous recruitment of PCNA. Fluorescence bleaching experiments (FRAP and FLIP revealed a stable association of PCNA with DNA repair sites, contrasting the high turnover of XRCC1. When cells were repeatedly challenged with multiple DNA lesions we observed a gradual depletion of the nuclear pool of PCNA, while XRCC1 dynamically redistributed even to lesions inflicted last. Conclusion These results show that PCNA and XRCC1 have distinct kinetic properties with functional consequences for their capacity to respond to successive DNA damage events.

  16. XRCC1 and PCNA are loading platforms with distinct kinetic properties and different capacities to respond to multiple DNA lesions

    Science.gov (United States)

    Mortusewicz, Oliver; Leonhardt, Heinrich

    2007-01-01

    Background Genome integrity is constantly challenged and requires the coordinated recruitment of multiple enzyme activities to ensure efficient repair of DNA lesions. We investigated the dynamics of XRCC1 and PCNA that act as molecular loading platforms and play a central role in this coordination. Results Local DNA damage was introduced by laser microirradation and the recruitment of fluorescent XRCC1 and PCNA fusion proteins was monitored by live cell microscopy. We found an immediate and fast recruitment of XRCC1 preceding the slow and continuous recruitment of PCNA. Fluorescence bleaching experiments (FRAP and FLIP) revealed a stable association of PCNA with DNA repair sites, contrasting the high turnover of XRCC1. When cells were repeatedly challenged with multiple DNA lesions we observed a gradual depletion of the nuclear pool of PCNA, while XRCC1 dynamically redistributed even to lesions inflicted last. Conclusion These results show that PCNA and XRCC1 have distinct kinetic properties with functional consequences for their capacity to respond to successive DNA damage events. PMID:17880707

  17. Multiple ways to prevent transmission of paternal mitochondrial DNA for maternal inheritance in animals.

    Science.gov (United States)

    Sato, Ken; Sato, Miyuki

    2017-10-01

    Mitochondria contain their own DNA (mtDNA). In most sexually reproducing organisms, mtDNA is inherited maternally (uniparentally); this type of inheritance is thus referred to as 'maternal (uniparental) inheritance'. Recent studies have revealed various mechanisms to prevent the transmission of sperm-derived paternal mtDNA to the offspring, thereby ensuring maternal inheritance of mtDNA. In the nematode Caenorhabditis elegans, paternal mitochondria and their mtDNA degenerate almost immediately after fertilization and are selectively degraded by autophagy, which is referred to as 'allophagy' (allogeneic [non-self] organelle autophagy). In the fruit fly Drosophila melanogaster, paternal mtDNA is largely eliminated by an endonuclease G-mediated mechanism. Paternal mitochondria are subsequently removed by endocytic and autophagic pathways after fertilization. In many mammals, including humans, paternal mitochondria enter fertilized eggs. However, the fate of paternal mitochondria and their mtDNA in mammals is still a matter of debate. In this review, we will summarize recent knowledge on the molecular mechanisms underlying the prevention of paternal mtDNA transmission, which ensures maternal mtDNA inheritance in animals. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  18. A linear concatenation strategy to construct 5'-enriched amplified cDNA libraries using multiple displacement amplification.

    Science.gov (United States)

    Gadkar, Vijay J; Filion, Martin

    2013-06-01

    In various experimental systems, limiting available amounts of RNA may prevent a researcher from performing large-scale analyses of gene transcripts. One way to circumvent this is to 'pre-amplify' the starting RNA/cDNA, so that sufficient amounts are available for any downstream analysis. In the present study, we report the development of a novel protocol for constructing amplified cDNA libraries using the Phi29 DNA polymerase based multiple displacement amplification (MDA) system. Using as little as 200 ng of total RNA, we developed a linear concatenation strategy to make the single-stranded cDNA template amenable for MDA. The concatenation, made possible by the template switching property of the reverse transcriptase enzyme, resulted in the amplified cDNA library with intact 5' ends. MDA generated micrograms of template, allowing large-scale polymerase chain reaction analyses or other large-scale downstream applications. As the amplified cDNA library contains intact 5' ends, it is also compatible with 5' RACE analyses of specific gene transcripts. Empirical validation of this protocol is demonstrated on a highly characterized (tomato) and an uncharacterized (corn gromwell) experimental system.

  19. Hair dye poisoning

    Science.gov (United States)

    Hair tint poisoning ... Different types of hair dye contain different harmful ingredients. The harmful ingredients in permanent dyes are: Naphthylamine Other aromatic amino compounds Phenylenediamines Toluene ...

  20. Multiple homoplasious insertions and deletions of a Triticeae (Poaceae DNA transposon: a phylogenetic perspective

    Directory of Open Access Journals (Sweden)

    Mason-Gamer Roberta J

    2007-06-01

    Full Text Available Abstract Background Stowaway elements are short, non-autonomous DNA transposons categorized as miniature inverted-repeat transposable elements (MITEs. The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed. Thus, a phylogenetic perspective on presence vs. absence of elements in an aligned data set can provide valuable historical insights into the dynamics of MITE acquisition and loss. Results A Stowaway-like element resides within the fourth intron of a β-amylase gene in representatives of five genera in the wheat tribe, Triticeae. Its presence vs. absence was examined with reference to the β-amylase gene tree topology, and in light of sequence comparisons of the β-amylase elements to Triticeae Stowaway elements in the Entrez nucleotide database. Among the sequences lacking the element, there are five distinct putative excision footprints (one widespread and four restricted to unrelated lineages and two flanking deletions. The sequences that do contain elements are polyphyletic on the β-amylase tree, and their elements are divergent at the sequence level. The β-amylase elements do not form a monophyletic group relative to other Stowaway elements in Entrez; most are more similar to elements from other loci in other Triticeae genomes than they are to one another. Conclusion Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway-like element has undergone multiple deletions from and insertions into the same site in β-amylase intron 4 during the history of the tribe. The elements currently at the site represent multiple, distinct lineages that transcend generic boundaries. While patterns of Stowaway polymorphism across a phylogenetic data set do not allow evolutionary mechanisms to be inferred with certainty, they do provide

  1. MELAS syndrome associated with both A3243G-tRNALeu mutation and multiple mitochondrial DNA deletions.

    Science.gov (United States)

    Aharoni, Sharon; Traves, Teres A; Melamed, Eldad; Cohen, Sarit; Silver, Esther Leshinsky

    2010-09-15

    The syndrome of mitochondrial encephalopathy, lactic acidosis, and stroke-like episode (MELAS) is characterized clinically by recurrent focal neurological deficits, epilepsy, and short stature. The phenotypic spectrum is extremely diverse, with multisystemic organ involvement leading to isolated diabetes, deafness, renal tubulopathy, hypertrophic cardiomyopathy, and retinitis pigmentosa. In 80% of cases, the syndrome is associated with an AG transmission mutation (A3243G) in the tRNALeu gene of the mitochondrial DNA (mtDNA). We describe a woman with a unique combination of the MELAS A3243G mutation and multiple mtDNA deletions with normal POLG sequence. The patient presented with diabetes mellitus, sensorineural deafness, short stature, and mental disorientation. All her three children died in early adolescence. 2010 Elsevier B.V. All rights reserved.

  2. Mitochondrial DNA T4216C and A4917G variations in multiple sclerosis

    DEFF Research Database (Denmark)

    Andalib, Sasan; Talebi, Mahnaz; Sakhinia, Ebrahim

    2015-01-01

    DNA gene and A4917G variation in the mtDNA NADH Dehydrogenase 2 (ND2) gene are associated with MS in an Iranian population. MATERIAL AND METHODS: Blood samples were collected from 100 patients with MS and 100 unrelated healthy controls, and DNA extraction was performed by salting-out. By means.......637). Logistic regression analysis revealed an odds ratio (OR) of 1.2 with 95% CI of 0.4-3.5. CONCLUSION: The present study revealed no association between MS and T4216C variation in the ND1 mtDNA gene and A4917G variation in the mtDNA ND2 gene in the Iranian population....... focuses on the neurogenetics of the complex pathogenesis of MS in relation to factors such as mitochondrial DNA (mtDNA) variations. T4216C and A4917G are common mitochondrial gene variations associated with MS. The present study tested whether mtDNA T4216C variation in the NADH Dehydrogenase 1 (ND1) mt...

  3. Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre

    DEFF Research Database (Denmark)

    Lisby, M.; Mortensen, Uffe Hasbro; Rothstein, R.

    2003-01-01

    DNA double-strand break repair (DSBR) is an essential process for preserving genomic integrity in all organisms. To investigate this process at the cellular level, we engineered a system of fluorescently marked DNA double-strand breaks (DSBs) in the yeast Saccharomyces cerevisiae to visualize in ...

  4. Enhanced post wash retention of combed DNA molecules by varying multiple combing parameters.

    Science.gov (United States)

    Yadav, Hemendra; Sharma, Pulkit

    2017-11-01

    Recent advances in genomics have created a need for efficient techniques for deciphering information hidden in various genomes. Single molecule analysis is one such technique to understand molecular processes at single molecule level. Fiber- FISH performed with the help of DNA combing can help us in understanding genetic rearrangements and changes in genome at single DNA molecule level. For performing Fiber-FISH we need high retention of combed DNA molecules post wash as Fiber-FISH requires profuse washing. We optimized combing process involving combing solution, method of DNA mounting on glass slides and coating of glass slides to enhance post-wash retention of DNA molecules. It was found that average number of DNA molecules observed post-wash per field of view was maximum with our optimized combing solution. APTES coated glass slides showed lesser retention than PEI surface but fluorescent intensity was higher in case of APTES coated surface. Capillary method used to mount DNA on glass slides also showed lesser retention but straight DNA molecules were observed as compared to force flow method. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Identification of multiple mRNA and DNA sequences from small tissue samples isolated by laser-assisted microdissection.

    Science.gov (United States)

    Bernsen, M R; Dijkman, H B; de Vries, E; Figdor, C G; Ruiter, D J; Adema, G J; van Muijen, G N

    1998-10-01

    Molecular analysis of small tissue samples has become increasingly important in biomedical studies. Using a laser dissection microscope and modified nucleic acid isolation protocols, we demonstrate that multiple mRNA as well as DNA sequences can be identified from a single-cell sample. In addition, we show that the specificity of procurement of tissue samples is not compromised by smear contamination resulting from scraping of the microtome knife during sectioning of lesions. The procedures described herein thus allow for efficient RT-PCR or PCR analysis of multiple nucleic acid sequences from small tissue samples obtained by laser-assisted microdissection.

  6. Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

    Directory of Open Access Journals (Sweden)

    Suryani Lukman

    Full Text Available The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD. In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs. Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3. Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart. Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1 a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2 possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.

  7. Evaluation of simultaneous binding of Chromomycin A3 to the multiple sites of DNA by the new restriction enzyme assay.

    Science.gov (United States)

    Murase, Hirotaka; Noguchi, Tomoharu; Sasaki, Shigeki

    2018-06-01

    Chromomycin A3 (CMA3) is an aureolic acid-type antitumor antibiotic. CMA3 forms dimeric complexes with divalent cations, such as Mg 2+ , which strongly binds to the GC rich sequence of DNA to inhibit DNA replication and transcription. In this study, the binding property of CMA3 to the DNA sequence containing multiple GC-rich binding sites was investigated by measuring the protection from hydrolysis by the restriction enzymes, AccII and Fnu4HI, for the center of the CGCG site and the 5'-GC↓GGC site, respectively. In contrast to the standard DNase I footprinting method, the DNA substrates are fully hydrolyzed by the restriction enzymes, therefore, the full protection of DNA at all the cleavable sites indicates that CMA3 simultaneously binds to all the binding sites. The restriction enzyme assay has suggested that CMA3 has a high tendency to bind the successive CGCG sites and the CGG repeat. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. An inverse switch in DNA base excision and strand break repair contributes to melphalan resistance in multiple myeloma cells.

    Directory of Open Access Journals (Sweden)

    Mirta M L Sousa

    Full Text Available Alterations in checkpoint and DNA repair pathways may provide adaptive mechanisms contributing to acquired drug resistance. Here, we investigated the levels of proteins mediating DNA damage signaling and -repair in RPMI8226 multiple myeloma cells and its Melphalan-resistant derivative 8226-LR5. We observed markedly reduced steady-state levels of DNA glycosylases UNG2, NEIL1 and MPG in the resistant cells and cross-resistance to agents inducing their respective DNA base lesions. Conversely, repair of alkali-labile sites was apparently enhanced in the resistant cells, as substantiated by alkaline comet assay, autoribosylation of PARP-1, and increased sensitivity to PARP-1 inhibition by 4-AN or KU58684. Reduced base-excision and enhanced single-strand break repair would both contribute to the observed reduction in genomic alkali-labile sites, which could jeopardize productive processing of the more cytotoxic Melphalan-induced interstrand DNA crosslinks (ICLs. Furthermore, we found a marked upregulation of proteins in the non-homologous end-joining (NHEJ pathway of double-strand break (DSB repair, likely contributing to the observed increase in DSB repair kinetics in the resistant cells. Finally, we observed apparent upregulation of ATR-signaling and downregulation of ATM-signaling in the resistant cells. This was accompanied by markedly increased sensitivity towards Melphalan in the presence of ATR-, DNA-PK, or CHK1/2 inhibitors whereas no sensitizing effect was observed subsequent to ATM inhibition, suggesting that replication blocking lesions are primary triggers of the DNA damage response in the Melphalan resistant cells. In conclusion, Melphalan resistance is apparently contributed by modulation of the DNA damage response at multiple levels, including downregulation of specific repair pathways to avoid repair intermediates that could impair efficient processing of cytotoxic ICLs and ICL-induced DSBs. This study has revealed several novel

  9. Anaerobic azo dye reduction

    OpenAIRE

    Zee, van der, F.P.

    2002-01-01

    Azo dyes, aromatic moieties linked together by azo (-N=N-) chromophores, represent the largest class of dyes used in textile-processing and other industries. The release of these compounds into the environment is undesirable, not only because of their colour, but also because many azo dyes and their breakdown products are toxic and/or mutagenic to life. To remove azo dyes from wastewater, a biological treatment strategy based on anaerobic reduction of the azo dye...

  10. Hypervariability of ribosomal DNA at multiple chromosomal sites in lake trout (Salvelinus namaycush).

    Science.gov (United States)

    Zhuo, L; Reed, K M; Phillips, R B

    1995-06-01

    Variation in the intergenic spacer (IGS) of the ribosomal DNA (rDNA) of lake trout (Salvelinus namaycush) was examined. Digestion of genomic DNA with restriction enzymes showed that almost every individual had a unique combination of length variants with most of this variation occurring within rather than between populations. Sequence analysis of a 2.3 kilobase (kb) EcoRI-DraI fragment spanning the 3' end of the 28S coding region and approximately 1.8 kb of the IGS revealed two blocks of repetitive DNA. Putative transcriptional termination sites were found approximately 220 bases (b) downstream from the end of the 28S coding region. Comparison of the 2.3-kb fragments with two longer (3.1 kb) fragments showed that the major difference in length resulted from variation in the number of short (89 b) repeats located 3' to the putative terminator. Repeat units within a single nucleolus organizer region (NOR) appeared relatively homogeneous and genetic analysis found variants to be stably inherited. A comparison of the number of spacer-length variants with the number of NORs found that the number of length variants per individual was always less than the number of NORs. Examination of spacer variants in five populations showed that populations with more NORs had more spacer variants, indicating that variants are present at different rDNA sites on nonhomologous chromosomes.

  11. Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation.

    Science.gov (United States)

    Kuan, Pei Fen; Chiang, Derek Y

    2012-09-01

    DNA methylation has emerged as an important hallmark of epigenetics. Numerous platforms including tiling arrays and next generation sequencing, and experimental protocols are available for profiling DNA methylation. Similar to other tiling array data, DNA methylation data shares the characteristics of inherent correlation structure among nearby probes. However, unlike gene expression or protein DNA binding data, the varying CpG density which gives rise to CpG island, shore and shelf definition provides exogenous information in detecting differential methylation. This article aims to introduce a robust testing and probe ranking procedure based on a nonhomogeneous hidden Markov model that incorporates the above-mentioned features for detecting differential methylation. We revisit the seminal work of Sun and Cai (2009, Journal of the Royal Statistical Society: Series B (Statistical Methodology)71, 393-424) and propose modeling the nonnull using a nonparametric symmetric distribution in two-sided hypothesis testing. We show that this model improves probe ranking and is robust to model misspecification based on extensive simulation studies. We further illustrate that our proposed framework achieves good operating characteristics as compared to commonly used methods in real DNA methylation data that aims to detect differential methylation sites. © 2012, The International Biometric Society.

  12. Single-cell multiple gene expression analysis based on single-molecule-detection microarray assay for multi-DNA determination

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lu [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Xianwei [School of Life Sciences, Shandong University, Jinan 250100 (China); Zhang, Xiaoli [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Jinxing [School of Life Sciences, Shandong University, Jinan 250100 (China); Jin, Wenrui, E-mail: jwr@sdu.edu.cn [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)

    2015-01-07

    Highlights: • A single-molecule-detection (SMD) microarray for 10 samples is fabricated. • The based-SMD microarray assay (SMA) can determine 8 DNAs for each sample. • The limit of detection of SMA is as low as 1.3 × 10{sup −16} mol L{sup −1}. • The SMA can be applied in single-cell multiple gene expression analysis. - Abstract: We report a novel ultra-sensitive and high-selective single-molecule-detection microarray assay (SMA) for multiple DNA determination. In the SMA, a capture DNA (DNAc) microarray consisting of 10 subarrays with 9 spots for each subarray is fabricated on a silanized glass coverslip as the substrate. On the subarrays, the spot-to-spot spacing is 500 μm and each spot has a diameter of ∼300 μm. The sequence of the DNAcs on the 9 spots of a subarray is different, to determine 8 types of target DNAs (DNAts). Thus, 8 types of DNAts are captured to their complementary DNAcs at 8 spots of a subarray, respectively, and then labeled with quantum dots (QDs) attached to 8 types of detection DNAs (DNAds) with different sequences. The ninth spot is used to detect the blank value. In order to determine the same 8 types of DNAts in 10 samples, the 10 DNAc-modified subarrays on the microarray are identical. Fluorescence single-molecule images of the QD-labeled DNAts on each spot of the subarray are acquired using a home-made single-molecule microarray reader. The amounts of the DNAts are quantified by counting the bright dots from the QDs. For a microarray, 8 types of DNAts in 10 samples can be quantified in parallel. The limit of detection of the SMA for DNA determination is as low as 1.3 × 10{sup −16} mol L{sup −1}. The SMA for multi-DNA determination can also be applied in single-cell multiple gene expression analysis through quantification of complementary DNAs (cDNAs) corresponding to multiple messenger RNAs (mRNAs) in single cells. To do so, total RNA in single cells is extracted and reversely transcribed into their cDNAs. Three

  13. DNA mediated wire-like clusters of self-assembled TiO₂ nanomaterials: supercapacitor and dye sensitized solar cell applications.

    Science.gov (United States)

    Nithiyanantham, U; Ramadoss, Ananthakumar; Ede, Sivasankara Rao; Kundu, Subrata

    2014-07-21

    A new route for the formation of wire-like clusters of TiO₂ nanomaterials self-assembled in DNA scaffold within an hour of reaction time is reported. TiO₂ nanomaterials are synthesized by the reaction of titanium-isopropoxide with ethanol and water in the presence of DNA under continuous stirring and heating at 60 °C. The individual size of the TiO₂ NPs self-assembled in DNA and the diameter of the wires can be tuned by controlling the DNA to Ti-salt molar ratios and other reaction parameters. The eventual diameter of the individual particles varies between 15 ± 5 nm ranges, whereas the length of the nanowires varies in the 2-3 μm range. The synthesized wire-like DNA-TiO₂ nanomaterials are excellent materials for electrochemical supercapacitor and DSSC applications. From the electrochemical supercapacitor experiment, it was found that the TiO₂ nanomaterials showed different specific capacitance (Cs) values for the various nanowires, and the order of Cs values are as follows: wire-like clusters (small size) > wire-like clusters (large size). The highest Cs of 2.69 F g(-1) was observed for TiO₂ having wire-like structure with small sizes. The study of the long term cycling stability of wire-like clusters (small size) electrode were shown to be stable, retaining ca. 80% of the initial specific capacitance, even after 5000 cycles. The potentiality of the DNA-TiO₂ nanomaterials was also tested in photo-voltaic applications and the observed efficiency was found higher in the case of wire-like TiO₂ nanostructures with larger sizes compared to smaller sizes. In future, the described method can be extended for the synthesis of other oxide based materials on DNA scaffold and can be further used in other applications like sensors, Li-ion battery materials or treatment for environmental waste water.

  14. A novel GMO biosensor for rapid ultrasensitive and simultaneous detection of multiple DNA components in GMO products.

    Science.gov (United States)

    Huang, Lin; Zheng, Lei; Chen, Yinji; Xue, Feng; Cheng, Lin; Adeloju, Samuel B; Chen, Wei

    2015-04-15

    Since the introduction of genetically modified organisms (GMOs), there has been on-going and continuous concern and debates on the commercialization of products derived from GMOs. There is an urgent need for development of highly efficient analytical methods for rapid and high throughput screening of GMOs components, as required for appropriate labeling of GMO-derived foods, as well as for on-site inspection and import/export quarantine. In this study, we describe, for the first time, a multi-labeling based electrochemical biosensor for simultaneous detection of multiple DNA components of GMO products on the same sensing interface. Two-round signal amplification was applied by using both an exonuclease enzyme catalytic reaction and gold nanoparticle-based bio-barcode related strategies, respectively. Simultaneous multiple detections of different DNA components of GMOs were successfully achieved with satisfied sensitivity using this electrochemical biosensor. Furthermore, the robustness and effectiveness of the proposed approach was successfully demonstrated by application to various GMO products, including locally obtained and confirmed commercial GMO seeds and transgenetic plants. The proposed electrochemical biosensor demonstrated unique merits that promise to gain more interest in its use for rapid and on-site simultaneous multiple screening of different components of GMO products. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Assessing flow paths in a karst aquifer based on multiple dye tracing tests using stochastic simulation and the MODFLOW-CFP code

    Science.gov (United States)

    Assari, Amin; Mohammadi, Zargham

    2017-09-01

    Karst systems show high spatial variability of hydraulic parameters over small distances and this makes their modeling a difficult task with several uncertainties. Interconnections of fractures have a major role on the transport of groundwater, but many of the stochastic methods in use do not have the capability to reproduce these complex structures. A methodology is presented for the quantification of tortuosity using the single normal equation simulation (SNESIM) algorithm and a groundwater flow model. A training image was produced based on the statistical parameters of fractures and then used in the simulation process. The SNESIM algorithm was used to generate 75 realizations of the four classes of fractures in a karst aquifer in Iran. The results from six dye tracing tests were used to assign hydraulic conductivity values to each class of fractures. In the next step, the MODFLOW-CFP and MODPATH codes were consecutively implemented to compute the groundwater flow paths. The 9,000 flow paths obtained from the MODPATH code were further analyzed to calculate the tortuosity factor. Finally, the hydraulic conductivity values calculated from the dye tracing experiments were refined using the actual flow paths of groundwater. The key outcomes of this research are: (1) a methodology for the quantification of tortuosity; (2) hydraulic conductivities, that are incorrectly estimated (biased low) with empirical equations that assume Darcian (laminar) flow with parallel rather than tortuous streamlines; and (3) an understanding of the scale-dependence and non-normal distributions of tortuosity.

  16. Tunable Microfluidic Dye Laser

    DEFF Research Database (Denmark)

    Olsen, Brian Bilenberg; Helbo, Bjarne; Kutter, Jörg Peter

    2003-01-01

    We present a tunable microfluidic dye laser fabricated in SU-8. The tunability is enabled by integrating a microfluidic diffusion mixer with an existing microfluidic dye laser design by Helbo et al. By controlling the relative flows in the mixer between a dye solution and a solvent......, the concentration of dye in the laser cavity can be adjusted, allowing the wavelength to be tuned. Wavelength tuning controlled by the dye concentration was demonstrated with macroscopic dye lasers already in 1971, but this principle only becomes practically applicable by the use of microfluidic mixing...

  17. Human embryonic stem cells have enhanced repair of multiple forms of DNA damage

    DEFF Research Database (Denmark)

    Maynard, Scott; Swistowska, Anna Maria; Lee, Jae Wan

    2008-01-01

    cells compared with various differentiated murine cells. Using single-cell gel electrophoresis (comet assay) we found that human embryonic stem cells (BG01, I6) have more efficient repair of different types of DNA damage (generated from H2O2, UV-C, ionizing radiation, or psoralen) than human primary...

  18. PicoGreen dye as an active medium for plastic lasers

    Science.gov (United States)

    Pradeep, C.; Vallabhan, C. P. G.; Radhakrishnan, P.; Nampoori, V. P. N.

    2015-08-01

    Deoxyribonucleic acid lipid complex thin films are used as a host material for laser dyes. We tested PicoGreen dye, which is commonly used for the quantification of single and double stranded DNA, for its applicability as lasing medium. PicoGreen dye exhibits enhanced fluorescence on intercalation with DNA. This enormous fluorescence emission is amplified in a planar microcavity to achieve yellow lasing. Here the role of DNA is not only a host medium, but also as a fluorescence dequencher. With the obtained results we have ample reasons to propose PicoGreen dye as a lasing medium, which can lead to the development of DNA based bio-lasers.

  19. Diagnostic value of stool DNA testing for multiple markers of colorectal cancer and advanced adenoma: a meta-analysis.

    Science.gov (United States)

    Yang, Hua; Xia, Bing-Qing; Jiang, Bo; Wang, Guozhen; Yang, Yi-Peng; Chen, Hao; Li, Bing-Sheng; Xu, An-Gao; Huang, Yun-Bo; Wang, Xin-Ying

    2013-08-01

    The diagnostic value of stool DNA (sDNA) testing for colorectal neoplasms remains controversial. To compensate for the lack of large-scale unbiased population studies, a meta-analysis was performed to evaluate the diagnostic value of sDNA testing for multiple markers of colorectal cancer (CRC) and advanced adenoma. The PubMed, Science Direct, Biosis Review, Cochrane Library and Embase databases were systematically searched in January 2012 without time restriction. Meta-analysis was performed using a random-effects model using sensitivity, specificity, diagnostic OR (DOR), summary ROC curves, area under the curve (AUC), and 95% CIs as effect measures. Heterogeneity was measured using the χ(2) test and Q statistic; subgroup analysis was also conducted. A total of 20 studies comprising 5876 individuals were eligible. There was no heterogeneity for CRC, but adenoma and advanced adenoma harboured considerable heterogeneity influenced by risk classification and various detection markers. Stratification analysis according to risk classification showed that multiple markers had a high DOR for the high-risk subgroups of both CRC (sensitivity 0.759 [95% CI 0.711 to 0.804]; specificity 0.883 [95% CI 0.846 to 0.913]; AUC 0.906) and advanced adenoma (sensitivity 0.683 [95% CI 0.584 to 0.771]; specificity 0.918 [95% CI 0.866 to 0.954]; AUC 0.946) but not for the average-risk subgroups of either. In the methylation subgroup, sDNA testing had significantly higher DOR for CRC (sensitivity 0.753 [95% CI 0.685 to 0.812]; specificity 0.913 [95% CI 0.860 to 0.950]; AUC 0.918) and advanced adenoma (sensitivity 0.623 [95% CI 0.527 to 0.712]; specificity 0.926 [95% CI 0.882 to 0.958]; AUC 0.910) compared with the mutation subgroup. There was no significant heterogeneity among studies for subgroup analysis. sDNA testing for multiple markers had strong diagnostic significance for CRC and advanced adenoma in high-risk subjects. Methylation makers had more diagnostic value than mutation

  20. Chemistry of Natural Dyes

    Indian Academy of Sciences (India)

    scientific principles, and the interaction between the dye and the dyed material is ... Dyes are classified based on their structure, source, method of application .... the right source that gives not only beautiful tones, but colourfast shades as well.

  1. Visual Detection of Potato leafroll virus by One-step Reverse Transcription Loop-Mediated Isothermal Amplification of DNA with Hydroxynaphthol Blue Dye

    NARCIS (Netherlands)

    Ahmadi, S.; Almasi, A.M.; Fatehi, F.; Struik, P.C.; Moradi, A.

    2013-01-01

    Loop-mediated isothermal amplification (LAMP) assay is a novel technique for amplifying DNA under constant temperature, with high specificity, sensitivity, rapidity and efficiency. We applied reverse transcription loop-mediated isothermal amplification (RT-LAMP) to visually detect Potato leafroll

  2. Tumor-specific histone signature and DNA methylation in multiple myeloma and leukemia cells

    Czech Academy of Sciences Publication Activity Database

    Foltánková, Veronika; Legartová, Soňa; Kozubek, Stanislav; Bártová, Eva

    2012-01-01

    Roč. 59, č. 4 (2012), s. 450-462 ISSN 0028-2685 R&D Projects: GA ČR(CZ) GAP302/10/1022; GA ČR GBP302/12/G157 Institutional research plan: CEZ:AV0Z50040702 Keywords : ChIP * histones * DNA methylation Subject RIV: BO - Biophysics Impact factor: 1.574, year: 2012

  3. Evidence for multiple repair pathways of double-strand DNA breaks in Chinese hamster cells

    International Nuclear Information System (INIS)

    Giaccia, A.J.; Weistein, R.; Stamato, T.D.; Roosa, R.

    1984-01-01

    XR-1 is a mutant of the Chinese hamster cell (CHO-K1) which is abnormally sensitive to killing by gamma rays in G/sub 1/ (D37 = 27 rads vs. 318 for parent) and early S phases of the cell cycle but has near normal resistance in late S and early G/sub 2/ (Somatic Cell Genetics, 9:165-173, 1983). Complementation studies between XR-1 and its parent indicate that this sensitivity to gamma rays is a recessive phenotype. Both the XR-1 and its parent cell are able to repair single strand DNA breaks. However, in comparison to its parental cell, the XR-1 cell is markedly deficient in the repair of double strand DNA breaks introduced by gamma irradiation during the sensitive G/sub 1/-early S period, while in the late S-G/sub 2/ resistant period the repair is similar in both cells. This correlation suggests that an unrepaired double strand DNA break is the lethal lesion and that at least two pathways for the repair of these lesions exist in mammalian cells

  4. Multiple pathways of DNA double-strand break processing in a mutant Indian muntjac cell line

    International Nuclear Information System (INIS)

    Bouffler, S.D.; Jha, B.; Johnson, R.T.

    1990-01-01

    DNA break processing is compared in the Indian muntjac cell lines, SVM and DM. The initial frequencies and resealing of X-ray generated single- and double-strand breaks are similar in the two cell lines. Inhibiting the repair of UV damage leads to greater double-strand breakage in SVM than in DM, and some of these breaks are not repaired; however, repair-associated single-strand breakage and resealing are normal. Dimethylsulfate also induces excess double-strand breakage in SVM, and these breaks are irreparable. Restricted plasmids are reconstituted correctly in SVM at approximately 30% of the frequency observed in DM. Thus SVM has a reduced capacity to repair certain types of double-strand break. This defect is not due to a DNA ligase deficiency. We conclude that DNA double-strand breaks are repaired by a variety of pathways within mammalian cells and that the structure of the break or its mode of formation determines its subsequent fate

  5. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

    Directory of Open Access Journals (Sweden)

    Athma A Pai

    2011-02-01

    Full Text Available The modification of DNA by methylation is an important epigenetic mechanism that affects the spatial and temporal regulation of gene expression. Methylation patterns have been described in many contexts within and across a range of species. However, the extent to which changes in methylation might underlie inter-species differences in gene regulation, in particular between humans and other primates, has not yet been studied. To this end, we studied DNA methylation patterns in livers, hearts, and kidneys from multiple humans and chimpanzees, using tissue samples for which genome-wide gene expression data were also available. Using the multi-species gene expression and methylation data for 7,723 genes, we were able to study the role of promoter DNA methylation in the evolution of gene regulation across tissues and species. We found that inter-tissue methylation patterns are often conserved between humans and chimpanzees. However, we also found a large number of gene expression differences between species that might be explained, at least in part, by corresponding differences in methylation levels. In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%-18% of differences in gene expression levels between humans and chimpanzees.

  6. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

    Science.gov (United States)

    Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

    2014-11-01

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. uv dye lasers

    International Nuclear Information System (INIS)

    Abakumov, G.A.; Fadeev, V.V.; Khokhlov, R.V.; Simonov, A.P.

    1975-01-01

    The most important property of visible dye lasers, that is, continuous wavelength tuning, stimulated the search for dyes capable to lase in uv. They were found in 1968. Now the need for tunable uv lasers for applications in spectroscopy, photochemistry, isotope separation, remote air and sea probing, etc. is clearly seen. A review of some recent advances in uv dye lasers is reviewed

  8. DNA mediated wire-like clusters of self-assembled TiO2 nanomaterials: supercapacitor and dye sensitized solar cell applications

    Science.gov (United States)

    Nithiyanantham, U.; Ramadoss, Ananthakumar; Ede, Sivasankara Rao; Kundu, Subrata

    2014-06-01

    A new route for the formation of wire-like clusters of TiO2 nanomaterials self-assembled in DNA scaffold within an hour of reaction time is reported. TiO2 nanomaterials are synthesized by the reaction of titanium-isopropoxide with ethanol and water in the presence of DNA under continuous stirring and heating at 60 °C. The individual size of the TiO2 NPs self-assembled in DNA and the diameter of the wires can be tuned by controlling the DNA to Ti-salt molar ratios and other reaction parameters. The eventual diameter of the individual particles varies between 15 +/- 5 nm ranges, whereas the length of the nanowires varies in the 2-3 μm range. The synthesized wire-like DNA-TiO2 nanomaterials are excellent materials for electrochemical supercapacitor and DSSC applications. From the electrochemical supercapacitor experiment, it was found that the TiO2 nanomaterials showed different specific capacitance (Cs) values for the various nanowires, and the order of Cs values are as follows: wire-like clusters (small size) > wire-like clusters (large size). The highest Cs of 2.69 F g-1 was observed for TiO2 having wire-like structure with small sizes. The study of the long term cycling stability of wire-like clusters (small size) electrode were shown to be stable, retaining ca. 80% of the initial specific capacitance, even after 5000 cycles. The potentiality of the DNA-TiO2 nanomaterials was also tested in photo-voltaic applications and the observed efficiency was found higher in the case of wire-like TiO2 nanostructures with larger sizes compared to smaller sizes. In future, the described method can be extended for the synthesis of other oxide based materials on DNA scaffold and can be further used in other applications like sensors, Li-ion battery materials or treatment for environmental waste water.A new route for the formation of wire-like clusters of TiO2 nanomaterials self-assembled in DNA scaffold within an hour of reaction time is reported. TiO2 nanomaterials are

  9. Purification, crystallization and preliminary crystallographic analysis of a multiple cofactor-dependent DNA ligase from Sulfophobococcus zilligii

    International Nuclear Information System (INIS)

    Supangat, Supangat; An, Young Jun; Sun, Younguk; Kwon, Suk-Tae; Cha, Sun-Shin

    2010-01-01

    A recombinant multiple cofactor-dependent DNA ligase from S. zilligii has been purified and crystallized. X-ray diffraction data were collected to 2.9 Å resolution and the crystals belonged to space group P1. A recombinant DNA ligase from Sulfophobococcus zilligii that shows multiple cofactor specificity (ATP, ADP and GTP) was expressed in Escherichia coli and purified under reducing conditions. Crystals were obtained by the microbatch crystallization method at 295 K in a drop containing 1 µl protein solution (10 mg ml −1 ) and an equal volume of mother liquor [0.1 M HEPES pH 7.5, 10%(w/v) polyethylene glycol 10 000]. A data set was collected to 2.9 Å resolution using synchrotron radiation. The crystals belonged to space group P1, with unit-cell parameters a = 63.7, b = 77.1, c = 77.8 Å, α = 83.4, β = 82.4, γ = 74.6°. Assuming the presence of two molecules in the unit cell, the solvent content was estimated to be about 53.4%

  10. Unraveling the rat blood genome-wide transcriptome after oral administration of lavender oil by a two-color dye-swap DNA microarray approach

    Directory of Open Access Journals (Sweden)

    Motohide Hori

    2016-06-01

    Full Text Available Lavender oil (LO is a commonly used essential oil in aromatherapy as non-traditional medicine. With an aim to demonstrate LO effects on the body, we have recently established an animal model investigating the influence of orally administered LO in rat tissues, genome-wide. In this brief, we investigate the effect of LO ingestion in the blood of rat. Rats were administered LO at usual therapeutic dose (5 mg/kg in humans, and following collection of the venous blood from the heart and extraction of total RNA, the differentially expressed genes were screened using a 4 × 44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA in conjunction with a two-color dye-swap approach. A total of 834 differentially expressed genes in the blood were identified: 362 up-regulated and 472 down-regulated. These genes were functionally categorized using bioinformatics tools. The gene expression inventory of rat blood transcriptome under LO, a first report, has been deposited into the Gene Expression Omnibus (GEO: GSE67499. The data will be a valuable resource in examining the effects of natural products, and which could also serve as a human model for further functional analysis and investigation.

  11. Hair Dye–DNA Interaction: Plausible Cause of Mutation

    Directory of Open Access Journals (Sweden)

    Swati Maiti

    2015-09-01

    Full Text Available Hair dye is one of the most popular cosmetic products which are used more widely and frequently to improve an individual’s appearance. Although the genotoxic effects of dye ingredients are widely reported, hair dye in its usable form is not reported extensively. In this contribution, we report the possible mode of interaction of hair dye with DNA which leads to genotoxicity. The effect of dye DNA interaction was studied on the most popular and globally used hair dye with Calf Thymus DNA and plasmid DNA. This interaction of dye DNA was studied by spectroscopic analyses and gel electrophoresis. The result had shown positive interaction of dye with DNA. Gel electrophoresis study confirms the binding of dye with DNA which results in linearization and fragmentation of the plasmid DNA. Dye–DNA interaction causes fragmentation and oxidation of DNA in absence of any catalyst, implies high toxicity of commercial hair dyes. Thus, it can be deduced from the present studies that hair dye in its usable form may lead to its penetration through skin affecting genomic DNA possesses genotoxic property and can be treated as one of the most common mutagen.

  12. Lipophilic Polycation Vehicles Display High Plasmid DNA Delivery to Multiple Cell Types.

    Science.gov (United States)

    Wu, Yaoying; Smith, Adam E; Reineke, Theresa M

    2017-08-16

    A class of cationic poly(alkylamidoamine)s (PAAAs) containing lipophilic methylene linkers were designed and examined as in vitro plasmid DNA (pDNA) delivery agents. The PAAAs were synthesized via step-growth polymerization between a diamine monomer and each of four different diacid chloride monomers with varying methylene linker lengths, including glutaryl chloride, adipoyl chloride, pimeloyl chloride, and suberoyl chloride, which served to systematically increase the lipophilicity of the polymers. The synthesized polymers successfully complexed with pDNA in reduced serum medium at N/P ratios of 5 and greater, resulting in polyplexes with hydrodynamic diameters of approximately 1 μm. These polyplexes were tested for in vitro transgene expression and cytotoxicity using HDFa (human dermal fibroblast), HeLa (human cervical carcinoma), HMEC (human mammary epithelial), and HUVEC (human umbilical vein endothelial) cells. Interestingly, select PAAA polyplex formulations were found to be more effective than Lipofectamine 2000 at promoting transgene expression (GFP) while maintaining comparable or higher cell viability. Transgene expression was highest in HeLa cells (∼90% for most formulations) and lowest in HDFa cells (up to ∼20%) as measured by GFP fluorescence. In addition, the cytotoxicity of PAAA polyplex formulations was significantly increased as the molecular weight, N/P ratio, and methylene linker length were increased. The PAAA vehicles developed herein provide a new delivery vehicle design strategy of displaying attributes of both polycations and lipids, which show promise as a tunable scaffold for refining the structure-activity-toxicity profiles for future genome editing studies.

  13. DNA methylation–based immune response signature improves patient diagnosis in multiple cancers

    Science.gov (United States)

    Jeschke, Jana; Bizet, Martin; Calonne, Emilie; Dedeurwaerder, Sarah; Garaud, Soizic; Koch, Alexander; Larsimont, Denis; Salgado, Roberto; Van den Eynden, Gert; Willard Gallo, Karen; Defrance, Matthieu; Sotiriou, Christos

    2017-01-01

    BACKGROUND. The tumor immune response is increasingly associated with better clinical outcomes in breast and other cancers. However, the evaluation of tumor-infiltrating lymphocytes (TILs) relies on histopathological measurements with limited accuracy and reproducibility. Here, we profiled DNA methylation markers to identify a methylation of TIL (MeTIL) signature that recapitulates TIL evaluations and their prognostic value for long-term outcomes in breast cancer (BC). METHODS. MeTIL signature scores were correlated with clinical endpoints reflecting overall or disease-free survival and a pathologic complete response to preoperative anthracycline therapy in 3 BC cohorts from the Jules Bordet Institute in Brussels and in other cancer types from The Cancer Genome Atlas. RESULTS. The MeTIL signature measured TIL distributions in a sensitive manner and predicted survival and response to chemotherapy in BC better than did histopathological assessment of TILs or gene expression–based immune markers, respectively. The MeTIL signature also improved the prediction of survival in other malignancies, including melanoma and lung cancer. Furthermore, the MeTIL signature predicted differences in survival for malignancies in which TILs were not known to have a prognostic value. Finally, we showed that MeTIL markers can be determined by bisulfite pyrosequencing of small amounts of DNA from formalin-fixed, paraffin-embedded tumor tissue, supporting clinical applications for this methodology. CONCLUSIONS. This study highlights the power of DNA methylation to evaluate tumor immune responses and the potential of this approach to improve the diagnosis and treatment of breast and other cancers. FUNDING. This work was funded by the Fonds National de la Recherche Scientifique (FNRS) and Télévie, the INNOVIRIS Brussels Region BRUBREAST Project, the IUAP P7/03 program, the Belgian “Foundation against Cancer,” the Breast Cancer Research Foundation (BCRF), and the Fonds Gaston Ithier

  14. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

    Czech Academy of Sciences Publication Activity Database

    Reshetnikov, R.V.; Šponer, Jiří; Rassokhina, O.I.; Kopylov, A.M.; Tsvetkov, P.O.; Makarov, A.A.; Golovin, A.V.

    2011-01-01

    Roč. 39, č. 22 (2011), s. 9789-9802 ISSN 0305-1048 R&D Projects: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA MŠk(CZ) LC06030 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : QM/MM * quadruplex DNA * molecular dynamics simulation Subject RIV: BO - Biophysics Impact factor: 8.026, year: 2011

  15. A defined role for multiple Fanconi anemia gene products in DNA-damage-associated ubiquitination.

    Science.gov (United States)

    Tan, Winnie; Deans, Andrew J

    2017-06-01

    Fanconi anemia (FA) is an inherited blood disorder that causes bone marrow failure and high predisposition to cancers. The FA pathway guards the cell's genome stability by orchestrating the repair of interstrand cross-linking during the S phase of the cell cycle, preventing the chromosomal instability that is a key event in bone marrow failure syndrome. Central to the FA pathway is loss of monoubiquitinated forms of the Fanconi proteins FANCI and FANCD2, a process that is normally mediated by a "core complex" of seven other Fanconi proteins. Each protein, when mutated, can cause FA. The FA core-complex-catalyzed reaction is critical for signaling DNA cross-link damage such as that induced by chemotherapies. Here, we present a perspective on the current understanding of FANCI and FANCD2 monoubiquitination-mediated DNA repair. Our recent biochemical reconstitution of the monoubiquitination (and deubiquitination) reactions creates a paradigm for understanding FA. Further biochemical analysis will create new opportunities to address the leukemic phenotype of FA patients. Copyright © 2017 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

  16. Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers.

    Science.gov (United States)

    Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S; Garcia-Closas, Montserrat; Sherman, Mark E; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P; Khan, Javed; Chanock, Stephen

    2011-01-17

    Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  17. Detection of somatic mutations by high-resolution DNA melting (HRM analysis in multiple cancers.

    Directory of Open Access Journals (Sweden)

    Jesus Gonzalez-Bosquet

    Full Text Available Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each. HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  18. Assessment of Multiple Types of DNA Damage in Human Placentas from Smoking and Non-smoking Women in the Czech Republic

    Science.gov (United States)

    Margaret Pratt, M.; King, Leon C.; Adams, Linda D.; John, Kaarthik; Sirajuddin, Paul; Olivero, Ofelia A.; Manchester, David K.; Sram, Radim J.; DeMarini, David M.; Poirier, Miriam C.

    2010-01-01

    Three classes of DNA damage were assessed in human placentas collected (in 2000-4) from 51 women living in the Teplice region of the Czech Republic, a mining area considered to have some of the worst environmental pollution in Europe in the 1980s. Polycyclic aromatic hydrocarbon (PAH)-DNA adducts were localized and semiquantified using immunohistochemistry (IHC) and the Automated Cellular Imaging System (ACIS). More generalized DNA damage was measured both by 32P-postlabeling and by abasic (AB) site analysis. Placenta stained with antiserum elicited against DNA modified with r7, t8-dihydroxy-t-9, 10-oxy-7,8,9,10-tetrahydro-benzo[a]pyrene (BPDE) revealed PAH-DNA adduct localization in nuclei of the cytotrophoblast (CT) cells and syncytiotrophoblast (ST) knots lining the chorionic villi. The highest levels of DNA damage, 49–312 PAH-DNA adducts/108 nucleotides, were found by IHC/ACIS in 14 immediately-fixed placenta samples. An additional 37 placenta samples were stored frozen before fixation and embedding, and because PAH-DNA adducts were largely undetectable in these samples, freezing was implicated in the loss of IHC signal. The same placentas (n = 37) contained 1.7 – 8.6 stable/bulky DNA adducts/108 nucleotides and 0.6 – 47.2 AB sites/105 nucleotides. For all methods there was no correlation among types of DNA damage and no difference in extent of DNA damage between smokers and non-smokers. Therefore, the data show that DNA from placentas obtained in Teplice contained multiple types of DNA damage, which likely arose from various environmental exposures. In addition, PAH-DNA adducts were present at high concentrations in the CT cells and ST knots of the chorionic villi. PMID:20839217

  19. Hair dye contact allergy

    DEFF Research Database (Denmark)

    Søsted, Heidi; Rastogi, Suresh Chandra; Andersen, Klaus Ejner

    2004-01-01

    Colouring of hair can cause severe allergic contact dermatitis. The most frequently reported hair dye allergens are p-phenylenediamine (PPD) and toluene-2,5-diamine, which are included in, respectively, the patch test standard series and the hairdressers series. The aim of the present study...... was to identify dye precursors and couplers in hair dyeing products causing clinical hair dye dermatitis and to compare the data with the contents of these compounds in a randomly selected set of similar products. The patient material comprised 9 cases of characteristic clinical allergic hair dye reaction, where...... exposure history and patch testing had identified a specific hair dye product as the cause of the reaction. The 9 products used by the patients were subjected to chemical analysis. 8 hair dye products contained toluene-2,5-diamine (0.18 to 0.98%). PPD (0.27%) was found in 1 product, and m-aminophenol (0...

  20. A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans.

    Science.gov (United States)

    Mauchline, T H; Mohan, S; Davies, K G; Schaff, J E; Opperman, C H; Kerry, B R; Hirsch, P R

    2010-05-01

    To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR-based diagnostic tool for P. penetrans. An optimized method to decontaminate endospores, release and purify DNA enabled multiple strand amplification. DNA purity was assessed by cloning and sequencing gyrB and 16S rRNA gene fragments obtained from PCR using generic primers. Samples indicated to be 100%P. penetrans by the gyrB assay were estimated at 46% using the 16S rRNA gene. No bias was detected on cloning and sequencing 12 housekeeping and sporulation gene fragments from amplified DNA. The detection limit by PCR with Pasteuria-specific 16S rRNA gene primers following multiple strand amplification of DNA extracted using the method was a single endospore. Generation of large quantities DNA will facilitate genomic sequencing of P. penetrans. Apparent differences in sample purity are explained by variations in 16S rRNA gene copy number in Eubacteria leading to exaggerated estimations of sample contamination. Detection of single endospores will facilitate investigations of P. penetrans molecular ecology. These methods will advance studies on P. penetrans and facilitate research on other obligate and fastidious micro-organisms where it is currently impractical to obtain DNA in sufficient quantity and quality.

  1. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    Science.gov (United States)

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  2. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

    Directory of Open Access Journals (Sweden)

    Qing-Yan Dai

    Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

  3. Emergence of Tetracycline Resistance in Helicobacter pylori: Multiple Mutational Changes in 16S Ribosomal DNA and Other Genetic Loci

    Science.gov (United States)

    Dailidiene, Daiva; Bertoli, M. Teresita; Miciuleviciene, Jolanta; Mukhopadhyay, Asish K.; Dailide, Giedrius; Pascasio, Mario Alberto; Kupcinskas, Limas; Berg, Douglas E.

    2002-01-01

    Tetracycline is useful in combination therapies against the gastric pathogen Helicobacter pylori. We found 6 tetracycline-resistant (Tetr) strains among 159 clinical isolates (from El Salvador, Lithuania, and India) and obtained the following four results: (i) 5 of 6 Tetr isolates contained one or two nucleotide substitutions in one part of the primary tetracycline binding site in 16S rRNA (AGA965-967 [Escherichia coli coordinates] changed to gGA, AGc, guA, or gGc [lowercase letters are used to represent the base changes]), whereas the sixth (isolate Ind75) retained AGA965-967; (ii) PCR products containing mutant 16S ribosomal DNA (rDNA) alleles transformed recipient strains to Tetr phenotypes, but transformants containing alleles with single substitutions (gGA and AGc) were less resistant than their Tetr parents; (iii) each of 10 Tetr mutants of reference strain 26695 (in which mutations were induced with metronidazole, a mutagenic anti-H. pylori agent) contained the normal AGA965-967 sequence; and (iv) transformant derivatives of Ind75 and of one of the Tetr 26695 mutants that had acquired mutant rDNA alleles were resistant to tetracycline at levels higher than those to which either parent strain was resistant. Thus, tetracycline resistance in H. pylori results from an accumulation of changes that may affect tetracycline-ribosome affinity and/or other functions (perhaps porins or efflux pumps). We suggest that the rarity of tetracycline resistance among clinical isolates reflects this need for multiple mutations and perhaps also the deleterious effects of such mutations on fitness. Formally equivalent mutations with small but additive effects are postulated to contribute importantly to traits such as host specificity and virulence and to H. pylori's great genetic diversity. PMID:12435699

  4. The long persistence of pyrrolizidine alkaloid-derived DNA adducts in vivo: kinetic study following single and multiple exposures in male ICR mice.

    Science.gov (United States)

    Zhu, Lin; Xue, Junyi; Xia, Qingsu; Fu, Peter P; Lin, Ge

    2017-02-01

    Pyrrolizidine alkaloid (PA)-containing plants are widespread in the world and the most common poisonous plants affecting livestock, wildlife, and humans. Our previous studies demonstrated that PA-derived DNA adducts can potentially be a common biological biomarker of PA-induced liver tumor formation. In order to validate the use of these PA-derived DNA adducts as a biomarker, it is necessary to understand the basic kinetics of the PA-derived DNA adducts formed in vivo. In this study, we studied the dose-dependent response and kinetics of PA-derived DNA adduct formation and removal in male ICR mice orally administered with a single dose (40 mg/kg) or multiple doses (10 mg/kg/day) of retrorsine, a representative carcinogenic PA. In the single-dose exposure, the PA-derived DNA adducts exhibited dose-dependent linearity and persisted for up to 4 weeks. The removal of the adducts following a single-dose exposure to retrorsine was biphasic with half-lives of 9 h (t 1/2α ) and 301 h (~12.5 days, t 1/2β ). In the 8-week multiple exposure study, a marked accumulation of PA-derived DNA adducts without attaining a steady state was observed. The removal of adducts after the multiple exposure also demonstrated a biphasic pattern but with much extended half-lives of 176 h (~7.33 days, t 1/2α ) and 1736 h (~72.3 days, t 1/2β ). The lifetime of PA-derived DNA adducts was more than 8 weeks following the multiple-dose treatment. The significant persistence of PA-derived DNA adducts in vivo supports their role in serving as a biomarker of PA exposure.

  5. Application of four dyes in gene expression analyses by microarrays

    Directory of Open Access Journals (Sweden)

    van Schooten Frederik J

    2005-07-01

    Full Text Available Abstract Background DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed simultaneously by applying four different fluorescent dyes. Results Following tests for cross-talk of fluorescence signals, Alexa 488, Alexa 594, Cyanine 3 and Cyanine 5 were selected for hybridizations. For self-hybridizations, a single RNA sample was labelled with all dyes and hybridized on commercial cDNA arrays or on in-house spotted oligonucleotide arrays. Correlation coefficients for all combinations of dyes were above 0.9 on the cDNA array. On the oligonucleotide array they were above 0.8, except combinations with Alexa 488, which were approximately 0.5. Standard deviation of expression differences for replicate spots were similar on the cDNA array for all dye combinations, but on the oligonucleotide array combinations with Alexa 488 showed a higher variation. Conclusion In conclusion, the four dyes can be used simultaneously for gene expression experiments on the tested cDNA array, but only three dyes can be used on the tested oligonucleotide array. This was confirmed by hybridizations of control with test samples, as all combinations returned similar numbers of differentially expressed genes with comparable effects on gene expression.

  6. Multiple Ethnic Origins of Mitochondrial DNA Lineages for the Population of Mauritius

    Science.gov (United States)

    Betancor, Eva; Suárez, Nicolás M.; Calaon, Diego; Čaval, Saša; Janoo, Anwar; Pestano, Jose

    2014-01-01

    This article reports on the first genetic assessment of the contemporary Mauritian population. Small island nodes such as Mauritius played a critical role in historic globalization processes and revealing high-resolution details of labour sourcing is crucial in order to better understand early-modern diaspora events. Mauritius is a particularly interesting case given detailed historic accounts attesting to European (Dutch, French and British), African and Asian points of origin. Ninety-seven samples were analysed for mitochondrial DNA to begin unravelling the complex dynamics of the island's modern population. In corroboration with general demographic information, the majority of maternal lineages were derived from South Asia (58.76%), with Malagasy (16.60%), East/Southeast Asian (11.34%) and Sub-Saharan African (10.21%) also making significant contributions. This study pinpoints specific regional origins for the South Asian genetic contribution, showing a greater influence on the contemporary population from northern and southeast India. Moreover, the analysis of lineages related to the slave trade demonstrated that Madagascar and East Asia were the main centres of origin, with less influence from West Africa. PMID:24676463

  7. WATERLESS DYEING [REVIEW

    Directory of Open Access Journals (Sweden)

    DEVRENT Nalan

    2015-05-01

    Full Text Available The textile industry is believed to be one of the biggest consumers of water. Water consumption and exhaustion in dyeing textile materials in conventional methods is an important environmental problem. The cost of waste water treatment will cause a prominent problem in the future as it does today. Increasing consideration of ecologic consequences of industrial processes as well as legislation enforcing the avoidance of environmental problems have caused a reorientation of thinking and promoted projects for replacement of conventional technologies. One of these new technologies is dyeing in supercritical fluids. Dyeing with supercritical carbon dioxide is a favourable concept considering the value of water as a natural resource and the cost of waste water treatment. This dyeing method offers many advantages over conventional aqueous dyeing: During this dyeing process no water is used, therefore there is no waste water problem, no other chemicals are required; the carbon dioxide can be recycled; the dystuff which is not adsorbed on the substrate can be collected and reused; The necessary energy consumption in this process is relatively lower than is needed to heat water in conventional methods of dyeing. Due to unnecessary of drying process, it helps to save both energy and time; and dyeing cycle is shorter compared with traditional methods. In addition carbon dioxide is non-toxic and non-flammable. Supercritical fluid, supercritical dyeing, disperse dyestuffs, solid-fluid equilibrium

  8. Deficiency of Double-Strand DNA Break Repair Does Not Impair Mycobacterium tuberculosis Virulence in Multiple Animal Models of Infection

    OpenAIRE

    Heaton, Brook E.; Barkan, Daniel; Bongiorno, Paola; Karakousis, Petros C.; Glickman, Michael S.

    2014-01-01

    Mycobacterium tuberculosis persistence within its human host requires mechanisms to resist the effector molecules of host immunity, which exert their bactericidal effects through damaging pathogen proteins, membranes, and DNA. Substantial evidence indicates that bacterial pathogens, including M. tuberculosis, require DNA repair systems to repair the DNA damage inflicted by the host during infection, but the role of double-strand DNA break (DSB) repair systems is unclear. Double-strand DNA bre...

  9. Nitrogen-doped multiple graphene aerogel/gold nanostar as the electrochemical sensing platform for ultrasensitive detection of circulating free DNA in human serum.

    Science.gov (United States)

    Ruiyi, Li; Ling, Liu; Hongxia, Bei; Zaijun, Li

    2016-05-15

    Graphene aerogel has attracted increasing attention due to its large specific surface area, high-conductivity and electronic interaction. The paper reported a facile synthesis of nitrogen-doped multiple graphene aerogel/gold nanostar (termed as N-doped MGA/GNS) and its use as the electrochemical sensing platform for detection of double stranded (dsDNA). On the one hand, the N-doped MGA offers a much better electrochemical performance compared with classical graphene aerogel. Interestingly, the performance can be enhanced by only increasing the cycle number of graphene oxide gelation. On the other hand, the hybridization with GNS further enhances the electrocatalytic activity towards Fe(CN)6(3-/4-). In addition, the N-doped MGA/GNS provides a well-defined three-dimensional architecture. The unique structure make it is easy to combine with dsDNA to form the electroactive bioconjugate. The integration not only triggers an ultrafast DNA electron and charge transfer, but also realizes a significant synergy between N-doped MGA, GNS and dsDNA. As a result, the electrochemical sensor based on the hybrid exhibits highly sensitive differential pulse voltammetric response (DPV) towards dsDNA. The DPV signal linearly increases with the increase of dsDNA concentration in the range from 1.0×10(-)(21) g ml(-)(1) to 1.0×10(-16) g ml(-1) with the detection limit of 3.9×10(-22) g ml(-1) (S/N=3). The sensitivity is much more than that of all reported DNA sensors. The analytical method was successfully applied in the electrochemical detection of circulating free DNA in human serum. The study also opens a window on the electrical properties of multiple graphene aerogel and DNA as well their hybrids to meet the needs of further applications as special nanoelectronics in molecule diagnosis, bioanalysis and catalysis. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Anaerobic azo dye reduction

    NARCIS (Netherlands)

    Zee, van der F.P.

    2002-01-01

    Azo dyes, aromatic moieties linked together by azo (-N=N-) chromophores, represent the largest class of dyes used in textile-processing and other industries. The release of these compounds into the environment is undesirable, not only because of their colour, but also

  11. for aqueous dye lasers

    Indian Academy of Sciences (India)

    2014-02-12

    Feb 12, 2014 ... inclusion complex of RhB with the container molecule cucurbit[7]uril (CB[7]). Keywords. Temperature-dependent fluorescence; Rhodamine B; cucurbit[7]uril; host–guest complex; dye laser. PACS Nos 36.20.kd; 83.60.pq; 87.64.kv. 1. Introduction. Rhodamine B (RhB) is an efficient and photostable laser dye ...

  12. Extraction of dye

    African Journals Online (AJOL)

    Dyes of natural origins are great for color appreciation as any variation in the concentration of dye, mordant, type of water, soil and climate give variations in ... Grey scale and blue dyed silk were used for color fastness rating. ..... Down to Earth.

  13. Multiple differences in calling songs and other traits between solitary and gregarious Mormon crickets from allopatric mtDNA clades

    Directory of Open Access Journals (Sweden)

    Bailey William V

    2007-01-01

    Full Text Available Abstract Background In acoustic species, traits such as male calling song are likely to diverge quickly between allopatric populations due to sexual selection, and divergence in parameters such as carrier frequency, chirp structure, and other important song characters can influence sexual isolation. Here we make use of two forms of Mormon crickets to examine differences in a broad suite of traits that have the potential to influence speciation via sexual isolation. Mormon crickets in "gregarious" populations aggregate into dense migratory bands, and females are the sexually competitive sex (sex-role reversal. There is also a non-outbreak "solitary" form. These two forms are largely but not perfectly correlated with a significant mtDNA subdivision within the species that is thought to have arisen in allopatry. Combined information about multiple, independently evolving traits, such as morphology and structural and behavioural differences in calling song, provides greater resolution of the overall differences between these allopatric populations, and allows us to assess their stage of divergence. We test two predictions, first that the forms differ in song and second that gregarious males are more reluctant to sing than solitary males due to sex role reversal. We also tested for a difference in the relationship between the size of the forewing resonator, the mirror, and carrier frequency, as most models of sound production in crickets indicate that mirror size should predict carrier frequency. Results Multivariate analyses showed that solitary and gregarious individuals from different populations representing the two mtDNA clades had almost non-overlapping distributions based on multiple song and morphological measurements. Carrier frequency differed between the two, and gregarious males were more reluctant to sing overall. Mirror size predicted carrier frequency; however, the relationship between mirror size and surface area varied between

  14. Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple-displacement amplification.

    Science.gov (United States)

    Arakaki, Atsushi; Shibusawa, Mie; Hosokawa, Masahito; Matsunaga, Tadashi

    2010-03-01

    Magnetotactic bacteria comprise a phylogenetically diverse group that is capable of synthesizing intracellular magnetic particles. Although various morphotypes of magnetotactic bacteria have been observed in the environment, bacterial strains available in pure culture are currently limited to a few genera due to difficulties in their enrichment and cultivation. In order to obtain genetic information from uncultured magnetotactic bacteria, a genome preparation method that involves magnetic separation of cells, flow cytometry, and multiple displacement amplification (MDA) using phi29 polymerase was used in this study. The conditions for the MDA reaction using samples containing 1 to 100 cells were evaluated using a pure-culture magnetotactic bacterium, "Magnetospirillum magneticum AMB-1," whose complete genome sequence is available. Uniform gene amplification was confirmed by quantitative PCR (Q-PCR) when 100 cells were used as a template. This method was then applied for genome preparation of uncultured magnetotactic bacteria from complex bacterial communities in an aquatic environment. A sample containing 100 cells of the uncultured magnetotactic coccus was prepared by magnetic cell separation and flow cytometry and used as an MDA template. 16S rRNA sequence analysis of the MDA product from these 100 cells revealed that the amplified genomic DNA was from a single species of magnetotactic bacterium that was phylogenetically affiliated with magnetotactic cocci in the Alphaproteobacteria. The combined use of magnetic separation, flow cytometry, and MDA provides a new strategy to access individual genetic information from magnetotactic bacteria in environmental samples.

  15. Intelligent layered nanoflare: ``lab-on-a-nanoparticle'' for multiple DNA logic gate operations and efficient intracellular delivery

    Science.gov (United States)

    Yang, Bin; Zhang, Xiao-Bing; Kang, Li-Ping; Huang, Zhi-Mei; Shen, Guo-Li; Yu, Ru-Qin; Tan, Weihong

    2014-07-01

    DNA strand displacement cascades have been engineered to construct various fascinating DNA circuits. However, biological applications are limited by the insufficient cellular internalization of naked DNA structures, as well as the separated multicomponent feature. In this work, these problems are addressed by the development of a novel DNA nanodevice, termed intelligent layered nanoflare, which integrates DNA computing at the nanoscale, via the self-assembly of DNA flares on a single gold nanoparticle. As a ``lab-on-a-nanoparticle'', the intelligent layered nanoflare could be engineered to perform a variety of Boolean logic gate operations, including three basic logic gates, one three-input AND gate, and two complex logic operations, in a digital non-leaky way. In addition, the layered nanoflare can serve as a programmable strategy to sequentially tune the size of nanoparticles, as well as a new fingerprint spectrum technique for intelligent multiplex biosensing. More importantly, the nanoflare developed here can also act as a single entity for intracellular DNA logic gate delivery, without the need of commercial transfection agents or other auxiliary carriers. By incorporating DNA circuits on nanoparticles, the presented layered nanoflare will broaden the applications of DNA circuits in biological systems, and facilitate the development of DNA nanotechnology.DNA strand displacement cascades have been engineered to construct various fascinating DNA circuits. However, biological applications are limited by the insufficient cellular internalization of naked DNA structures, as well as the separated multicomponent feature. In this work, these problems are addressed by the development of a novel DNA nanodevice, termed intelligent layered nanoflare, which integrates DNA computing at the nanoscale, via the self-assembly of DNA flares on a single gold nanoparticle. As a ``lab-on-a-nanoparticle'', the intelligent layered nanoflare could be engineered to perform a variety of

  16. Fluorescent nanohybrids based on asymmetrical cyanine dyes decorated carbon nanotubes

    OpenAIRE

    Çavuşlar, Özge; Cavuslar, Ozge

    2015-01-01

    In this thesis, we focused on imparting new optical properties to carbon nanotubes (CNTs) to allow their optical detection and visualization in biomedical applications. We investigated the interactions of CNTs and DNA wrapped CNTs with asymmetrical cyanine dye molecules to study the applicability of resulting hybrid materials to fluorescent based systems. When CNTs interacted with asymmetrical cyanine dyes, they constructed a light absorbing nanoarray. However, the fluorescence emission of th...

  17. Direct thermal dyes

    Science.gov (United States)

    Ehlinger, Edward

    1990-07-01

    Direct thermal dyes are members of a class of compounds referred to in the imaging industry as color formers or leuco dyes. The oldest members of that class have simple triarylmethane structures, and have been employed for years in various dyeing applications. More complex triarylmethane compounds, such as phthalides and fluorans, are now used in various imaging systems to produce color. Color is derived from all of these compounds via the same mechanism, on a molecular level. That is, an event of activation produces a highly resonating cationic system whose interaction with incident light produces reflected light of a specific color. The activation event in the case of a direct thermal system is the creation of a melt on the paper involving dye and an acidic developer. The three major performance parameters in a thermal system are background color, image density, and image stability. The three major dye physical parameters affecting thermal performance are chemical constituency, purity, and particle size. Those dyes having the best combination of characteristics which can also be manufactured economically dominate the marketplace. Manufacturing high performance dyes for the thermal market involves multi-step, convergent reaction sequences performed on large scale. Intermediates must be manufactured at the right time, and at the right quality to be useful.

  18. Dyes for displays

    Science.gov (United States)

    Claussen, U.

    1984-01-01

    The improvement of contrast and visibility of LCD by two different means was undertaken. The two methods are: (1) development of fluorescent dyes to increase the visibility of fluorescent activated displays (FLAD); and (2) development of dichroic dyes to increase the contrast of displays. This work was done in close cooperation with the electronic industry, where the newly synthesized dyes were tested. The targets for the chemical synthesis were selected with the help of computer model calculations. A marketable range of dyes was developed. Since the interest of the electronic industries concerning FLAD was low, the investigations were stopped. Dichroic dyes, especially black mixtures with good light fastness, order parameter, and solubility in nematic phases were developed. The application of these dyes is restricted to indoor use because of an increase of viscosity below -10 C. Applications on a technical scale, e.g., for the automotive industry, will be possible if the displays work at temperatures down to -40 C. This problem requires a complex optimization of the dye/nematic phase system.

  19. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Neufeld, Josh D; Bodrossy, Levente; Stralis-Pavese, Nancy; McNamara, Niall P; Ostle, Nick; Briones, Maria J I; Murrell, J Colin

    2008-10-01

    Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

  20. Interlaboratory study of DNA extraction from multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for individual kernel detection system of genetically modified maize.

    Science.gov (United States)

    Akiyama, Hiroshi; Sakata, Kozue; Makiyma, Daiki; Nakamura, Kosuke; Teshima, Reiko; Nakashima, Akie; Ogawa, Asako; Yamagishi, Toru; Futo, Satoshi; Oguchi, Taichi; Mano, Junichi; Kitta, Kazumi

    2011-01-01

    In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.

  1. Dyeing of Polyester with Disperse Dyes: Part 2. Synthesis and Dyeing Characteristics of Some Azo Disperse Dyes for Polyester Fabrics

    Directory of Open Access Journals (Sweden)

    Alya M. Al-Etaibi

    2016-06-01

    Full Text Available The goal of this study was to utilize carrier for accelerating the rate of dyeing not only to enhance dyeing of polyester fabrics dyed with disperse dyes 3a,b, but also to save energy. Both the color strength expressed as dye uptake and the fastness properties of the dyed fabrics were evaluated.

  2. A polarized view on DNA under tension

    Science.gov (United States)

    van Mameren, Joost; Vermeulen, Karen; Wuite, Gijs J. L.; Peterman, Erwin J. G.

    2018-03-01

    In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of double-stranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.

  3. Mycobacterial UvrD1 is a Ku-dependent DNA helicase that plays a role in multiple DNA repair events, including double-strand break repair.

    Science.gov (United States)

    Sinha, Krishna Murari; Stephanou, Nicolas C; Gao, Feng; Glickman, Michael S; Shuman, Stewart

    2007-05-18

    Mycobacterium tuberculosis and other bacterial pathogens have a Ku-dependent nonhomologous end joining pathway of DNA double-strand break repair. Here we identify mycobacterial UvrD1 as a novel interaction partner for Ku in a genome-wide yeast two-hybrid screen. UvrD1 per se is a vigorous DNA-dependent ATPase but a feeble DNA helicase. Ku stimulates UvrD1 to catalyze ATP-dependent unwinding of 3'-tailed DNAs. UvrD1, Ku, and DNA form a stable ternary complex in the absence of ATP. The Ku binding determinants are located in the distinctive C-terminal segment of UvrD1. A second mycobacterial paralog, UvrD2, is a vigorous Ku-independent DNA helicase. Ablation of UvrD1 sensitizes Mycobacterium smegmatis to killing by ultraviolet and ionizing radiation and to a single chromosomal break generated by I-SceI endonuclease. The physical and functional interactions of bacterial Ku and UvrD1 highlight the potential for cross-talk between components of nonhomologous end joining and nucleotide excision repair pathways.

  4. Sequential strand displacement beacon for detection of DNA coverage on functionalized gold nanoparticles.

    Science.gov (United States)

    Paliwoda, Rebecca E; Li, Feng; Reid, Michael S; Lin, Yanwen; Le, X Chris

    2014-06-17

    Functionalizing nanomaterials for diverse analytical, biomedical, and therapeutic applications requires determination of surface coverage (or density) of DNA on nanomaterials. We describe a sequential strand displacement beacon assay that is able to quantify specific DNA sequences conjugated or coconjugated onto gold nanoparticles (AuNPs). Unlike the conventional fluorescence assay that requires the target DNA to be fluorescently labeled, the sequential strand displacement beacon method is able to quantify multiple unlabeled DNA oligonucleotides using a single (universal) strand displacement beacon. This unique feature is achieved by introducing two short unlabeled DNA probes for each specific DNA sequence and by performing sequential DNA strand displacement reactions. Varying the relative amounts of the specific DNA sequences and spacing DNA sequences during their coconjugation onto AuNPs results in different densities of the specific DNA on AuNP, ranging from 90 to 230 DNA molecules per AuNP. Results obtained from our sequential strand displacement beacon assay are consistent with those obtained from the conventional fluorescence assays. However, labeling of DNA with some fluorescent dyes, e.g., tetramethylrhodamine, alters DNA density on AuNP. The strand displacement strategy overcomes this problem by obviating direct labeling of the target DNA. This method has broad potential to facilitate more efficient design and characterization of novel multifunctional materials for diverse applications.

  5. Benzo(a)pyrene metabolism, DNA-binding and UV-induced repair of DNA damage in cultured skin fibroblasts from a patient with unilateral multiple basal cell carcinoma

    International Nuclear Information System (INIS)

    Don, P.S.C.; Mukhtar, H.; Das, M.; Berger, N.A.; Bickers, D.R.

    1989-01-01

    The metabolism of benzo(a)pyrene (BP), and its subsequent binding to DNA, and the repair of UV-induced DNA damage were studied in fibroblasts cultured from the skin of a 61-year-old male who had multiple basal cell carcinoma (BCC) (>100) on his left upper trunk. Results suggest that BP metabolism and repair of DNA are altered in tumor-bearing site (TSB) cells and that patients with this type of metabolic profile may be at higher risk of the development of cutaneous neoplasms. It is also possible that fibroblasts from tumour bearing skin undergo some as yet unexplained alteration in carcinogen metabolism as a consequence of the induction of neoplasia. (author)

  6. Significant accumulation of persistent organic pollutants and dysregulation in multiple DNA damage repair pathways in the electronic-waste-exposed populations

    Energy Technology Data Exchange (ETDEWEB)

    He, Xiaobo; Jing, Yaqing; Wang, Jianhai; Li, Keqiu [Basic Medical College, Tianjin Medical University, Tianjin 300070 (China); Yang, Qiaoyun [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China); Zhao, Yuxia [Basic Medical College, Tianjin Medical University, Tianjin 300070 (China); Li, Ran [State Key Joint Laboratory for Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering and Center for Environment and Health, Peking University, Beijing 100871 (China); Ge, Jie [Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060 (China); Key Laboratory of Breast Cancer Prevention and Treatment of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060 (China); Qiu, Xinghua, E-mail: xhqiu@pku.edu.cn [State Key Joint Laboratory for Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering and Center for Environment and Health, Peking University, Beijing 100871 (China); Li, Guang, E-mail: lig@tijmu.edu.cn [Basic Medical College, Tianjin Medical University, Tianjin 300070 (China)

    2015-02-15

    Electronic waste (e-waste) has created a worldwide environmental and health problem, by generating a diverse group of hazardous compounds such as persistent organic pollutants (POPs). Our previous studies demonstrated that populations from e-waste exposed region have a significantly higher level of chromosomal aberrancy and incidence of DNA damage. In this study, we further demonstrated that various POPs persisted at a significantly higher concentration in the exposed group than those in the unexposed group. The level of reactive oxygen species and micronucleus rate were also significantly elevated in the exposed group. RNA sequencing analysis revealed 31 genes in DNA damage responses and repair pathways that were differentially expressed between the two groups (Log 2 ratio >1 or <−1). Our data demonstrated that both females and males of the exposed group have activated a series of DNA damage response genes; however many important DNA repair pathways have been dysregulated. Expressions of NEIL1/3 and RPA3, which are critical in initiating base pair and nucleotide excision repairs respectively, have been downregulated in both females and males of the exposed group. In contrast, expression of RNF8, an E3 ligase involved in an error prone non-homologous end joining repair for DNA double strand break, was upregulated in both genders of the exposed group. The other genes appeared to be differentially expressed only when the males or females of the two groups were compared respectively. Importantly, the expression of cell cycle regulatory gene CDC25A that has been implicated in multiple kinds of malignant transformation was significantly upregulated among the exposed males while downregulated among the exposed females. In conclusion, our studies have demonstrated significant correlations between e-waste disposing and POPs accumulation, DNA lesions and dysregulation of multiple DNA damage repair mechanisms in the residents of the e-waste exposed region. - Highlights:

  7. Structural relationships among the multiple forms of DNA-dependent RNA polymerase II from cultured parsley cells

    International Nuclear Information System (INIS)

    Link, G.; Bogorad, L.; Kidd, G.H.; Richter, G.

    1978-01-01

    DNA-dependent RNA polymerase II (or B) was purified from cultured parsley cells, and its molecular structure was examined in detail. Upon centrifugation through glycerol gradients, RNA polymerase II sediments as a single band with an apparent sedimentation constant of 15S. No contamination with RNA polymerases I or III could be detected when the activity of purified RNA polymerase II was assayed in the presence of high concentrations of α-amanitin. Analysis of purified RNA polymerase II be nondenaturing and denaturing polyacrylamide gel electrophoresis revealed that this enzyme exists in multiple forms. They were designated II(O), II(A), and II(B). It is suggested that each form has a subunit of Mr = 140000 as well as smaller polypeptides in common. They differ, however, in the molecular weights of their largest subunits which is 220000 in form II(O), 200000 in form II(A), and 180000 in form II(B). These large subunits were labelled with 125 I, digested with trypsin, and tryptic digests were compared by two-dimensional analysis on thin-layer plates (Elder et al. (1977) J. Biol. Chem. 252, 6510-6515). Fingerprints of tryptic digests from the polypeptides with Mr = 220000, Mr = 200000, and Mr = 180000 were similar. It is, therefore, suggested that these subunits are stucturally related. A tryptic digest was also produced from the subunit with Mr = 140000. Its fingerprint was found to yield a considerably different distribution of peptides as compared to those from the three large subunits. (orig.) [de

  8. Geminin deploys multiple mechanisms to regulate Cdt1 before cell division thus ensuring the proper execution of DNA replication

    DEFF Research Database (Denmark)

    Ballabeni, Andrea; Zamponi, Raffaella; Moore, Jodene K

    2013-01-01

    the accumulation of Cdt1 in mitosis, because decreasing the Geminin levels prevents Cdt1 accumulation and impairs DNA replication. Geminin is known to inhibit Cdt1 function; its depletion during G2 leads to DNA rereplication and checkpoint activation. Here we show that, despite rapid Cdt1 protein turnover in G2...

  9. Successful treatment of multifocal pedal infection in a feline immunodeficiency virus-positive cat with multiple Bowenoid in situ carcinomas containing papillomaviral DNA sequences

    OpenAIRE

    Allan E Kessell; Derek McNair; John S Munday; Richard Savory; Catriona Halliday; Richard Malik

    2017-01-01

    Case summary A 16-year-old, castrated male, feline immunodeficiency virus (FIV)-positive, domestic shorthair cat developed multiple skin lesions. Most of these were Bowenoid carcinoma in situ and contained DNA sequences consistent with Felis catus papillomavirus type 2. Two additional lesions that developed in the skin and subcutaneous tissues between the digital and carpal pads on the left forelimb and right hindlimb were shown by cytology, histology and culture to be caused by Prototheca wi...

  10. Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies

    Science.gov (United States)

    Richardson, Ruth E.; Suzuki, Yo

    2015-01-01

    Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six double-stranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processes associated with most common applications of DNA assembly. We demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work. PMID:26348330

  11. DNA microarray technique for detecting food-borne pathogens

    Directory of Open Access Journals (Sweden)

    Xing GAO

    2012-08-01

    Full Text Available Objective To study the application of DNA microarray technique for screening and identifying multiple food-borne pathogens. Methods The oligonucleotide probes were designed by Clustal X and Oligo 6.0 at the conserved regions of specific genes of multiple food-borne pathogens, and then were validated by bioinformatic analyses. The 5' end of each probe was modified by amino-group and 10 Poly-T, and the optimized probes were synthesized and spotted on aldehyde-coated slides. The bacteria DNA template incubated with Klenow enzyme was amplified by arbitrarily primed PCR, and PCR products incorporated into Aminoallyl-dUTP were coupled with fluorescent dye. After hybridization of the purified PCR products with DNA microarray, the hybridization image and fluorescence intensity analysis was acquired by ScanArray and GenePix Pro 5.1 software. A series of detection conditions such as arbitrarily primed PCR and microarray hybridization were optimized. The specificity of this approach was evaluated by 16 different bacteria DNA, and the sensitivity and reproducibility were verified by 4 food-borne pathogens DNA. The samples of multiple bacteria DNA and simulated water samples of Shigella dysenteriae were detected. Results Nine different food-borne bacteria were successfully discriminated under the same condition. The sensitivity of genomic DNA was 102 -103pg/ μl, and the coefficient of variation (CV of the reproducibility of assay was less than 15%. The corresponding specific hybridization maps of the multiple bacteria DNA samples were obtained, and the detection limit of simulated water sample of Shigella dysenteriae was 3.54×105cfu/ml. Conclusions The DNA microarray detection system based on arbitrarily primed PCR can be employed for effective detection of multiple food-borne pathogens, and this assay may offer a new method for high-throughput platform for detecting bacteria.

  12. Surface plasmon resonance imaging reveals multiple binding modes of Agrobacterium transformation mediator VirE2 to ssDNA.

    Science.gov (United States)

    Kim, Sanghyun; Zbaida, David; Elbaum, Michael; Leh, Hervé; Nogues, Claude; Buckle, Malcolm

    2015-07-27

    VirE2 is the major secreted protein of Agrobacterium tumefaciens in its genetic transformation of plant hosts. It is co-expressed with a small acidic chaperone VirE1, which prevents VirE2 oligomerization. After secretion into the host cell, VirE2 serves functions similar to a viral capsid in protecting the single-stranded transferred DNA en route to the nucleus. Binding of VirE2 to ssDNA is strongly cooperative and depends moreover on protein-protein interactions. In order to isolate the protein-DNA interactions, imaging surface plasmon resonance (SPRi) studies were conducted using surface-immobilized DNA substrates of length comparable to the protein-binding footprint. Binding curves revealed an important influence of substrate rigidity with a notable preference for poly-T sequences and absence of binding to both poly-A and double-stranded DNA fragments. Dissociation at high salt concentration confirmed the electrostatic nature of the interaction. VirE1-VirE2 heterodimers also bound to ssDNA, though by a different mechanism that was insensitive to high salt. Neither VirE2 nor VirE1-VirE2 followed the Langmuir isotherm expected for reversible monomeric binding. The differences reflect the cooperative self-interactions of VirE2 that are suppressed by VirE1. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Dye Sensitizers for Photodynamic Therapy

    Directory of Open Access Journals (Sweden)

    Harold S. Freeman

    2013-03-01

    Full Text Available Photofrin® was first approved in the 1990s as a sensitizer for use in treating cancer via photodynamic therapy (PDT. Since then a wide variety of dye sensitizers have been developed and a few have been approved for PDT treatment of skin and organ cancers and skin diseases such as acne vulgaris. Porphyrinoid derivatives and precursors have been the most successful in producing requisite singlet oxygen, with Photofrin® still remaining the most efficient sensitizer (quantum yield = 0.89 and having broad food and drug administration (FDA approval for treatment of multiple cancer types. Other porphyrinoid compounds that have received approval from US FDA and regulatory authorities in other countries include benzoporphyrin derivative monoacid ring A (BPD-MA, meta-tetra(hydroxyphenylchlorin (m-THPC, N-aspartyl chlorin e6 (NPe6, and precursors to endogenous protoporphyrin IX (PpIX: 1,5-aminolevulinic acid (ALA, methyl aminolevulinate (MAL, hexaminolevulinate (HAL. Although no non-porphyrin sensitizer has been approved for PDT applications, a small number of anthraquinone, phenothiazine, xanthene, cyanine, and curcuminoid sensitizers are under consideration and some are being evaluated in clinical trials. This review focuses on the nature of PDT, dye sensitizers that have been approved for use in PDT, and compounds that have entered or completed clinical trials as PDT sensitizers.

  14. Treatment of dyeing wastewater including reactive dyes (Reactive ...

    African Journals Online (AJOL)

    Fungal growth was not observed at pH 2. Maximum fungal decolourisation ocurred at pH 3 for anionic reactive dyes (RR, RBB, RB) and pH 6 for cationic MB dye. The fungal dye bioremoval was associated with the surface charge of the fungus due to electrostatic interactions. Growing R. arrhizus strain decolourised 100% of ...

  15. Hair cosmetics: dyes.

    Science.gov (United States)

    Guerra-Tapia, A; Gonzalez-Guerra, E

    2014-11-01

    Hair plays a significant role in body image, and its appearance can be changed relatively easily without resort to surgical procedures. Cosmetics and techniques have therefore been used to change hair appearance since time immemorial. The cosmetics industry has developed efficient products that can be used on healthy hair or act on concomitant diseases of the hair and scalp. Dyes embellish the hair by bleaching or coloring it briefly, for temporary periods of longer duration, or permanently, depending on the composition of a dye (oxidative or nonoxidative) and its degree of penetration of the hair shaft. The dermatologist's knowledge of dyes, their use, and their possible side effects (contact eczema, cancer, increased porosity, brittleness) can extend to an understanding of cosmetic resources that also treat hair and scalp conditions. Copyright © 2013 Elsevier España, S.L.U. and AEDV. All rights reserved.

  16. Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence.

    Directory of Open Access Journals (Sweden)

    Joke J F A van Vugt

    Full Text Available BACKGROUND: Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. METHODOLOGY/PRINCIPAL FINDINGS: We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type and native RSC from yeast (SWI/SNF-type repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. CONCLUSIONS/SIGNIFICANCE: Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase

  17. Hair Dye and Hair Relaxers

    Science.gov (United States)

    ... For Consumers Consumer Information by Audience For Women Hair Dye and Hair Relaxers Share Tweet Linkedin Pin it More sharing ... products. If you have a bad reaction to hair dyes and relaxers, you should: Stop using the ...

  18. Dye filled security seal

    International Nuclear Information System (INIS)

    Wilson, D.C.

    1982-01-01

    A security seal for providing an indication of unauthorized access to a sealed object includes an elongate member to be entwined in the object such that access is denied unless the member is removed. The elongate member has a hollow, pressurizable chamber extending throughout its length that is filled with a permanent dye under greater than atmospheric pressure. Attempts to cut the member and weld it together are revealed when dye flows through a rupture in the chamber wall and stains the outside surface of the member

  19. The mitochondrial ND1 m.3337G>A mutation associated to multiple mitochondrial DNA deletions in a patient with Wolfram syndrome and cardiomyopathy.

    Science.gov (United States)

    Mezghani, Najla; Mnif, Mouna; Mkaouar-Rebai, Emna; Kallel, Nozha; Salem, Ikhlass Haj; Charfi, Nadia; Abid, Mohamed; Fakhfakh, Faiza

    2011-07-29

    Wolfram syndrome (WFS) is a rare hereditary disorder also known as DIDMOAD (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). It is a heterogeneous disease and full characterization of all clinical and biological features of this disorder is difficult. The wide spectrum of clinical expression, affecting several organs and tissues, and the similarity in phenotype between patients with Wolfram syndrome and those with certain types of respiratory chain diseases suggests mitochondrial DNA (mtDNA) involvement in Wolfram syndrome patients. We report a Tunisian patient with clinical features of moderate Wolfram syndrome including diabetes, dilated cardiomyopathy and neurological complications. The results showed the presence of the mitochondrial ND1 m.3337G>A mutation in almost homoplasmic form in 3 tested tissues of the proband (blood leukocytes, buccal mucosa and skeletal muscle). In addition, the long-range PCR amplifications revealed the presence of multiple deletions of the mitochondrial DNA extracted from the patient's skeletal muscle removing several tRNA and protein-coding genes. Our study reported a Tunisian patient with clinical features of moderate Wolfram syndrome associated with cardiomyopathy, in whom we detected the ND1 m.3337G>A mutation with mitochondrial multiple deletions. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

    Directory of Open Access Journals (Sweden)

    Wu Shi-Fang

    2011-07-01

    Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

  1. First description of a novel mitochondrial mutation in the MT-TI gene associated with multiple mitochondrial DNA deletion and depletion in family with severe dilated mitochondrial cardiomyopathy.

    Science.gov (United States)

    Alila-Fersi, Olfa; Tabebi, Mouna; Maalej, Marwa; Belguith, Neila; Keskes, Leila; Mkaouar-Rebai, Emna; Fakhfakh, Faiza

    2018-03-18

    Mitochondria are essential for early cardiac development and impaired mitochondrial function was described associated with heart diseases such as hypertrophic or dilated mitochondrial cardiomyopathy. In this study, we report a family including two individuals with severe dilated mitochondrial cardiomyopathy. The whole mitochondrial genome screening showed the presence of several variations and a novel homoplasmic mutation m.4318-4322delC in the MT-TI gene shared by the two patients and their mother and leading to a disruption of the tRNA Ile secondary structure. In addition, a mitochondrial depletion was present in blood leucocyte of the two affected brother whereas a de novo heteroplasmic multiple deletion in the major arc of mtDNA was present in blood leucocyte and mucosa of only one of them. These deletions in the major arc of the mtDNA resulted to the loss of several protein-encoding genes and also some tRNA genes. The mtDNA deletion and depletion could result to an impairment of the oxidative phosphorylation and energy metabolism in the respiratory chain in the studied patients. Our report is the first description of a family with severe lethal dilated mitochondrial cardiomyopathy and presenting several mtDNA abnormalities including punctual mutation, deletion and depletion. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Male infertility is significantly associated with multiple deletions in an 8.7-kb segment of sperm mtDNA in Pakistan.

    Science.gov (United States)

    Mughal, Irfan Afzal; Irfan, Asma; Jahan, Sarwat; Hameed, Abdul

    2017-06-12

    This study aimed to find a link between sperm mitochondrial DNA mutations and male infertility in Pakistan. DNA from semen samples was extracted and amplified by PCR using 7.8-kb deletion-specific primers. The PCR products were separated on agarose gel, visualized under UV-illumination, and then photographed. The results were genotyped and the data were analyzed using SPSS. Deletion analysis of the 8.7-kb fragment by long PCR revealed multiple deletions. The frequency of deletion was much higher in infertile groups as compared to the control group. Further, on comparison between different subtypes of infertile groups, the deletions were highest in the oligoasthenoteratozoospermia (OAT) group. The statistical analysis of case and control groups showed a significant association of the 8.7-kb deletion with human male infertile groups (P = 0.031), and particularly a very significant association with the OAT subgroup (P = 0.019). A significant association has been found between human male infertility and mtDNA deletions in an 8.7-kb segment of sperm mtDNA in a Pakistani population.

  3. Deficiency of double-strand DNA break repair does not impair Mycobacterium tuberculosis virulence in multiple animal models of infection.

    Science.gov (United States)

    Heaton, Brook E; Barkan, Daniel; Bongiorno, Paola; Karakousis, Petros C; Glickman, Michael S

    2014-08-01

    Mycobacterium tuberculosis persistence within its human host requires mechanisms to resist the effector molecules of host immunity, which exert their bactericidal effects through damaging pathogen proteins, membranes, and DNA. Substantial evidence indicates that bacterial pathogens, including M. tuberculosis, require DNA repair systems to repair the DNA damage inflicted by the host during infection, but the role of double-strand DNA break (DSB) repair systems is unclear. Double-strand DNA breaks are the most cytotoxic form of DNA damage and must be repaired for chromosome replication to proceed. M. tuberculosis elaborates three genetically distinct DSB repair systems: homologous recombination (HR), nonhomologous end joining (NHEJ), and single-strand annealing (SSA). NHEJ, which repairs DSBs in quiescent cells, may be particularly relevant to M. tuberculosis latency. However, very little information is available about the phenotype of DSB repair-deficient M. tuberculosis in animal models of infection. Here we tested M. tuberculosis strains lacking NHEJ (a Δku ΔligD strain), HR (a ΔrecA strain), or both (a ΔrecA Δku strain) in C57BL/6J mice, C3HeB/FeJ mice, guinea pigs, and a mouse hollow-fiber model of infection. We found no difference in bacterial load, histopathology, or host mortality between wild-type and DSB repair mutant strains in any model of infection. These results suggest that the animal models tested do not inflict DSBs on the mycobacterial chromosome, that other repair pathways can compensate for the loss of NHEJ and HR, or that DSB repair is not required for M. tuberculosis pathogenesis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  4. 5-aza-2′-deoxycytidine impairs mouse spermatogenesis at multiple stages through different usage of DNA methyltransferases

    International Nuclear Information System (INIS)

    Song, Ning; Endo, Daisuke; Song, Bin; Shibata, Yasuaki; Koji, Takehiko

    2016-01-01

    Mammalian spermatogenesis is a progressive process comprising spermatogonial proliferation, spermatocytic meiosis, and later spermiogenesis, which is considered to be under the regulation of epigenetic parameters. To gain insights into the significance of DNA methylation in early spermatogenesis, 5-azadC was used as a molecular biological tool to mimic the level of DNA methylation in vivo. Since the drug is incorporated into DNA during the S-phase, spermatogonia and spermatocytes would be affected primarily in mouse spermatogenesis. Adult male ICR mice were intraperitoneally injected with 5-azadC at a dose of 0.25 mg/kg/day for 10 consecutive days, allowing us to examine its maximum effect on the kinetics of spermatogonia and spermatocytes. In this short-term protocol, 5-azadC induced significant histological abnormalities, such as a marked increase in apoptosis of spermatogonia and spermatocytes, followed by severe loss of spermatids, while after termination of 5-azadC treatment, normal histology was restored in the testis within 35 days. Quantification of the methylation level of CCGG sites as well as whole DNA showed spermatogonial hypomethylation, which correlated with increased apoptosis of spermatogonia. Interestingly, the hypomethylated cells were simultaneously positive for tri-methylated histone H3 at K4. On the other hand, no changes in methylation level were found in spermatocytes, but PCNA staining clearly showed disordered accumulation of S-phase spermatocytes, which increased their apoptosis in stage XII. In addition, different immunohistochemical staining pattern was found for DNA methyltransferases (DNMTs); DNMT1was expressed in the majority of all germ cells, but DNMT3a and b were only expressed in spermatogonia. Our results indicate that 5-azadC caused DNA hypomethylation in spermatogonia, but induced prolongation of S-phase in spermatocytes, resulting in the induction of apoptosis in both cases. Thus, 5-azadC affects spermatogenesis at more than

  5. OPTIMIZATION OF DYEING PARAMETERS TO DYE COTTON WITH CARROT EXTRACTION

    Directory of Open Access Journals (Sweden)

    MIRALLES Verónica

    2017-05-01

    Full Text Available Natural dyes derived from flora and fauna are believed to be safe because of non-toxic, non-carcinogenic and biodegradable nature. Furthermore, natural dyes do not cause pollution and waste water problems. Natural dyes as well as synthetic dyes need the optimum parameters to get a good dyeing. On some occasions, It is necessary the use of mordants to increase the affinity between cellulose fiber and natural dye, but there are other conditions to optimize in the dyeing process, like time, temperature, auxiliary porducts, etc. In addition, the optimum conditions are different depends on the type of dye and the fiber nature. The aim of this work is the use of carrot extract to dye cotton fabric by exhaustion at diverse dyeing conditions. Diffferent dyeing processes were carried out to study the effect of pH condition and the temperature, using 7, 6 and 4 pH values and 95 ºC and 130ºC for an hour. As a result some images of dyed samples are shown. Moreover, to evaluate the colour of each sample CIELAB parameters are analysed obtained by reflexion spectrophotometre. The results showed that the temperature used has an important influence on the colour of the dyed sample.

  6. Microfluidic Dye Lasers

    DEFF Research Database (Denmark)

    Kristensen, Anders; Balslev, Søren; Gersborg-Hansen, Morten

    2006-01-01

    A technology for miniaturized, polymer based lasers, suitable for integration with planar waveguides and microfluidic networks is presented. The microfluidic dye laser device consists of a microfluidic channel with an embedded optical resonator. The devices are fabricated in a thin polymer film...

  7. (MTT) dye reduction assay.

    African Journals Online (AJOL)

    to inhibit proliferation of HeLa cells was determined using the 3443- dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) dye reduction assay. Extracts from roots of Agathisanthemum bojeri, Synaptolepis kirkii and Zanha africana and the leaf extract of Physalis peruviana at a concentration of 10 pg/ml inhibited cell ...

  8. Levitated droplet dye laser

    DEFF Research Database (Denmark)

    Azzouz, H.; Alkafadiji, L.; Balslev, Søren

    2006-01-01

    a high quality optical resonator. Our 750 nL lasing droplets consist of Rhodamine 6G dissolved in ethylene glycol, at a concentration of 0.02 M. The droplets are optically pumped at 532 nm light from a pulsed, frequency doubled Nd:YAG laser, and the dye laser emission is analyzed by a fixed grating...

  9. Dye laser principles with applications

    CERN Document Server

    Duarte, Frank J; Liao, Peter F; Kelley, Paul

    1990-01-01

    A tutorial introduction to the field of dye lasers, Dye Laser Principles also serves as an up-to-date overview for those using dye lasers as research and industrial tools. A number of the issues discussed in this book are pertinent not only to dye lasers but also to lasers in general. Most of the chapters in the book contain problem sets that expand on the material covered in the chapter.Key Features* Dye lasers are among the most versatile and successful laser sources currently available in use Offering both pulsed and continuous-wave operation and tunable from the near ultraviole

  10. B-G cDNA clones have multiple small repeats and hybridize to both chicken MHC regions

    DEFF Research Database (Denmark)

    Kaufman, J; Salomonsen, J; Skjødt, K

    1989-01-01

    We used rabbit antisera to the chicken MHC erythrocyte molecule B-G and to the class I alpha chain (B-F) to screen lambda gt11 cDNA expression libraries made with RNA selected by oligo-dT from bone marrow cells of anemic B19 homozygous chickens. Eight clones were found to encode B-G molecules which...

  11. Multiple origins of polyploidy in the phylogeny of southern African barbs (Cyprinidae) as inferred from mtDNA markers

    Czech Academy of Sciences Publication Activity Database

    Tsigenopoulos, C. S.; Ráb, Petr; Naran, D.; Berrebi, P.

    2002-01-01

    Roč. 88, - (2002), s. 466-473 ISSN 0018-067X R&D Projects: GA AV ČR IBS5045011; GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z5045916 Keywords : barbus * Cyprinidae * mitochondrial DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.687, year: 2002

  12. The mitochondrial ND1 m.3337G>A mutation associated to multiple mitochondrial DNA deletions in a patient with Wolfram syndrome and cardiomyopathy

    Energy Technology Data Exchange (ETDEWEB)

    Mezghani, Najla [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia); Mnif, Mouna [Service d' endocrinologie, C.H.U. Habib Bourguiba de Sfax (Tunisia); Mkaouar-Rebai, Emna, E-mail: emna_mkaouar@mail2world.com [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia); Kallel, Nozha [Service d' endocrinologie, C.H.U. Habib Bourguiba de Sfax (Tunisia); Salem, Ikhlass Haj [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia); Charfi, Nadia; Abid, Mohamed [Service d' endocrinologie, C.H.U. Habib Bourguiba de Sfax (Tunisia); Fakhfakh, Faiza [Laboratoire de Genetique Moleculaire Humaine, Faculte de Medecine de Sfax, Universite de Sfax (Tunisia)

    2011-07-29

    Highlights: {yields} We reported a patient with Wolfram syndrome and dilated cardiomyopathy. {yields} We detected the ND1 mitochondrial m.3337G>A mutation in 3 tested tissues (blood leukocytes, buccal mucosa and skeletal muscle). {yields} Long-range PCR amplification revealed the presence of multiple mitochondrial deletions in the skeletal muscle. {yields} The deletions remove several tRNA and protein-coding genes. -- Abstract: Wolfram syndrome (WFS) is a rare hereditary disorder also known as DIDMOAD (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). It is a heterogeneous disease and full characterization of all clinical and biological features of this disorder is difficult. The wide spectrum of clinical expression, affecting several organs and tissues, and the similarity in phenotype between patients with Wolfram syndrome and those with certain types of respiratory chain diseases suggests mitochondrial DNA (mtDNA) involvement in Wolfram syndrome patients. We report a Tunisian patient with clinical features of moderate Wolfram syndrome including diabetes, dilated cardiomyopathy and neurological complications. The results showed the presence of the mitochondrial ND1 m.3337G>A mutation in almost homoplasmic form in 3 tested tissues of the proband (blood leukocytes, buccal mucosa and skeletal muscle). In addition, the long-range PCR amplifications revealed the presence of multiple deletions of the mitochondrial DNA extracted from the patient's skeletal muscle removing several tRNA and protein-coding genes. Our study reported a Tunisian patient with clinical features of moderate Wolfram syndrome associated with cardiomyopathy, in whom we detected the ND1 m.3337G>A mutation with mitochondrial multiple deletions.

  13. The mitochondrial ND1 m.3337G>A mutation associated to multiple mitochondrial DNA deletions in a patient with Wolfram syndrome and cardiomyopathy

    International Nuclear Information System (INIS)

    Mezghani, Najla; Mnif, Mouna; Mkaouar-Rebai, Emna; Kallel, Nozha; Salem, Ikhlass Haj; Charfi, Nadia; Abid, Mohamed; Fakhfakh, Faiza

    2011-01-01

    Highlights: → We reported a patient with Wolfram syndrome and dilated cardiomyopathy. → We detected the ND1 mitochondrial m.3337G>A mutation in 3 tested tissues (blood leukocytes, buccal mucosa and skeletal muscle). → Long-range PCR amplification revealed the presence of multiple mitochondrial deletions in the skeletal muscle. → The deletions remove several tRNA and protein-coding genes. -- Abstract: Wolfram syndrome (WFS) is a rare hereditary disorder also known as DIDMOAD (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). It is a heterogeneous disease and full characterization of all clinical and biological features of this disorder is difficult. The wide spectrum of clinical expression, affecting several organs and tissues, and the similarity in phenotype between patients with Wolfram syndrome and those with certain types of respiratory chain diseases suggests mitochondrial DNA (mtDNA) involvement in Wolfram syndrome patients. We report a Tunisian patient with clinical features of moderate Wolfram syndrome including diabetes, dilated cardiomyopathy and neurological complications. The results showed the presence of the mitochondrial ND1 m.3337G>A mutation in almost homoplasmic form in 3 tested tissues of the proband (blood leukocytes, buccal mucosa and skeletal muscle). In addition, the long-range PCR amplifications revealed the presence of multiple deletions of the mitochondrial DNA extracted from the patient's skeletal muscle removing several tRNA and protein-coding genes. Our study reported a Tunisian patient with clinical features of moderate Wolfram syndrome associated with cardiomyopathy, in whom we detected the ND1 m.3337G>A mutation with mitochondrial multiple deletions.

  14. Characteristics of dye-sensitized solar cells using natural dye

    Energy Technology Data Exchange (ETDEWEB)

    Furukawa, Shoji, E-mail: furukawa@cse.kyutech.ac.j [Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka-ken 820-8502 (Japan); Iino, Hiroshi; Iwamoto, Tomohisa; Kukita, Koudai; Yamauchi, Shoji [Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka-ken 820-8502 (Japan)

    2009-11-30

    Dye-sensitized solar cells are expected to be used for future clean energy. Recently, most of the researchers in this field use Ruthenium complex as dye in the dye-sensitized solar cells. However, Ruthenium is a rare metal, so the cost of the Ruthenium complex is very high. In this paper, various dye-sensitized solar cells have been fabricated using natural dye, such as the dye of red-cabbage, curcumin, and red-perilla. As a result, it was found that the conversion efficiency of the solar cell fabricated using the mixture of red-cabbage and curcumin was about 0.6% (light source: halogen lamp), which was larger than that of the solar cells using one kind of dye. It was also found that the conversion efficiency was about 1.0% for the solar cell with the oxide semiconductor film fabricated using polyethylene glycol (PEG) whose molecular weight was 2,000,000 and red-cabbage dye. This indicates that the cost performance (defined by [conversion efficiency]/[cost of dye]) of the latter solar cell (dye: red-cabbage) is larger by more than 50 times than that of the solar cell using Ruthenium complex, even if the effect of the difference between the halogen lamp and the standard light source is taken into account.

  15. Assessment of multiple types of DNA damage in human placentas from smoking and nonsmoking women in the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Pratt, M. M.; King, L. C.; Adams, L. D.; John, K.; Sirajuddin, P.; Olivero, O. A.; Manchester, D. K.; Šrám, Radim; DeMarini, D. M.; Poirier, M. C.

    2011-01-01

    Roč. 52, č. 1 (2011), s. 58-68 ISSN 0893-6692 R&D Projects: GA MŽP(CZ) SP/1B3/8/08 Institutional research plan: CEZ:AV0Z50390512 Keywords : automated cellular imaging system * immunohistochemistry * BPDE-DNA antiserum Subject RIV: DN - Health Impact of the Environment Quality Impact factor: 3.709, year: 2011

  16. Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Xie, Fang-Fei; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Hong; Wu, Jian; Guo, Yu-Fan; Zeng, Ke-Qin; Wang, Ming-Jun; Zhu, Xiao-Wei; Xia, Wei; Wang, Lan; He, Pei; Bing, Peng-Fei; Lu, Xin; Zhang, Yong-Hong; Lei, Shu-Feng

    2018-01-01

    DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1 ) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P correlation (R T4  > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

  17. Random amplified polymorphic DNA based genetic characterization ...

    African Journals Online (AJOL)

    DIRECTOR

    2013-07-10

    Jul 10, 2013 ... Electrophoresis) buffer, 2 µl of SYBR-safe (DNA staining dye) was added to it, mixed properly, ..... tools in plant genetic resources conservation: a guide to the technologies. IPGRI. Rome ... Creating Capital. Seethalakshmi KK ...

  18. Recurring DNA copy number gain at chromosome 9p13 plays a role in the activation of multiple candidate oncogenes in progressing oral premalignant lesions

    International Nuclear Information System (INIS)

    Towle, Rebecca; Tsui, Ivy F L; Zhu, Yuqi; MacLellan, Sara; Poh, Catherine F; Garnis, Cathie

    2014-01-01

    Genomic alteration at chromosome 9p has been previously reported as a frequent and critical event in oral premalignancy. While this alteration is typically reported as a loss driven by selection for CDKN2A deactivation (at 9p21.3), we detect a recurrent DNA copy number gain of ∼2.49 Mbp at chromosome 9p13 in oral premalignant lesions (OPLs) that later progressed to invasive lesions. This recurrent alteration event has been validated using fluorescence in situ hybridization in an independent set of OPLs. Analysis of publicly available gene expression datasets aided in identifying three oncogene candidates that may have driven selection for DNA copy number increases in this region (VCP, DCTN3, and STOML2). We performed in vitro silencing and activation experiments for each of these genes in oral cancer cell lines and found that each gene is independently capable of upregulating proliferation and anchorage-independent growth. We next analyzed the activity of each of these genes in biopsies of varying histological grades that were obtained from a diseased oral tissue field in a single patient, finding further molecular evidence of parallel activation of VCP, DCTN3, and STOML2 during progression from normal healthy tissue to invasive oral carcinoma. Our results support the conclusion that DNA gain at 9p13 is important to the earliest stages of oral tumorigenesis and that this alteration event likely contributes to the activation of multiple oncogene candidates capable of governing oral cancer phenotypes

  19. Synthesis of azo pyridone dyes

    Directory of Open Access Journals (Sweden)

    Mijin Dušan Ž.

    2011-01-01

    Full Text Available Over 50% of all colorants which are used nowdays are azo dyes and pigments, and among them arylazo pyridone dyes (and pigments have became of interest in last several decades due to the high molar extinction coefficient, and the medium to high light and wet fastness properties. They find application generally as disperse dyes. The importance of disperse dyes increased in the 1970s and 1980s due to the use of polyester and nylon as the main synthetic fibers. Also, disperse dyes were used rapidly since 1970 in inks for the heat-transfer printing of polyester. The main synthetic route for the preparation of azo dyes is coupling reaction between an aromatic diazo compound and a coupling component. Of all dyes manufactured, about 60% are produced by this reaction. Arylazo pyridone dyes can be prepared from pyridone moiety as a coupling component, where substituent can be on nitrogen, and diazonim salts which can be derived from different substituted anilines or other heterocyclic derivatives. In addition, arylazo dyes containing pyridone ring can be prepared from arylazo diketones or arylazo ketoesters (obtained by coupling β-diketones or β-ketoesters with diazonim salts by condensation with cyanoacetamide. Disazo dyes can be prepared by tetrazotizing a dianiline and coupling it with a pyridone or by diazotizing aniline and coupling it with a dipyridone. Trisazo dyes can be also prepared by diazotizing of aniline and coupling it with a tripyridone or by hexazotizing a trianiline and coupling it with a pyridone. The main goal of this paper is to give a brief review on the synthesis of arylazo pyridone dyes due to the lack of such reviews. In addition, some properties of arylazo pyridone dyes as light fastness and azo-hydrazon tautomerism are disccused.

  20. Programmed coherent coupling in a synthetic DNA-based excitonic circuit

    Science.gov (United States)

    Boulais, Étienne; Sawaya, Nicolas P. D.; Veneziano, Rémi; Andreoni, Alessio; Banal, James L.; Kondo, Toru; Mandal, Sarthak; Lin, Su; Schlau-Cohen, Gabriela S.; Woodbury, Neal W.; Yan, Hao; Aspuru-Guzik, Alán; Bathe, Mark

    2018-02-01

    Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We first characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modelling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent circular dichroism, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.

  1. DNA-based identifications reveal multiple introductions of the vegetable leafminer Liriomyza sativae (Diptera: Agromyzidae) into the Torres Strait Islands and Papua New Guinea.

    Science.gov (United States)

    Blacket, M J; Rice, A D; Semeraro, L; Malipatil, M B

    2015-10-01

    Leafmining flies (Diptera: Agromyzidae) can be serious economic pests of horticultural crops. Some genera such as Liriomyza are particularly problematic with numerous species, some of which are highly polyphagous (wide host range), which can only be confidently identified morphologically from adult males. In our study, DNA barcoding was employed to establish new locality records of the vegetable leafminer fly, Liriomyza sativae, from the islands of Torres Strait (Queensland, Australia) and the central highlands of Papua New Guinea (PNG). These records represent significant range extensions of this highly invasive plant pest. Specimens of immature leafminers (from leaf mines) were collected over a 5-year period during routine plant health surveys in ethanol or on FTA® filter paper cards, both methods proved effective at preserving and transporting insect DNA under tropical conditions, with FTA cards possessing some additional logistical benefits. Specimens were identified through sequencing two sections of the cytochrome oxidase I gene and the utility of each was assessed for the identification of species and intra-specific genetic lineages. Our study indicates that multiple haplotypes of L. sativae occur in PNG, while a different haplotype is present in the Torres Strait, with genetic regionalization between these areas apart from a single possible instance - one haplotype 'S.7' appears to be common between these two regions - interestingly this has also been the most common haplotype detected in previous studies of invasive L. sativae populations. The DNA barcoding methods employed here not only identified multiple introductions of L. sativae, but also appear generally applicable to the identification of other agromyzid leafminers (Phytomyzinae and Agromyzinae) and should decrease the likelihood of potentially co-amplifying internal hymenopteran parasitoids. Currently, L. sativae is still not recorded from the Australian mainland; however, further sampling of

  2. Multiple group I introns in the small-subunit rDNA of Botryosphaeria dothidea: implication for intraspecific genetic diversity.

    Directory of Open Access Journals (Sweden)

    Chao Xu

    Full Text Available Botryosphaeria dothidea is a widespread and economically important pathogen on various fruit trees, and it often causes die-back and canker on limbs and fruit rot. In characterizing intraspecies genetic variation within this fungus, group I introns, rich in rDNA of fungi, may provide a productive region for exploration. In this research, we analysed complete small subunit (SSU ribosomal DNA (rDNA sequences of 37 B. dothidea strains, and found four insertions, designated Bdo.S943, Bdo.S1199-A, Bdo.S1199-B and Bdo.S1506, at three positions. Sequence analysis and structure prediction revealed that both Bdo.S943 and Bdo.S1506 belonged to subgroup IC1 of group I introns, whereas Bdo.S1199-A and Bdo.S1199-B corresponded to group IE introns. Moreover, Bdo.S1199-A was found to host an open reading frame (ORF for encoding the homing endonuclease (HE, whereas Bdo.S1199-B, an evolutionary descendant of Bdo.S1199-A, included a degenerate HE. The above four introns were novel, and were the first group I introns observed and characterized in this species. Differential distribution of these introns revealed that all strains could be separated into four genotypes. Genotype III (no intron and genotype IV (Bdo.S1199-B were each found in only one strain, whereas genotype I (Bdo.S1199-A and genotype II (Bdo.S943 and Bdo.S1506 occurred in 95% of the strains. There is a correlation between B. dothidea genotypes and hosts or geographic locations. Thus, these newly discovered group I introns can help to advance understanding of genetic differentiation within B. dothidea.

  3. Phylogeographical analysis of mtDNA data indicates postglacial expansion from multiple glacial refugia in woodland caribou (Rangifer tarandus caribou.

    Directory of Open Access Journals (Sweden)

    Cornelya F C Klütsch

    Full Text Available Glacial refugia considerably shaped the phylogeographical structure of species and may influence intra-specific morphological, genetic, and adaptive differentiation. However, the impact of the Quaternary ice ages on the phylogeographical structure of North American temperate mammalian species is not well-studied. Here, we surveyed ~1600 individuals of the widely distributed woodland caribou (Rangifer tarandus caribou using mtDNA control region sequences to investigate if glacial refugia contributed to the phylogeographical structure in this subspecies. Phylogenetic tree reconstruction, a median-joining network, and mismatch distributions supported postglacial expansions of woodland caribou from three glacial refugia dating back to 13544-22005 years. These three lineages consisted almost exclusively of woodland caribou mtDNA haplotypes, indicating that phylogeographical structure was mainly shaped by postglacial expansions. The putative centres of these lineages are geographically separated; indicating disconnected glacial refugia in the Rocky Mountains, east of the Mississippi, and the Appalachian Mountains. This is in congruence with the fossil record that caribou were distributed in these areas during the Pleistocene. Our results suggest that the last glacial maximum substantially shaped the phylogeographical structure of this large mammalian North American species that will be affected by climatic change. Therefore, the presented results will be essential for future conservation planning in woodland caribou.

  4. Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding.

    Science.gov (United States)

    Aizpurua, Ostaizka; Budinski, Ivana; Georgiakakis, Panagiotis; Gopalakrishnan, Shyam; Ibañez, Carlos; Mata, Vanessa; Rebelo, Hugo; Russo, Danilo; Szodoray-Parádi, Farkas; Zhelyazkova, Violeta; Zrncic, Vida; Gilbert, M Thomas P; Alberdi, Antton

    2018-02-01

    The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study, we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary niche is shaped by the extension and type of agricultural fields. We employed a dual-primer DNA metabarcoding approach to characterize arthropod 16S and COI DNA sequences within bat faecal pellets collected across 16 Southern European localities, to first characterize the bat species' dietary niche, second measure the incidence of agricultural pests across their ranges and third assess whether geographical dietary variation responds to climatic, landscape diversity, agriculture type and vegetation productivity factors. We detected 12 arthropod orders, among which lepidopterans were predominant. We identified >200 species, 44 of which are known to cause agricultural damage. Pest species were detected at all but one sampling site and in 94% of the analysed samples. Furthermore, the dietary diversity of M. schreibersii exhibited a negative linear relation with the area of intensive agricultural fields, thus suggesting crops restrict the dietary niche of bats to prey taxa associated with agricultural production within their foraging range. Overall, our results imply that M. schreibersii might be a valuable asset for biological pest suppression in a variety of agricultural productions and highlight the dynamic interplay between wildlife and agricultural systems. © 2017 John Wiley & Sons Ltd.

  5. DNA-based prenatal diagnosis for severe and variant forms of multiple acyl-CoA dehydrogenation deficiency

    DEFF Research Database (Denmark)

    Olsen, Rikke K J; Andresen, Brage S; Christensen, Ernst

    2005-01-01

    OBJECTIVES: Multiple acyl-CoA dehydrogenation deficiency (MADD) is a clinically heterogeneous disorder of mitochondrial fatty acid, amino acid, and choline oxidation due to mutations in the genes encoding electron transfer flavoprotein (ETF) or ETF ubiquinone oxidoreductase (ETFQO). So far...

  6. No evidence of association between optic neuritis and secondary LHON mtDNA mutations in patients with multiple sclerosis

    DEFF Research Database (Denmark)

    Andalib, Sasan; Talebi, Mahnaz; Sakhinia, Ebrahim

    2017-01-01

    Leber's Hereditary Optic Neuropathy (LHON) shares features with Multiple Sclerosis (MS). Both diseases develop optic lesions. Frequent secondary LHON mutations in MS patients may explain the optic damage. Here, we tested the hypothesis that secondary LHON mutations are associated with optic...

  7. Dye lasers in atomic spectroscopy

    International Nuclear Information System (INIS)

    Lange, W.; Luther, J.; Steudel, A.

    1974-01-01

    The properties of dye lasers which are relevant to atomic spectroscopy are discussed. Several experiments made possible by tunable dye lasers are discussed. Applications of high spectral density dye lasers are covered in areas such as absorption spectroscopy, fluorescence spectroscopy, photoionization and photodetachment, and two- and multi-photon processes. Applications which take advantage of the narrow bandwidth of tunable dye lasers are discussed, including saturation spectroscopy, fluorescence line narrowing, classic absorption and fluorescence spectroscopy, nonoptical detection of optical resonances, heterodyne spectroscopy, and nonlinear coherent resonant phenomena. (26 figures, 180 references) (U.S.)

  8. Chase the direct impact of rainfall into groundwater in Mt. Fuji from multiple analyses including microbial DNA

    Science.gov (United States)

    Kato, Kenji; Sugiyama, Ayumi; Nagaosa, Kazuyo; Tsujimura, Maki

    2016-04-01

    A huge amount of groundwater is stored in subsurface environment of Mt. Fuji, the largest volcanic mountain in Japan. Based on the concept of piston flow transport of groundwater an apparent residence time was estimated to ca. 30 years by 36Cl/Cl ratio (Tosaki et al., 2011). However, this number represents an averaged value of the residence time of groundwater which had been mixed before it flushes out. We chased signatures of direct impact of rainfall into groundwater to elucidate the routes of groundwater, employing three different tracers; stable isotopic analysis (delta 18O), chemical analysis (concentration of silica) and microbial DNA analysis. Though chemical analysis of groundwater shows an averaged value of the examined water which was blended by various water with different sources and routes in subsurface environment, microbial DNA analysis may suggest the place where they originated, which may give information of the source and transport routes of the water examined. Throughout the in situ observation of four rainfall events showed that stable oxygen isotopic ratio of spring water and shallow groundwater obtained from 726m a.s.l. where the average recharge height of rainfall was between 1500 and 1800 m became higher than the values before a torrential rainfall, and the concentration of silica decreased after this event when rainfall exceeded 300 mm in precipitation of an event. In addition, the density of Prokaryotes in spring water apparently increased. Those changes did not appear when rainfall did not exceed 100 mm per event. Thus, findings shown above indicated a direct impact of rainfall into shallow groundwater, which appeared within a few weeks of torrential rainfall in the studied geological setting. In addition, increase in the density of Archaea observed at deep groundwater after the torrential rainfall suggested an enlargement of the strength of piston flow transport through the penetration of rainfall into deep groundwater. This finding was

  9. Rectangular coordination polymer nanoplates: large-scale, rapid synthesis and their application as a fluorescent sensing platform for DNA detection.

    Directory of Open Access Journals (Sweden)

    Yingwei Zhang

    Full Text Available In this paper, we report on the large-scale, rapid synthesis of uniform rectangular coordination polymer nanoplates (RCPNs assembled from Cu(II and 4,4'-bipyridine for the first time. We further demonstrate that such RCPNs can be used as a very effective fluorescent sensing platform for multiple DNA detection with a detection limit as low as 30 pM and a high selectivity down to single-base mismatch. The DNA detection is accomplished by the following two steps: (1 RCPN binds dye-labeled single-stranded DNA (ssDNA probe, which brings dye and RCPN into close proximity, leading to fluorescence quenching; (2 Specific hybridization of the probe with its target generates a double-stranded DNA (dsDNA which detaches from RCPN, leading to fluorescence recovery. It suggests that this sensing system can well discriminate complementary and mismatched DNA sequences. The exact mechanism of fluorescence quenching involved is elucidated experimentally and its use in a human blood serum system is also demonstrated successfully.

  10. Dye Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Di Wei

    2010-03-01

    Full Text Available Dye sensitized solar cell (DSSC is the only solar cell that can offer both the flexibility and transparency. Its efficiency is comparable to amorphous silicon solar cells but with a much lower cost. This review not only covers the fundamentals of DSSC but also the related cutting-edge research and its development for industrial applications. Most recent research topics on DSSC, for example, applications of nanostructured TiO2, ZnO electrodes, ionic liquid electrolytes, carbon nanotubes, graphene and solid state DSSC have all been included and discussed.

  11. Dye solar cell research

    CSIR Research Space (South Africa)

    Cummings, F

    2009-11-01

    Full Text Available Cummings Energy and Processes Materials Science and Manufacturing Council for Scientific and Industrial Research P.O. Box 395 Pretoria 0001, South Africa 27 November 2009 CONTENT head2rightBackground head2rightCSIR Dye Solar Cell Research head2... rightCollaborations and Links © CSIR 2007 www.csir.co.za head2rightAcknowledgements BACKGROUND head2rightSA is dry: Annual rainfall average of 450 mm compared with a world average of 860 mm head2rightOn upside, we have some...

  12. CW organic dye laser

    International Nuclear Information System (INIS)

    Tuccio, S.A.; Peterson, O.G.

    1975-01-01

    A method and apparatus for producing continuous emission from a lasing medium comprising organic dye molecules in solution are described. Continuous emission is accomplished by flowing the medium through a focused optical cavity while simultaneously producing a population inversion in that portion of the medium flowing in close proximity to the focal point of the cavity. The population inversion is produced by pumping the medium longitudinally, along the optical axis of the cavity, preferably by the focused output of a continuous-wave argon laser. Sufficient thermal energy is continuously dissipated from the medium to maintain the optical homogeneity thereof at or above the quality required for continuous emission

  13. Intercalating dye as an acceptor in quantum-dot-mediated FRET

    International Nuclear Information System (INIS)

    Lim, Teck Chuan; Bailey, Vasudev J; Wang, T-H; Ho, Y-P

    2008-01-01

    Fluorescence resonance energy transfer (FRET) is a popular tool to study intermolecular distances and characterize structural or conformational changes of biological macromolecules. We investigate a novel inorganic/organic FRET pair with quantum dots (QDs) as donors and DNA intercalating dyes, BOBO-3, as acceptors by using DNA as a linker. Typically, FRET efficiency increases with the number of stained DNA linked to a QD. However, with the use of intercalating dyes, we demonstrate that FRET efficiency at a fixed DNA:QD ratio can be further enhanced by increasing the number of dyes stained to a DNA strand through the use of an increased staining dye/bp ratio. We exploit this flexibility in the staining ratio to maintain a high FRET efficiency of >0.90 despite a sixfold decrease in DNA concentration. Having characterized this new QD-mediated FRET system, we test this system in a cellular environment using nanocomplexes generated by encapsulating DNA with commercial non-viral gene carriers. Using this novel FRET pair, we are able to monitor the configuration changes and fate of the DNA nanocomplexes during intracellular delivery, thereby providing an insight into the mechanistic study of gene delivery

  14. Modification of azo dyes by lactic acid bacteria.

    Science.gov (United States)

    Pérez-Díaz, I M; McFeeters, R F

    2009-08-01

    The ability of Lactobacillus casei and Lactobacillus paracasei to modify the azo dye, tartrazine, was recently documented as the result of the investigation on red coloured spoilage in acidified cucumbers. Fourteen other lactic acid bacteria (LAB) were screened for their capability to modify the food colouring tartrazine and other azo dyes of relevance for the textile industry. Most LAB modified tartrazine under anaerobic conditions, but not under aerobic conditions in modified chemically defined media. Microbial growth was not affected by the presence of the azo dyes in the culture medium. The product of the tartrazine modification by LAB was identified as a molecule 111 daltons larger than its precursor by liquid chromatography-mass spectrometry. This product had a purple colour under aerobic conditions and was colourless under anaerobic conditions. It absorbed light at 361 and 553 nm. LAB are capable of anabolizing azo dyes only under anaerobic conditions. IMPACT AND SIGNIFICANCE OF THE STUDY: Although micro-organisms capable of reducing the azo bond on multiple dyes have been known for decades, this is the first report of anabolism of azo dyes by food related micro-organisms, such as LAB.

  15. Scanning fluorescence detector for high-throughput DNA genotyping

    Science.gov (United States)

    Rusch, Terry L.; Petsinger, Jeremy; Christensen, Carl; Vaske, David A.; Brumley, Robert L., Jr.; Luckey, John A.; Weber, James L.

    1996-04-01

    A new scanning fluorescence detector (SCAFUD) was developed for high-throughput genotyping of short tandem repeat polymorphisms (STRPs). Fluorescent dyes are incorporated into relatively short DNA fragments via polymerase chain reaction (PCR) and are separated by electrophoresis in short, wide polyacrylamide gels (144 lanes with well to read distances of 14 cm). Excitation light from an argon laser with primary lines at 488 and 514 nm is introduced into the gel through a fiber optic cable, dichroic mirror, and 40X microscope objective. Emitted fluorescent light is collected confocally through a second fiber. The confocal head is translated across the bottom of the gel at 0.5 Hz. The detection unit utilizes dichroic mirrors and band pass filters to direct light with 10 - 20 nm bandwidths to four photomultiplier tubes (PMTs). PMT signals are independently amplified with variable gain and then sampled at a rate of 2500 points per scan using a computer based A/D board. LabView software (National Instruments) is used for instrument operation. Currently, three fluorescent dyes (Fam, Hex and Rox) are simultaneously detected with peak detection wavelengths of 543, 567, and 613 nm, respectively. The detection limit for fluorescein-labeled primers is about 100 attomoles. Planned SCAFUD upgrades include rearrangement of laser head geometry, use of additional excitation lasers for simultaneous detection of more dyes, and the use of detector arrays instead of individual PMTs. Extensive software has been written for automatic analysis of SCAFUD images. The software enables background subtraction, band identification, multiple- dye signal resolution, lane finding, band sizing and allele calling. Whole genome screens are currently underway to search for loci influencing such complex diseases as diabetes, asthma, and hypertension. Seven production SCAFUDs are currently in operation. Genotyping output for the coming year is projected to be about one million total genotypes (DNA

  16. SFG characterization of a cationic ONLO dye in biological thin films

    Science.gov (United States)

    Johnson, Lewis E.; Casford, Michael T.; Elder, Delwin L.; Davies, Paul B.; Johal, Malkiat S.

    2013-10-01

    Biopolymer-based thin films, such as those composed of CTMA-DNA, can be used as a host material for NLOactive dyes for applications such as electro-optic (EO) switching and second harmonic generation. Previous work by Heckman et al. (Proc. SPIE 6401, 640108-2) has demonstrated functioning DNA-based EO modulators. Improved performance requires optimization of both the first hyperpolarizabilities (β) and degree of acentric ordering exhibited by the chromophores. The cationic dye DANPY-1 (Proc. SPIE 8464, 846409-D) has a high affinity for DNA and a substantial hyperpolarizability; however, its macroscopic ordering has not been previously characterized. We have characterized the acentric ordering of the dye using sum-frequency generation (SFG) vibrational spectroscopy in surface-immobilized DNA and on planar metal and dielectric surfaces.

  17. Absence of Mycoplasma-specific DNA sequence in brain, blood and CSF of patients with multiple sclerosis (MS): a study by PCR and real-time PCR.

    Science.gov (United States)

    Casserly, Georgina; Barry, Thomas; Tourtellotte, Wallace W; Hogan, Edward L

    2007-02-15

    Mycoplasmas are the smallest of the known self-replicating organisms. They lack cell walls and are associated with numerous diseases in humans and animals. We are exploring the possibility that infection by Mycoplasma may induce the inflammatory demyelinating disease of the central nervous system (CNS) that is MS. The presence of specific Mycoplasma species DNA was sought in brain, serum and cerebrospinal fluid (CSF) of patients diagnosed with multiple sclerosis (MS) and other neurological diseases (OND) including inflammatory disorders. The MS samples from patients with active and progressive MS, as well as in remission, a variety of other neurological disease controls, including inflammatory CNS diseases such as meningitis, cryptococcal meningitis and encephalitis and other neurological disorders such as migraine were also examined. Clinical samples were provided by the National Neurological Research Specimen Bank and the Human Brain and Spinal Fluid Resource Centre, Los Angeles. Analysis was carried out by conventional PCR using Mycoplasma-specific primers (McAuliffe et al., 2005) that target the 16S rDNA gene in Mycoplasma species. The Mycoplasma-specific primers could detect 102 Mycoplasma species. In this study, 30 samples of human brain and 57 pairs of serum and CSF and were examined. No Mycoplasma-specific nucleic acid sequence was detected, and the consistent observation of an endogenous gene, human serum albumin (HSA), as a positive control documented the adequacy of the method. Real-time PCR analysis of serum and CSF was done also targeting utilizing the Mycoplasma 16S rDNA gene, and this also demonstrated the lack of Mycoplasma in these samples. The presence of Mycoplasma at extraneural sites in MS patients is now being explored.

  18. Use of dyes in cariology.

    Science.gov (United States)

    van de Rijke, J W

    1991-04-01

    The property of dyes to enhance contrast by their colour can be used in clinical dentistry and in investigations in vitro or in vivo. They have been used for indication of affected dental tissues, improvement of diagnostic methods, enhancement of patient awareness and information about specific processes. The development of particular dye systems, aimed at clinical application, is often laborious because of toxic effects, lack of specificity, irreversible staining or difficulties with removal of the dye. Clinically used dyes are often visually observed, which means a qualitative assessment of the staining, while quantification of the staining, if performed at all, is confined mostly to laboratory experiments. In this paper the application of dyes, arranged according to their specific purpose in cariology, is discussed, and a brief historical overview is given of the development of two particular dye applications for which commercial dye systems are now available. If certain requirements are met, dyes can be of great help in detection and quantification when used with several diagnostic methods.

  19. ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly

    Directory of Open Access Journals (Sweden)

    Spang Rainer

    2009-12-01

    Full Text Available Abstract Background The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis. Results We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/. Conclusions ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.

  20. Parallel solid-phase isothermal amplification and detection of multiple DNA targets in microliter-sized wells of a digital versatile disc

    International Nuclear Information System (INIS)

    Santiago-Felipe, Sara; Tortajada-Genaro, Luis Antonio; Puchades, Rosa; Maquieira, Ángel

    2016-01-01

    An integrated method for the parallelized detection of multiple DNA target sequences is presented by using microstructures in a digital versatile disc (DVD). Samples and reagents were managed by using both the capillary and centrifugal forces induced by disc rotation. Recombinase polymerase amplification (RPA), in a bridge solid phase format, took place in separate wells, which thereby modified their optical properties. Then the DVD drive reader recorded the modifications of the transmitted laser beam. The strategy allowed tens of genetic determinations to be made simultaneously within <2 h, with small sample volumes (3 μL), low manipulation and at low cost. The method was applied to high-throughput screening of relevant safety threats (allergens, GMOs and pathogenic bacteria) in food samples. Satisfactory results were obtained in terms of sensitivity (48.7 fg of DNA) and reproducibility (below 18 %). This scheme warrants cost-effective multiplex amplification and detection and is perceived to represent a viable tool for screening of nucleic acid targets. (author)

  1. Optimization of a multi-gene HIV-1 recombinant subtype CRF02AG DNA vaccine for expression of multiple immunogenic forms

    International Nuclear Information System (INIS)

    Ellenberger, Dennis; Li Bin; Smith, James; Yi Hong; Folks, Thomas; Robinson, Harriet; Butera, Salvatore

    2004-01-01

    We developed an AIDS vaccine for Western and West-Central Africa based on a DNA plasmid vector expressing HIV-1 recombinant subtype CRF02 A G gag, pol, and env genes. To optimize the production of noninfectious HIV-like particles (VLPs) and potentially improve the effectiveness of the vaccine, we generated four potential vaccine constructs: the parental (IC2) and three modifications (IC25, IC48, and IC90) containing mutations within the HIV protease. While the parental construct IC2 expressed aggregates of Gag proteins, the IC25 construct resulted in the production of immature VLPs (the core comprises unprocessed Pr 55Gag ). The remaining two constructs (IC48 and IC90) produced mature VLPs (the core comprises processed capsid p24) in addition to immature VLPs and aggregates of Gag proteins. VLPs incorporated significant levels of mature gp120 envelope glycoprotein. Importantly, the mature VLPs were fusion competent and entered coreceptor-specific target cells. The production of multiple antigenic forms, including fusion-competent VLPs, by candidate DNA vaccine constructs may provide immunologic advantages for induction of protective cellular and humoral responses against HIV-1 proteins

  2. Multi-Locus Next-Generation Sequence Typing of DNA Extracted From Pooled Colonies Detects Multiple Unrelated Candida albicans Strains in a Significant Proportion of Patient Samples

    Directory of Open Access Journals (Sweden)

    Ningxin Zhang

    2018-06-01

    Full Text Available The yeast Candida albicans is an important opportunistic human pathogen. For C. albicans strain typing or drug susceptibility testing, a single colony recovered from a patient sample is normally used. This is insufficient when multiple strains are present at the site sampled. How often this is the case is unclear. Previous studies, confined to oral, vaginal and vulvar samples, have yielded conflicting results and have assessed too small a number of colonies per sample to reliably detect the presence of multiple strains. We developed a next-generation sequencing (NGS modification of the highly discriminatory C. albicans MLST (multilocus sequence typing method, 100+1 NGS-MLST, for detection and typing of multiple strains in clinical samples. In 100+1 NGS-MLST, DNA is extracted from a pool of colonies from a patient sample and also from one of the colonies. MLST amplicons from both DNA preparations are analyzed by high-throughput sequencing. Using base call frequencies, our bespoke DALMATIONS software determines the MLST type of the single colony. If base call frequency differences between pool and single colony indicate the presence of an additional strain, the differences are used to computationally infer the second MLST type without the need for MLST of additional individual colonies. In mixes of previously typed pairs of strains, 100+1 NGS-MLST reliably detected a second strain. Inferred MLST types of second strains were always more similar to their real MLST types than to those of any of 59 other isolates (22 of 31 inferred types were identical to the real type. Using 100+1 NGS-MLST we found that 7/60 human samples, including three superficial candidiasis samples, contained two unrelated strains. In addition, at least one sample contained two highly similar variants of the same strain. The probability of samples containing unrelated strains appears to differ considerably between body sites. Our findings indicate the need for wider surveys to

  3. Multiple effects of fluorescent light on repair of ultraviolet-induced DNA lesions in cultured goldfish cells

    International Nuclear Information System (INIS)

    Uchida, Nobuhiro; Mitani, Hiroshi; Shima, Akihiro

    1995-01-01

    It is known that fluorescent light illumination prior to UV irradiation (FL preillumination) of cultured fish cells increases photorepair (PR) ability. In the present study, it was found that FL preillumination also enhanced UV resistance of logarithmically growing cells in the dark. This enhancement of UV resistance differs from induction of PR because it was not suppressed by cyclohexamide (CH) and it occurred immediately after FL preillumination. The effects of FL preillumination on repair of UV-induced DNA lesions in the dark were examined by an endonuclease-sensitive site assay to measure the repair of cyclobutyl pyrimidine dimers, and by enzyme-linked immunosorbent assay to quantitate the repair of (6-4) photoproducts. It was found that excision repair ability for (6-4) photoproducts in the genome overall was increased by FL preillumination. Moreover, a decrease in (6-4) photoproducts by FL illumination immediately after UV irradiation of the cells was found, the decrement being enhanced by FL preillumination with or without CH. (author)

  4. Multiple effects of fluorescent light on repair of ultraviolet-induced DNA lesions in cultured goldfish cells

    Energy Technology Data Exchange (ETDEWEB)

    Uchida, Nobuhiro; Mitani, Hiroshi; Shima, Akihiro [Tokyo Univ. (Japan). Lab. of Radiation Biology

    1995-01-01

    It is known that fluorescent light illumination prior to UV irradiation (FL preillumination) of cultured fish cells increases photorepair (PR) ability. In the present study, it was found that FL preillumination also enhanced UV resistance of logarithmically growing cells in the dark. This enhancement of UV resistance differs from induction of PR because it was not suppressed by cyclohexamide (CH) and it occurred immediately after FL preillumination. The effects of FL preillumination on repair of UV-induced DNA lesions in the dark were examined by an endonuclease-sensitive site assay to measure the repair of cyclobutyl pyrimidine dimers, and by enzyme-linked immunosorbent assay to quantitate the repair of (6-4) photoproducts. It was found that excision repair ability for (6-4) photoproducts in the genome overall was increased by FL preillumination. Moreover, a decrease in (6-4) photoproducts by FL illumination immediately after UV irradiation of the cells was found, the decrement being enhanced by FL preillumination with or without CH. (author).

  5. Successful treatment of multifocal pedal infection in a feline immunodeficiency virus-positive cat with multiple Bowenoid in situ carcinomas containing papillomaviral DNA sequences

    Directory of Open Access Journals (Sweden)

    Allan E Kessell

    2017-01-01

    Full Text Available Case summary A 16-year-old, castrated male, feline immunodeficiency virus (FIV-positive, domestic shorthair cat developed multiple skin lesions. Most of these were Bowenoid carcinoma in situ and contained DNA sequences consistent with Felis catus papillomavirus type 2. Two additional lesions that developed in the skin and subcutaneous tissues between the digital and carpal pads on the left forelimb and right hindlimb were shown by cytology, histology and culture to be caused by Prototheca wickerhamii . These lesions failed to improve in response to systemic therapy treatment with itraconazole, but excision by sharp en bloc resection with follow-up oral itraconazole therapy proved curative for one lesion, although the other lesion recurred, necessitating a second surgery. Relevance and novel information This is only the second reported case of feline protothecosis from Australia and the first case that has been cultured and identified to the species level. Also of great interest was the presence of multiple papillomavirus-associated neoplastic lesions, which may have afforded a portal of entry for the algal pathogen and the cat’s positive FIV status; the latter might have impacted on both viral and algal pathogenesis by effects on immunocompetence.

  6. Successful treatment of multifocal pedal Prototheca wickerhamii infection in a feline immunodeficiency virus-positive cat with multiple Bowenoid in situ carcinomas containing papillomaviral DNA sequences

    Science.gov (United States)

    Kessell, Allan E; McNair, Derek; Munday, John S; Savory, Richard; Halliday, Catriona; Malik, Richard

    2017-01-01

    Case summary A 16-year-old, castrated male, feline immunodeficiency virus (FIV)-positive, domestic shorthair cat developed multiple skin lesions. Most of these were Bowenoid carcinoma in situ and contained DNA sequences consistent with Felis catus papillomavirus type 2. Two additional lesions that developed in the skin and subcutaneous tissues between the digital and carpal pads on the left forelimb and right hindlimb were shown by cytology, histology and culture to be caused by Prototheca wickerhamii. These lesions failed to improve in response to systemic therapy treatment with itraconazole, but excision by sharp en bloc resection with follow-up oral itraconazole therapy proved curative for one lesion, although the other lesion recurred, necessitating a second surgery. Relevance and novel information This is only the second reported case of feline protothecosis from Australia and the first case that has been cultured and identified to the species level. Also of great interest was the presence of multiple papillomavirus-associated neoplastic lesions, which may have afforded a portal of entry for the algal pathogen and the cat’s positive FIV status; the latter might have impacted on both viral and algal pathogenesis by effects on immunocompetence. PMID:28491447

  7. Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes† †Electronic supplementary information (ESI) available: Chemicals, materials and DNA sequences used in the investigation, the construction of YES, AND, OR, XOR and INH logic gates, CD and PAGE experimental results. See DOI: 10.1039/c7sc05246d

    Science.gov (United States)

    Lin, Xiaodong; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei

    2018-01-01

    The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way. PMID:29675221

  8. Tracking the direct impact of rainfall on groundwater at Mt. Fuji by multiple analyses including microbial DNA

    Science.gov (United States)

    Sugiyama, Ayumi; Masuda, Suguru; Nagaosa, Kazuyo; Tsujimura, Maki; Kato, Kenji

    2018-02-01

    the heavy rain transported archaeal particles from the geologic layer along the groundwater route. This finding was supported by changes in constituents of Archaea, dominated by Halobacteriales and Methanobacteriales, which were not seen from other observations. Those two groups of Archaea are believed to be relatively tightly embedded in the geologic layer and were extracted from the environment to the examined groundwater through enforced piston flow. Microbial DNA can thus give information about the groundwater route, which may not be shown by analysis of chemical materials dissolved in the groundwater.

  9. Multiple origins of polyploidy in the phylogeny of southern African barbs (Cyprinidae) as inferred from mtDNA markers.

    Science.gov (United States)

    Tsigenopoulos, C S; Ráb, P; Naran, D; Berrebi, P

    2002-06-01

    The cyprinid genus Barbus, with more than 800 nominal species, is an apparently polyphyletic assemblage to which a number of unrelated species, groups and/or assemblages have been assigned. It includes species that exhibit three different ploidy levels: diploid, tetraploid and hexaploid. Several lineages of the family Cyprinidae constitute a major component of the African freshwater ichthyofauna, having about 500 species, and fishes assigned to the genus 'Barbus' have the most species on the continent. We used complete sequences of the mitochondrial cytochrome b gene in order to infer phylogenetic relationships between diploid, tetraploid and hexaploid species of 'Barbus' occurring in southern Africa, the only region where representatives of all of the three ploidy levels occur. The results indicate that most of the lineages are incorrectly classified in the genus 'Barbus'. The southern African tetraploids probably originated from southern African diploids. They constitute a monophyletic group distinct from tetraploids occurring in the Euro-Mediterranean region (Barbus sensu stricto). The 'small' African diploid species seem to be paraphyletic, while the 'large' African hexaploid barbs species are of a single, recent origin and form a monophyletic group. The evidence of multiple, independent origins of polyploidy occurring in the African cyprinine cyprinids thus provides a significant contribution to the knowledge on the systematic diversity of these fishes, and warrants a thorough taxonomic reorganization of the genus.

  10. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterization of currently unrecognized taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 573 cox1 sequences from 110 currently recognized species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognized taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g., morphology, life history, ecology) are necessary before any taxonomic changes are formalized.

  11. JS-K, a GST-activated nitric oxide generator, induces DNA double-strand breaks, activates DNA damage response pathways, and induces apoptosis in vitro and in vivo in human multiple myeloma cells.

    Science.gov (United States)

    Kiziltepe, Tanyel; Hideshima, Teru; Ishitsuka, Kenji; Ocio, Enrique M; Raje, Noopur; Catley, Laurence; Li, Chun-Qi; Trudel, Laura J; Yasui, Hiroshi; Vallet, Sonia; Kutok, Jeffery L; Chauhan, Dharminder; Mitsiades, Constantine S; Saavedra, Joseph E; Wogan, Gerald N; Keefer, Larry K; Shami, Paul J; Anderson, Kenneth C

    2007-07-15

    Here we investigated the cytotoxicity of JS-K, a prodrug designed to release nitric oxide (NO(*)) following reaction with glutathione S-transferases, in multiple myeloma (MM). JS-K showed significant cytotoxicity in both conventional therapy-sensitive and -resistant MM cell lines, as well as patient-derived MM cells. JS-K induced apoptosis in MM cells, which was associated with PARP, caspase-8, and caspase-9 cleavage; increased Fas/CD95 expression; Mcl-1 cleavage; and Bcl-2 phosphorylation, as well as cytochrome c, apoptosis-inducing factor (AIF), and endonuclease G (EndoG) release. Moreover, JS-K overcame the survival advantages conferred by interleukin-6 (IL-6) and insulin-like growth factor 1 (IGF-1), or by adherence of MM cells to bone marrow stromal cells. Mechanistic studies revealed that JS-K-induced cytotoxicity was mediated via NO(*) in MM cells. Furthermore, JS-K induced DNA double-strand breaks (DSBs) and activated DNA damage responses, as evidenced by neutral comet assay, as well as H2AX, Chk2 and p53 phosphorylation. JS-K also activated c-Jun NH(2)-terminal kinase (JNK) in MM cells; conversely, inhibition of JNK markedly decreased JS-K-induced cytotoxicity. Importantly, bortezomib significantly enhanced JS-K-induced cytotoxicity. Finally, JS-K is well tolerated, inhibits tumor growth, and prolongs survival in a human MM xenograft mouse model. Taken together, these data provide the preclinical rationale for the clinical evaluation of JS-K to improve patient outcome in MM.

  12. Development of AVLIS dye laser system

    International Nuclear Information System (INIS)

    Sugiyama, Akira; Nakayama, Tsuyoshi; Kato, Masaaki; Arisawa, Takashi

    1995-01-01

    CVL pumped single mode dye laser was performed. It was found that pressure tuning has some excellent feature in comparison to mechanical tuning in dye laser frequency control. For evaluation of dye laser amplifier, two-dimensional rate equation was proposed. Calculated data by this equation agreed with experimental data in large diameter input dye laser beam condition. (author)

  13. Tracking the direct impact of rainfall on groundwater at Mt. Fuji by multiple analyses including microbial DNA

    Directory of Open Access Journals (Sweden)

    A. Sugiyama

    2018-02-01

    after the event. This suggests that strengthened piston flow caused by the heavy rain transported archaeal particles from the geologic layer along the groundwater route. This finding was supported by changes in constituents of Archaea, dominated by Halobacteriales and Methanobacteriales, which were not seen from other observations. Those two groups of Archaea are believed to be relatively tightly embedded in the geologic layer and were extracted from the environment to the examined groundwater through enforced piston flow. Microbial DNA can thus give information about the groundwater route, which may not be shown by analysis of chemical materials dissolved in the groundwater.

  14. Treatment of dye house effluents

    International Nuclear Information System (INIS)

    Waheed, S.; Ashraf, C.M.

    1999-01-01

    Environmental considerations play an increasingly important role in processing of textiles. For textile, limits on particular substances have been and are being laid down either by law or as a result of the demands of clothing manufactures. One of the most complex areas in textile processing is textile printing and dyeing. Here, virtually all dye classes are used. In some printing processes such as reactive printing, many of products used end up in the wastewater. A study of the optimisation of wastewater treatment systems and the systematic management of water and the problems of dyeing are reviewed in this article. (author)

  15. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

  16. Simultaneous detection of multiple HPV DNA via bottom-well microfluidic chip within an infra-red PCR platform.

    Science.gov (United States)

    Liu, Wenjia; Warden, Antony; Sun, Jiahui; Shen, Guangxia; Ding, Xianting

    2018-03-01

    Portable Polymerase Chain Reaction (PCR) devices combined with microfluidic chips or lateral flow stripes have shown great potential in the field of point-of-need testing (PoNT) as they only require a small volume of patient sample and are capable of presenting results in a short time. However, the detection for multiple targets in this field leaves much to be desired. Herein, we introduce a novel PCR platform by integrating a bottom-well microfluidic chip with an infra-red (IR) excited temperature control method and fluorescence co-detection of three PCR products. Microfluidic chips are utilized to partition different samples into individual bottom-wells. The oil phase in the main channel contains multi-walled carbon nanotubes which were used as a heat transfer medium that absorbs energy from the IR-light-emitting diode (LED) and transfers heat to the water phase below. Cyclical rapid heating and cooling necessary for PCR are achieved by alternative power switching of the IR-LED and Universal Serial Bus (USB) mini-fan with a pulse width modulation scheme. This design of the IR-LED PCR platform is economic, compact, and fully portable, making it a promising application in the field of PoNT. The bottom-well microfluidic chip and IR-LED PCR platform were combined to fulfill a three-stage thermal cycling PCR for 40 cycles within 90 min for Human Papilloma Virus (HPV) detection. The PCR fluorescent signal was successfully captured at the end of each cycle. The technique introduced here has broad applications in nucleic acid amplification and PoNT devices.

  17. Survery on Actual Conditions of Food Dyes

    OpenAIRE

    佐藤, ひろみ

    1981-01-01

    Many food dyes are widely used as food additives in Japan, and many investigations have been pointed the problems of safety of these food dyes used in Japanese food. There are two types of commercial food dyes, one is synthetic dyes and the other is natural dyes.Recently Japanese food is not stained so colourfully, but it is stained faintly in colour near to natural food by using of mixed synthetic dyes. On their hand, many consumers have a tendency to prefer natural food dyes because they ha...

  18. Laser desorption mass spectrometry for high-throughput DNA analysis and its applications

    Science.gov (United States)

    Chen, C. H. Winston; Golovlev, Valeri V.; Taranenko, N. I.; Allman, S. L.; Isola, Narayana R.; Potter, N. T.; Matteson, K. J.; Chang, Linus Y.

    1999-05-01

    Laser desorption mass spectrometry (LDMS) has been developed for DNA sequencing, disease diagnosis, and DNA fingerprinting for forensic applications. With LDMS, the speed of DNA analysis can be much faster than conventional gel electrophoresis. No dye or radioactive tagging to DNA segments for detection is needed. LDMS is emerging as a new alternative technology for DNA analysis.

  19. Polyethylenimine-coated Fe3O4 nanoparticles effectively quench fluorescent DNA, which can be developed as a novel platform for protein detection.

    Science.gov (United States)

    Ma, Long; Sun, Nana; Zhang, Jinyan; Tu, Chunhao; Cao, Xiuqi; Duan, Demin; Diao, Aipo; Man, Shuli

    2017-11-23

    We report a novel assembly of polyethyleneimine (PEI)-coated Fe 3 O 4 nanoparticles (NPs) with single-stranded DNA (ssDNA), and the fluorescence of the dye labeled in the DNA is remarkably quenched. In the presence of a target protein, the protein-DNA aptamer mutual interaction releases the ssDNA from this assembly and hence restores the fluorescence. This feature could be adopted to develop an aptasensor for protein detection. As a proof-of-concept, for the first time, we have used this proposed sensing strategy to detect thrombin selectively and sensitively. Furthermore, simultaneous multiple detection of thrombin and lysozyme in a complex protein mixture has been proven to be possible.

  20. Association of oxidative stress and DNA damage with grafting time in patients with multiple myeloma and lymphoma submitted to autologous hematopoietic stem cell transplantation

    Directory of Open Access Journals (Sweden)

    Thayna Nogueira dos Santos

    Full Text Available ABSTRACT The aim of the study was to investigate the association between oxidative stress and DNA damage with grafting time in patients submitted to autologous hematopoietic stem-cell transplantation (HSCT. The study included 37 patients submitted to autologous HSCT diagnosed with Multiple Myeloma (MM and lymphoma (Hodgkin’s and non-Hodgkin’s. Biomarkers of oxidative stress and DNA damage index (DI were performed at baseline (pre-CR of the disease and during the conditioning regimen (CR, one day after the HSCT, ten days after HSCT and twenty days after HSCT, as well as in the control group consisting of 30 healthy individuals. The outcomes showed that both groups of patients had an hyperoxidative state with high DI when compared to baseline and to the control group and that the CR exacerbated this condition. However, after the follow-up period of the study, this picture was re-established to the baseline levels of each pathology. The study patients with MM showed a mean grafting time of 10.75 days (8 to 13 days, with 10.15 days (8 to 15 days for the lymphoma patients. In patients with MM, there was a negative correlation between the grafting time and the basal levels of GPx (r = -0.54; p = 0.034, indicating that lower levels of this important enzyme are associated with a longer grafting time. For the DI, the correlation was a positive one (r = 0.529; p = 0.030. In the group with lymphoma, it was observed that the basal levels of NOx were positively correlated with grafting time (r = 0.4664, p = 0.032. The data indicate the potential of these biomarkers as predictors of toxicity and grafting time in patients with MM and Lymphomas submitted to autologous HSCT.

  1. An efficient and reproducible method for in vitro clonal multiplication of Rauvolfia tetraphylla L. and evaluation of genetic stability using DNA-based markers.

    Science.gov (United States)

    Faisal, Mohammad; Alatar, Abdulrahman A; Ahmad, Naseem; Anis, Mohammad; Hegazy, Ahmad K

    2012-12-01

    An efficient protocol is described for the rapid in vitro clonal propagation of an endangered medicinal plant, Rauvolfia tetraphylla L., through high frequency shoot induction from nodal explants collected from young shoots of a field grown plant. Effects of growth regulators [6-benzyladenine (BA), kinetin (Kin) 2iP, or α-naphthalene acetic acid (NAA)], carbohydrates, different medium [Murashige and Skoog (MS), Woody Plant Medium (WPM), Gamborg medium (B5), Linsmier and Skoog medium (LS)], and various pH levels on in vitro morphogenesis were investigated. The highest frequency of shoot regeneration (90 %) and maximum number of shoot (35.4 ± 2.3) per explant were observed on WPM medium supplemented with 7.5 μM BA, 2.5 μM NAA, and 30 g/l sucrose at pH 5.8. Well-developed shoots, 4-5 cm in length, were successfully rooted ex vitro at 90 % by a 30-min pulse treatment with 150 μM IBA prior to their transfer in planting substrates. The survival rate of transplantation reached 90 % when transferred to field condition. Genetic stability of micropropagated plantlets was assessed and compared with mother plant using Random Amplified Polymorphic DNA and Inter Simple Sequence Repeats markers. No variation was observed in DNA fingerprinting patterns among the micropropagated plants, which were similar to that of the donor plant illustrating their genetic uniformity and clonal fidelity. This confirms that clonal propagation of this plant using axillary shoot buds can be used for commercial exploitation of the selected genotype where a high degree of fidelity is an essential prerequisite. The work contributed to a better in vitro regeneration and clonal mass multiplication of R. tetraphylla and to develop a strategy for the germplasm conservation of this endangered medicinal plant.

  2. Hair Dyes and Cancer Risk

    Science.gov (United States)

    ... http://www.fda.gov/aboutfda/centersoffices/officeoffoods/cfsan/default.htm . Selected References Huncharek M, Kupelnick B. Personal use of hair dyes and the risk of bladder cancer: results of a meta-analysis. ...

  3. Dimeric fluorescent energy transfer dyes comprising asymmetric cyanine azole-indolenine chromophores

    Science.gov (United States)

    Glazer, Alexander N.; Benson, Scott C.

    1998-01-01

    Novel fluorescent heterodimeric DNA-staining energy transfer dyes are provided combining asymmetric cyanine azole-indolenine dyes, which provide for strong DNA affinity, large Stokes shifts and emission in the red region of the spectrum. The dyes find particular application in gel electrophoresis and for labels which may be bound to a variety of compositions in a variety of contexts. Kits and individual compounds are provided, where the kits find use for simultaneous detection of a variety of moieties, particularly using a single narrow wavelength irradiation source. The individual compounds are characterized by high donor quenching and high affinity to dsDNA as a result of optimizing the length of the linking group separating the two chromophores.

  4. Ultrasound for low temperature dyeing of wool with acid dye.

    Science.gov (United States)

    Ferrero, F; Periolatto, M

    2012-05-01

    The possibility of reducing the temperature of conventional wool dyeing with an acid levelling dye using ultrasound was studied in order to reach exhaustion values comparable to those obtained with the standard procedure at 98 °C, obtaining dyed samples of good quality. The aim was to develop a laboratory method that could be transferred at industrial level, reducing both the energy consumption and fiber damage caused by the prolonged exposure to high temperature without the use of polluting auxiliary agents. Dyeings of wool fabrics were carried out in the temperature range between 60 °C and 80 °C using either mechanical or ultrasound agitation of the bath and coupling the two methods to compare the results. For each dyeing, the exhaustion curves of the dye bath were determined and the better results of dyeing kinetics were obtained with ultrasound coupled with mechanical stirring. Hence the corresponding half dyeing times, absorption rate constants according to Cegarra-Puente modified equation and ultrasonic efficiency were calculated in comparison with mechanical stirring alone. In the presence of ultrasound the absorption rate constants increased by at least 50%, at each temperature, confirming the synergic effect of sonication on the dyeing kinetics. Moreover the apparent activation energies were also evaluated and the positive effect of ultrasound was ascribed to the pre-exponential factor of the Arrhenius equation. It was also shown that the effect of ultrasound at 60 °C was just on the dye bath, practically unaffecting the wool fiber surface, as confirmed by the results of SEM analysis. Finally, fastness tests to rubbing and domestic laundering yielded good values for samples dyed in ultrasound assisted process even at the lower temperature. These results suggest the possibility, thanks to the use of ultrasound, to obtain a well equalized dyeing on wool working yet at 60°C, a temperature process strongly lower than 98°C, currently used in industry

  5. Comparison of five DNA quantification methods

    DEFF Research Database (Denmark)

    Nielsen, Karsten; Mogensen, Helle Smidt; Hedman, Johannes

    2008-01-01

    Six commercial preparations of human genomic DNA were quantified using five quantification methods: UV spectrometry, SYBR-Green dye staining, slot blot hybridization with the probe D17Z1, Quantifiler Human DNA Quantification kit and RB1 rt-PCR. All methods measured higher DNA concentrations than...... Quantification kit in two experiments. The measured DNA concentrations with Quantifiler were 125 and 160% higher than expected based on the manufacturers' information. When the Quantifiler human DNA standard (Raji cell line) was replaced by the commercial human DNA preparation G147A (Promega) to generate the DNA...... standard curve in the Quantifiler Human DNA Quantification kit, the DNA quantification results of the human DNA preparations were 31% higher than expected based on the manufacturers' information. The results indicate a calibration problem with the Quantifiler human DNA standard for its use...

  6. Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

    Institute of Scientific and Technical Information of China (English)

    Xiao-Rong Wu; Chen-Wei Wu; Fei Ding; Cheng Tian; Wen Jiang; Cheng-De Mao; Chuan Zhang

    2017-01-01

    Discrete and symmetric three-dimensional (3D) DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization (e.g.dye molecules,proteins,inorganic nanoparticles,etc.) to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA pointstar motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron (E-TET),rhombic dodecahedron (R-DOD),and rhombic triacontahedron (R-TRI) are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis (PAGE),atomic force microscope (AFM) imaging,and cryogenic transmission electron microscope imaging (cryo-TEM) associated with single particle reconstruction.

  7. A DNA vaccine encoding multiple HIV CD4 epitopes elicits vigorous polyfunctional, long-lived CD4+ and CD8+ T cell responses.

    Directory of Open Access Journals (Sweden)

    Daniela Santoro Rosa

    Full Text Available T-cell based vaccines against HIV have the goal of limiting both transmission and disease progression by inducing broad and functionally relevant T cell responses. Moreover, polyfunctional and long-lived specific memory T cells have been associated to vaccine-induced protection. CD4(+ T cells are important for the generation and maintenance of functional CD8(+ cytotoxic T cells. We have recently developed a DNA vaccine encoding 18 conserved multiple HLA-DR-binding HIV-1 CD4 epitopes (HIVBr18, capable of eliciting broad CD4(+ T cell responses in multiple HLA class II transgenic mice. Here, we evaluated the breadth and functional profile of HIVBr18-induced immune responses in BALB/c mice. Immunized mice displayed high-magnitude, broad CD4(+/CD8(+ T cell responses, and 8/18 vaccine-encoded peptides were recognized. In addition, HIVBr18 immunization was able to induce polyfunctional CD4(+ and CD8(+ T cells that proliferate and produce any two cytokines (IFNγ/TNFα, IFNγ/IL-2 or TNFα/IL-2 simultaneously in response to HIV-1 peptides. For CD4(+ T cells exclusively, we also detected cells that proliferate and produce all three tested cytokines simultaneously (IFNγ/TNFα/IL-2. The vaccine also generated long-lived central and effector memory CD4(+ T cells, a desirable feature for T-cell based vaccines. By virtue of inducing broad, polyfunctional and long-lived T cell responses against conserved CD4(+ T cell epitopes, combined administration of this vaccine concept may provide sustained help for CD8(+ T cells and antibody responses- elicited by other HIV immunogens.

  8. Natural dyes as photosensitizers for dye-sensitized solar cell

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Sancun; Wu, Jihuai; Huang, Yunfang; Lin, Jianming [Institute of Materials Physical Chemistry, Huaqiao University, Quanzhou, Fujian 362021 (China)

    2006-02-15

    The dye-sensitized solar cells (DSC) were assembled by using natural dyes extracted from black rice, capsicum, erythrina variegata flower, rosa xanthina, and kelp as sensitizers. The I{sub SC} from 1.142mA to 0.225mA, the V{sub OC} from 0.551V to 0.412V, the fill factor from 0.52 to 0.63, and P{sub max} from 58{mu}W to 327{mu}W were obtained from the DSC sensitized with natural dye extracts. In the extracts of natural fruit, leaves and flower chosen, the black rice extract performed the best photosensitized effect, which was due to the better interaction between the carbonyl and hydroxyl groups of anthocyanin molecule on black rice extract and the surface of TiO{sub 2} porous film. The blue-shift of absorption wavelength of the black rice extract in ethanol solution on TiO{sub 2} film and the blue-shift phenomenon from absorption spectrum to photoaction spectrum of DSC sensitized with black rice extract are discussed in the paper. Because of the simple preparation technique, widely available and low cheap cost natural dye as an alternative sensitizer for dye-sensitized solar cell is promising. (author)

  9. Unraveling the Rat Intestine, Spleen and Liver Genome-Wide Transcriptome after the Oral Administration of Lavender Oil by a Two-Color Dye-Swap DNA Microarray Approach.

    Science.gov (United States)

    Kubo, Hiroko; Shibato, Junko; Saito, Tomomi; Ogawa, Tetsuo; Rakwal, Randeep; Shioda, Seiji

    2015-01-01

    The use of lavender oil (LO)--a commonly, used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate--in non-traditional medicine is increasing globally. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model in this current study, investigating the orally administered LO effects genome wide in the rat small intestine, spleen, and liver. The rats were administered LO at 5 mg/kg (usual therapeutic dose in humans) followed by the screening of differentially expressed genes in the tissues, using a 4×44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA) in conjunction with a dye-swap approach, a novelty of this study. Fourteen days after LO treatment and compared with a control group (sham), a total of 156 and 154 up (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, 174 and 66 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, and 222 and 322 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively. The reverse transcription-polymerase chain reaction (RT-PCR) validation of highly up- and down-regulated genes confirmed the regulation of the Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes by LO as examples in these tissues. Using bioinformatics, including Ingenuity Pathway Analysis (IPA), differentially expressed genes were functionally categorized by their Gene Ontology (GO) and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat. Further IPA analysis in particular unraveled the presence of novel genes, such as Papd4, Or8k5, Gprc5b, Taar5, Trpc6, Pld2 and Onecut3 (up-regulated top molecules) and Tnf, Slc45a4, Slc25a23 and Samt4 (down-regulated top molecules), to be influenced by LO treatment in the small intestine, spleen and liver

  10. Unraveling the Rat Intestine, Spleen and Liver Genome-Wide Transcriptome after the Oral Administration of Lavender Oil by a Two-Color Dye-Swap DNA Microarray Approach.

    Directory of Open Access Journals (Sweden)

    Hiroko Kubo

    Full Text Available The use of lavender oil (LO--a commonly, used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate--in non-traditional medicine is increasing globally. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model in this current study, investigating the orally administered LO effects genome wide in the rat small intestine, spleen, and liver. The rats were administered LO at 5 mg/kg (usual therapeutic dose in humans followed by the screening of differentially expressed genes in the tissues, using a 4×44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA in conjunction with a dye-swap approach, a novelty of this study. Fourteen days after LO treatment and compared with a control group (sham, a total of 156 and 154 up (≧ 1.5-fold- and down (≦ 0.75-fold-regulated genes, 174 and 66 up- (≧ 1.5-fold- and down (≦ 0.75-fold-regulated genes, and 222 and 322 up- (≧ 1.5-fold- and down (≦ 0.75-fold-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively. The reverse transcription-polymerase chain reaction (RT-PCR validation of highly up- and down-regulated genes confirmed the regulation of the Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes by LO as examples in these tissues. Using bioinformatics, including Ingenuity Pathway Analysis (IPA, differentially expressed genes were functionally categorized by their Gene Ontology (GO and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat. Further IPA analysis in particular unraveled the presence of novel genes, such as Papd4, Or8k5, Gprc5b, Taar5, Trpc6, Pld2 and Onecut3 (up-regulated top molecules and Tnf, Slc45a4, Slc25a23 and Samt4 (down-regulated top molecules, to be influenced by LO treatment in the small intestine, spleen and

  11. Van Gieson's picrofuchsin. The staining mechanisms for collagen and cytoplasm, and an examination of the dye diffusion rate model of differential staining

    DEFF Research Database (Denmark)

    Prentø, P

    1993-01-01

    this and experiments with additives (sodium dodecylsulphate, urea etc.) and organic solvents, it is proposed that coagulant interchain cross-linking at the high protein concentration of the cytoplasm masks potential dye-binding sites. This affects high affinity dyes with multiple binding sites more than small dyes......, and so puts AcF at a disadvantage compared to PA. Staining of non-collagen proteins is mainly by hydrophobic bonding, involving ionic attractions, apolar bonds, and release of water. This mode of binding is relatively strong, decreases swelling and leads to slow dye exchange. Dye binding to collagen...

  12. OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

    Directory of Open Access Journals (Sweden)

    Kevin M. Bradley

    2014-08-01

    Full Text Available Synthetic biologists wishing to self-assemble large DNA (L-DNA constructs from small DNA fragments made by automated synthesis need fragments that hybridize predictably. Such predictability is difficult to obtain with nucleotides built from just the four standard nucleotides. Natural DNA's peculiar combination of strong and weak G:C and A:T pairs, the context-dependence of the strengths of those pairs, unimolecular strand folding that competes with desired interstrand hybridization, and non-Watson–Crick interactions available to standard DNA, all contribute to this unpredictability. In principle, adding extra nucleotides to the genetic alphabet can improve the predictability and reliability of autonomous DNA self-assembly, simply by increasing the information density of oligonucleotide sequences. These extra nucleotides are now available as parts of artificially expanded genetic information systems (AEGIS, and tools are now available to generate entirely standard DNA from AEGIS DNA during PCR amplification. Here, we describe the OligArch (for "oligonucleotide architecting" software, an application that permits synthetic biologists to engineer optimally self-assembling DNA constructs from both six- and eight-letter AEGIS alphabets. This software has been used to design oligonucleotides that self-assemble to form complete genes from 20 or more single-stranded synthetic oligonucleotides. OligArch is therefore a key element of a scalable and integrated infrastructure for the rapid and designed engineering of biology.

  13. The DNA relaxation activity and covalent complex accumulation of Mycobacterium tuberculosis topoisomerase I can be assayed in Escherichia coli: application for identification of potential FRET-dye labeling sites

    Directory of Open Access Journals (Sweden)

    Abrenica Maria V

    2010-09-01

    Full Text Available Abstract Background Mycobacterium tuberculosis topoisomerase I (MtTOP1 and Escherichia coli topoisomerase I have highly homologous transesterification domains, but the two enzymes have distinctly different C-terminal domains. To investigate the structure-function of MtTOP1 and to target its activity for development of new TB therapy, it is desirable to have a rapid genetic assay for its catalytic activity, and potential bactericidal consequence from accumulation of its covalent complex. Results We show that plasmid-encoded recombinant MtTOP1 can complement the temperature sensitive topA function of E. coli strain AS17. Moreover, expression of MtTOP1-G116 S enzyme with the TOPRIM mutation that inhibits DNA religation results in SOS induction and loss of viability in E. coli. The absence of cysteine residues in the MtTOP1 enzyme makes it an attractive system for introduction of potentially informative chemical or spectroscopic probes at specific positions via cysteine mutagenesis. Such probes could be useful for development of high throughput screening (HTS assays. We employed the AS17 complementation system to screen for sites in MtTOP1 that can tolerate cysteine substitution without loss of complementation function. These cysteine substitution mutants were confirmed to have retained the relaxation activity. One such mutant of MtTOP1 was utilized for fluorescence probe incorporation and fluorescence resonance energy transfer measurement with fluorophore-labeled oligonucleotide substrate. Conclusions The DNA relaxation and cleavage complex accumulation of M. tuberculosis topoisomerase I can be measured with genetic assays in E. coli, facilitating rapid analysis of its activities, and discovery of new TB therapy targeting this essential enzyme.

  14. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  15. Bacterial reduction in genotoxicity of Direct Red 28 dye.

    Science.gov (United States)

    Bafana, Amit; Jain, Minakshi; Agrawal, Gaurav; Chakrabarti, Tapan

    2009-03-01

    Direct Red 28 (DR28) is a benzidine-based azo dye widely used in several countries. It has also been a subject of intense research for its anti-prion activity. Like other benzidine-based azo dyes, it is also carcinogenic and toxic. However, there are very few studies addressing its detoxification. In the present study, a Bacillus velezensis strain was used for detoxification of DR28. Toxicity was checked by a battery of highly sensitive genotoxicity assays like comet assay, DNA ladder formation, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay and flow cytometric Annexin V binding assay. HL-60 cell line was used as the test system. All the assays showed an initial increase in toxicity upon biodegradation due to release of mutagenic products, like benzidine and 4-aminobiphenyl, from the dye. These intermediates caused significant DNA damage and induced apoptosis in HL-60 cells. Then the culture degraded these mutagenic intermediates, due to which the toxicity was reduced gradually, finally resulting in nearly complete detoxification.

  16. Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

    Science.gov (United States)

    Kang, Hongzhang; Sun, Xiao; Yin, Shan; Du, Hongmei; Yamanaka, Norikazu; Gapare, Washington; Wu, Harry X.; Liu, Chunjiang

    2012-01-01

    The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N ST = 0.751> G ST = 0.690, Ptree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia. PMID:23115642

  17. Phylogeography of Quercus variabilis based on chloroplast DNA sequence in East Asia: multiple glacial refugia and Mainland-migrated island populations.

    Directory of Open Access Journals (Sweden)

    Dongmei Chen

    Full Text Available The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N(ST= 0.751> G(ST= 0.690, P<0.05. Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu's F(S indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s, a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.

  18. Dye-sensitized solar cells: Atomic scale investigation of interface structure and dynamics

    International Nuclear Information System (INIS)

    Ma Wei; Zhang Fan; Meng Sheng

    2014-01-01

    Recent progress in dye-sensitized solar cells (DSC) research is reviewed, focusing on atomic-scale investigations of the interface electronic structures and dynamical processes, including the structure of dye adsorption onto TiO 2 , ultrafast electron injection, hot-electron injection, multiple-exciton generation, and electron—hole recombination. Advanced experimental techniques and theoretical approaches are briefly summarized, and then progressive achievements in photovoltaic device optimization based on insights from atomic scale investigations are introduced. Finally, some challenges and opportunities for further improvement of dye solar cells are presented. (invited review — international conference on nanoscience and technology, china 2013)

  19. Feasibility of solar-pumped dye lasers

    Science.gov (United States)

    Lee, Ja H.; Kim, Kyung C.; Kim, Kyong H.

    1987-01-01

    Dye laser gains were measured at various pump-beam irradiances on a dye cell in order to evaluate the feasibility of solar pumping. Rhodamine 6G dye was considered as a candidate for the solar-pumped laser because of its high utilization of the solar spectrum and high quantum efficiency. Measurements show that a solar concentration of 20,000 is required to reach the threshold of the dye.

  20. Natural dyes versus lysochrome dyes in cheiloscopy: A comparative evaluation.

    Science.gov (United States)

    Singh, Narendra Nath; Brave, V R; Khanna, Shally

    2010-01-01

    Cheiloscopy is the study of lip prints. Lip prints are genotypically determined and are unique, and stable. At the site of crime, lip prints can be either visible or latent. To develop lip prints for study purpose various chemicals such as lysochrome dyes, fluorescent dyes, etc. are available which are very expensive. Vermilion (Sindoor used by married Indian women) and indigo dye (fabric whitener) are readily available, naturally derived, and cost-effective reagents available in India. To compare the efficacy of sudan black, vermilion, and indigo in developing visible and latent lip prints made on bone china cup, satin fabric, and cotton fabric. Out of 45 Volunteers 15 lip prints were made on bone China cup 15 lip prints on Satin fabric and 15 on Cotton fabric. Sudan black, vermilion and indigo were applied on visible and latent lip prints and graded as good (+,+), fair (+), and poor (-) and statistically evaluated. The vermilion and indigo dye gives comparable results to that of sudan black for developing visible and latent lip prints.

  1. Effect of dye structure and redox mediators on anaerobic azo and anthraquinone dye reduction

    Directory of Open Access Journals (Sweden)

    Mayara Carantino Costa

    2012-01-01

    Full Text Available We investigated the biological decolourisation of dyes with different molecular structures. The kinetic constant values (k1 achieved with azo dye Reactive Red 120 were 7.6 and 10.1 times higher in the presence of RM (redox mediators AQDS and riboflavin, respectively, than the assays lacking RM. The kinetic constant achieved with the azo dye Congo Red was 42 times higher than that obtained with the anthraquinone dye Reactive Blue 4. The effect of RM on dye reduction was more evident for azo dyes resistant to reductive processes, and ineffective for anthraquinone dyes because of the structural stability of the latter.

  2. Characterising the potential of sheep wool for ancient DNA analyses

    DEFF Research Database (Denmark)

    Brandt, Luise Ørsted; Tranekjer, Lena D.; Mannering, Ulla

    2011-01-01

    can be PCR-amplified from wool derived from a variety of breeds, regardless of the body location or natural pigmentation. Furthermore, although DNA can be PCR-amplified from wool dyed with one of four common plant dyes (tansy, woad, madder, weld), the use of mordants such as alum or iron leads...... and content of DNA in hair shafts are known to vary, and it is possible that common treatments of wool such as dyeing may negatively impact the DNA. Using quantitative real-time polymerase chain reaction (PCR), we demonstrate that in general, short fragments of both mitochondrial and single-copy nuclear DNA...

  3. Quirks of dye nomenclature. 1. Evans blue.

    Science.gov (United States)

    Cooksey, C J

    2014-02-01

    The history, origin, identity, chemistry and use of Evans blue dye are described along with the first application to staining by Herbert McLean Evans in 1914. In the 1930s, the dye was marketed under the name, Evans blue dye, which was profoundly more acceptable than the ponderous chemical name.

  4. Dye-sensitized solar cell with natural gel polymer electrolytes and f-MWCNT as counter-electrode

    Science.gov (United States)

    Nwanya, A. C.; Amaechi, C. I.; Ekwealor, A. B. C.; Osuji, R. U.; Maaza, M.; Ezema, F. I.

    2015-05-01

    Samples of DSSCs were made with gel polymer electrolytes using agar, gelatin and DNA as the polymer hosts. Anthocyanine dye from Hildegardia barteri flower is used to sensitize the TiO2 electrode, and the spectrum of the dye indicates strong absorptions in the blue region of the solar spectrum. The XRD pattern of the TiO2 shows that the adsorption of the dye did not affect the crystallinity of the electrode. The f-MWCNT indicates graphite structure of the MWCNTs were acid oxidized without significant damage. Efficiencies of 3.38 and 0.1% were obtained using gelatin and DNA gel polymer electrolytes, respectively, for the fabricated dye-sensitized solar cells.

  5. Ethnobotany of dye plants in Dong communities of China.

    Science.gov (United States)

    Liu, Yujing; Ahmed, Selena; Liu, Bo; Guo, Zhiyong; Huang, Weijuan; Wu, Xianjin; Li, Shenghua; Zhou, Jiangju; Lei, Qiyi; Long, Chunlin

    2014-02-19

    Dyes derived from plants have an extensive history of use for coloring food and clothing in Dong communities and other indigenous areas in the uplands of China. In addition to use as coloring agents, Dong communities have historically utilized dye plants for their value for enhancing the nutritive, medicinal and preservative properties of foods. However, the persistence of plant-derived dyes and associated cultural practices and traditional knowledge is threatened with rapid socio-economic change in China. Research is needed to document the ethnobotany of dye plants in indigenous communities towards their conservation and potential commercialization as a sustainable means of supporting local development initiatives. Semi-structured surveys on plants used for coloring agents and associated traditional knowledge were conducted in fifteen Dong villages of Tongdao County in Hunan Province of South Central China during 2011-2012. Transect walks were carried out with key informants identified from semi-structured surveys to collect samples and voucher specimens for each documented plant species for taxonomic identification. Dong households at the study sites utilize the flowers, bark, stems, tubers and roots of 13 plant species from 9 families as dyes to color their customary clothing and food. Out of the documented plants, a total of 7 are used for coloring food, 3 for coloring clothing and 3 for both food and clothing. Documented plants consist of 3 species that yield black pigments, 3 for brownish red/russet pigments, 3 for red pigments, 2 for dark blue pigments and 2 for yellow pigments. In addition to dyes, the plants have multiple uses including medicinal, ornamental, sacrificial, edible, and for timber. The use of dyes derived from plants persists at the study sites for their important role in expressing Dong cultural identity through customary clothing and food. Further research is needed to evaluate the safety of dye plants, their efficacy in enhancing food

  6. Cosensitization process effect of D-A-π-A featured dyes on photovoltaic performances

    Directory of Open Access Journals (Sweden)

    Bo Liu

    2016-04-01

    Full Text Available Cosensitization based on two or multiple dyes as “dye cocktails” can hit the target on compensating and broadening light-harvesting region. Two indoline D-A-π-A motif sensitizers (WS-2 and WS-39 that possess similar light response area but distinctly reversed feature in photovoltaic performance are selected as the specific cosensitization couple. That is, WS-2 shows quite high photocurrent but low photovoltage, and WS-39 gives relatively low photocurrent but quite high photovoltage. Due to the obvious “barrel effect”, both dyes show medium PCE around 8.50%. In contrast with the previous cosensitization strategy mostly focused on the compensation of light response region, herein we perform different cosensitization sequence, for taking insight into the balance of photocurrent and photovoltage, and achieving the synergistic improvement in power conversion efficiency (PCE. Electronic impedance spectra (EIS indicate that exploiting dye WS-39 with high VOC value as the primary sensitizer can repress the charge recombination more effectively, resulting in superior VOC rather than using dye WS-2 with high JSC as the primary sensitizer. As a consequence, a high PCE value of 9.48% is obtained with the delicate cosensitization using WS-39 as primary dye and WS-2 as accessory dye, which is higher than the corresponding devices sensitized by each individual dye (around 8.48–8.67%. It provides an effective optimizing strategy of cosensitization how to combine the individual dye advantages for developing highly efficient solar cells. Keywords: Indoline dye, Cosensitization, Adsorption sequence, Charge recombination, Photovoltaic performances

  7. Studies on Dyeing Performance of Novel Acid Azo Dyes and Mordent Acid Azo Dyes Based on 2,4-Dihydroxybenzophenone

    Directory of Open Access Journals (Sweden)

    Bharat C. Dixit

    2009-01-01

    Full Text Available Novel acid azo and mordent acid azo dyes have been prepared by the coupling of diazo solution of different aminonaphthol sulphonic acids and aromatic amino acids with 2,4-dihydroxybenzophenone. The resultant dyes were characterized by elemental analysis as well as IR and 1H NMR spectral studies. The UV-visible spectral data have also been discussed in terms of structure property relationship. The dyeing assessments of all the dyes were evaluated on wool and silk textile fibers. The dyeing of chrome pretreated wool and silk have also been monitored. The result shows that better hue was obtained on mordented fiber. Results of bactericidal studies of chrome pretreated fibers revealed that the toxicity of mordented dyes against bacteria is fairly good. Dyeing on wool and silk fibers resulted in yellowish pink to reddish brown colourations having excellent light fastness and washing fastness.

  8. Induction of a M/sub r/ 21,000 polypeptide in an Arthrobacter Sp. by dye-sensitized photooxidation

    International Nuclear Information System (INIS)

    Franzi, J.J.

    1985-01-01

    Irradiation of aerobic cultures of an Arthrobacter species with near-UV light and oxygen induced synthesis of a cell surface protein, M/sub r/ 21,000 polypeptide. Visible light, oxygen and a sensitizing dye were also effective in induction. Far-UV light, bleomycin and nalidixic acid, all inducers of the recA protein in Escherichia coli, were ineffective inducers of this protein. Furthermore, X-irradiation and radical-generating oxidants failed to induce synthesis of the M/sub r/ 21,000 polypeptide. DNA binding dyes proved to be capable of inducing synthesis of this protein or inhibiting dye-mediated stimulation of synthesis of this protein. For example, dGdC-specific dyes (e.g. methylene blue, neutral red, acridine orange or ethidium bromide) were efficient inducers of the M/sub r/ 21,000 polypeptide. Also methylene blue and neutral red were more efficient inducers than were acridine orange or ethidium bromide, which could be explained by the greater dGdC specificity and, possibly by the greater photoreactivity of methylene blue and neutral red. dAdT-specific dyes such as methyl green or daunomycin effectively inhibited dye-mediated induction. Rose bengal is an anionic dye which does not bind to DNA but does mediate the photooxidation of deoxyguanosine residues in DNA. It is an efficient inducer of the M/sub r/ 21,000 polypeptide. Induction with this dye is nearly eliminated when novobiocin, an inhibitor of DNA gyrase (topoisomerase II) which mediates relaxation, is added in conjunction with rose bengal

  9. Induction of a M/sub r/ 21,000 polypeptide in an Arthrobacter Sp. by dye-sensitized photooxidation

    Energy Technology Data Exchange (ETDEWEB)

    Franzi, J.J.

    1985-01-01

    Irradiation of aerobic cultures of an Arthrobacter species with near-UV light and oxygen induced synthesis of a cell surface protein, M/sub r/ 21,000 polypeptide. Visible light, oxygen and a sensitizing dye were also effective in induction. Far-UV light, bleomycin and nalidixic acid, all inducers of the recA protein in Escherichia coli, were ineffective inducers of this protein. Furthermore, X-irradiation and radical-generating oxidants failed to induce synthesis of the M/sub r/ 21,000 polypeptide. DNA binding dyes proved to be capable of inducing synthesis of this protein or inhibiting dye-mediated stimulation of synthesis of this protein. For example, dGdC-specific dyes (e.g. methylene blue, neutral red, acridine orange or ethidium bromide) were efficient inducers of the M/sub r/ 21,000 polypeptide. Also methylene blue and neutral red were more efficient inducers than were acridine orange or ethidium bromide, which could be explained by the greater dGdC specificity and, possibly by the greater photoreactivity of methylene blue and neutral red. dAdT-specific dyes such as methyl green or daunomycin effectively inhibited dye-mediated induction. Rose bengal is an anionic dye which does not bind to DNA but does mediate the photooxidation of deoxyguanosine residues in DNA. It is an efficient inducer of the M/sub r/ 21,000 polypeptide. Induction with this dye is nearly eliminated when novobiocin, an inhibitor of DNA gyrase (topoisomerase II) which mediates relaxation, is added in conjunction with rose bengal.

  10. Photoelectrochemical studies of dye-sensitized solar cells using organic dyes

    Energy Technology Data Exchange (ETDEWEB)

    Marinado, Tannia

    2009-10-15

    The dye-sensitized solar cell (DSC) is a promising efficient low-cost molecular photovoltaic device. One of the key components in DSCs is the dye, as it is responsible for the capture of sunlight. State-of-the-art DSC devices, based on ruthenium dyes, show record efficiencies of 10-12 %. During the last decade, metal-free organic dyes have been extensively explored as sensitizers for DSC application. The use of organic dyes is particularly attractive as it enables easy structural modifications, due to fairly short synthetic routes and reduced material cost. Novel dye should in addition to the light-harvesting properties also be compatible with the DSC components. In this thesis, a series of new organic dyes are investigated, both when integrated in the DSC device and as individual components. The evaluation methods consisted of different electrochemical and photoelectrochemical techniques. Whereas the light-harvesting properties of the dyes were fairly easily improved, the behavior of the dye integrated in the DSC showed less predictable photovoltaic results. The dye series studied in Papers II and IV revealed that their dye energetics limited vital electron-transfer processes, the dye regeneration (Paper II) and injection quantum yield (Paper IV). Further, in Papers III-VI, it was observed that different dye structures seemed to alter the interfacial electron recombination with the electrolyte. In addition to the dye structure sterics, some organic dyes appear to enhance the interfacial recombination, possibly due to specific dye-redox acceptor interaction (Paper V). The impact of dye sterical modifications versus the use of coadsorbent was explored in Paper VI. The dye layer properties in the presence and absence of various coadsorbents were further investigated in Paper VII. The core of this thesis is the identification of the processes and properties limiting the performance of the DSC device, aiming at an overall understanding of the compatibility between the

  11. Radiative characteristics of CVL pumped dye laser

    Energy Technology Data Exchange (ETDEWEB)

    Kubo, Uichi; Ishiguro, Takahide

    1987-09-01

    This paper describes the radiative characteristics of CVL pumped dye laser. It is compared YAG-SH (530 nm) with CVL (511, 578 nm) and CVL (511 nm) for pumping source. Influence of solvent in dye laser power was examined. The present experimental results show that efficiency of CVL (511 nm) pumped dye laser was most high. When the dye solution is at a standstill, the efficiency of dye laser with water and Sodium Lauryl Sulfate (S.L.S., 2 %wt.) was most high among the four kinds of solvent. In the condition of dye solution flow, the water and S.L.S. or ethylene glycol was useful solvent for dye laser.

  12. Radiative characteristics of CVL pumped dye laser

    International Nuclear Information System (INIS)

    Kubo, Uichi; Ishiguro, Takahide.

    1987-01-01

    This paper describes the radiative characteristics of CVL pumped dye laser. It is compared YAG-SH (530 nm) with CVL (511, 578 nm) and CVL (511 nm) for pumping source. Influence of solvent in dye laser power was examined. The present experimental results show that efficiency of CVL (511 nm) pumped dye laser was most high. When the dye solution is at a standstill, the efficiency of dye laser with water and Sodium Lauryl Sulfate (S.L.S., 2 %wt.) was most high among the four kinds of solvent. In the condition of dye solution flow, the water and S.L.S. or Ethylene Glycol was useful solvent for dye laser. (author)

  13. BODIPYs for Dye-Sensitized Solar Cells.

    Science.gov (United States)

    Klfout, Hafsah; Stewart, Adam; Elkhalifa, Mahmoud; He, Hongshan

    2017-11-22

    BODIPY, abbreviation of boron-dipyrromethene, is one class of robust organic molecules that has been used widely in bioimaging, sensing, and logic gate design. Recently, BODIPY dyes have been explored for dye-sensitized solar cells (DSCs). Studies demonstrate their potential as light absorbers for the conversion of solar energy to electricity. However, their photovoltaic performance is inferior to many other dyes, including porphyrin dyes. In this review, several synthetic strategies of BODIPY dyes for DSCs and their further functionalization are described. The photophysical properties of dye molecules and their photovoltaic performances in DSCs are summarized. We aim to provide readers a clear picture of the field and expect to shed light on the next generation of BODIPY dyes for their applications in solar energy conversion.

  14. Influence of styryl dyes on blood erythrocytes

    Science.gov (United States)

    Nizomov, Negmat; Barakaeva, Mubaro; Kurtaliev, Eldar N.; Rahimov, Sherzod I.; Khakimova, Dilorom P.; Khodjayev, Gayrat; Yashchuk, Valeriy N.

    2008-08-01

    It was studied the influence of F, Sbt, Sil, Sbo monomer and homodimer Dst-5, Dst-10, Dbt-5, Dbt-10, Dil-10, Dbo-10 styryl dyes on blood erythrocytes of white rats. It was shown that the homodimer styryl dyes Dst-5, Dbt-5 and Dbo-10 decrease the erythrocytes quantity by 1.5-2 times more as compared with monomer dyes Sbt and Sbo. The main cause of dyes different action is the different oxidation degree of intracellular hemoglobin evoked by these dyes. It was established that the observed effects was connected with different penetration of these dyes through membrane of erythrocytes and with interaction of these dyes with albumin localized in membranes of cells.

  15. Characteristics of a Broadband Dye Laser Using Pyrromethene and Rhodamine Dyes

    Science.gov (United States)

    Tedder, Sarah A.; Danehy, Paul M.; Wheeler, Jeffrey L.

    2011-01-01

    A broadband dye laser pumped by a frequency-doubled Nd:YAG laser with a full-width half-maximum (FWHM) from 592 to 610 nm was created for the use in a dual-pump broadband CARS system called WIDECARS. The desired broadband dye laser was generated with a mixture of Pyrromethene dyes as an oscillator gain medium and a spectral selective optic in the oscillator cavity. A mixture of Rhodamine dyes were used in the amplifier dye cell. To create this laser a study was performed to characterize the spectral behavior of broadband dye lasers created with Rhodamine dyes 590, 610, and 640, Pyrromethene dyes 597 and 650 as well as mixture of these dyes.

  16. Octane-Assisted Reverse Micellar Dyeing of Cotton with Reactive Dyes

    Directory of Open Access Journals (Sweden)

    Alan Yiu-lun Tang

    2017-12-01

    Full Text Available In this study, we investigated the computer colour matching (CCM of cotton fabrics dyed with reactive dye using the octane-assisted reverse micellar approach. The aim of this study is to evaluate the colour quality and compare the accuracy between CCM forecasting and simulated dyeing produced by conventional water-based dyeing and octane-assisted reverse micellar dyeing. First, the calibration of dyeing databases for both dyeing methods was established. Standard samples were dyed with known dye concentrations. Computer colour matching was conducted by using the colour difference formula of International Commission on Illumination (CIE L*a*b*. Experimental results revealed that the predicted concentrations were nearly the same as the expected known concentrations for both dyeing methods. This indicates that octane-assisted reverse micellar dyeing system can achieve colour matching as good as the conventional water-based dyeing system. In addition, when comparing the colour produced by the conventional water-based dyeing system and the octane-assisted reverse micellar dyeing system, the colour difference (ΔE is ≤1, which indicates that the reverse micellar dyeing system could be applied for industrial dyeing with CCM.

  17. Binding and Inhibitory Effect of the Dyes Amaranth and Tartrazine on Amyloid Fibrillation in Lysozyme.

    Science.gov (United States)

    Basu, Anirban; Suresh Kumar, Gopinatha

    2017-02-16

    Interaction of two food colorant dyes, amaranth and tartrazine, with lysozyme was studied employing multiple biophysical techniques. The dyes exhibited hypochromic changes in the presence of lysozyme. The intrinsic fluorescence of lysozyme was quenched by both dyes; amaranth was a more efficient quencher than tartrazine. The equilibrium constant of amaranth was higher than that of tartarzine. From FRET analysis, the binding distances for amaranth and tartrazine were calculated to be 4.51 and 3.93 nm, respectively. The binding was found to be dominated by non-polyelectrolytic forces. Both dyes induced alterations in the microenvironment surrounding the tryptophan and tyrosine residues of the protein, with the alterations being comparatively higher for the tryptophans than the tyrosines. The interaction caused significant loss in the helicity of lysozyme, the change being higher with amaranth. The binding of both dyes was exothermic. The binding of amaranth was enthalpy driven, while that of tartrazine was predominantly entropy driven. Amaranth delayed lysozyme fibrillation at 25 μM, while tartrazine had no effect even at 100 μM. Nevertheless, both dyes had a significant inhibitory effect on fibrillogenesis. The present study explores the potential antiamyloidogenic property of these azo dyes used as food colorants.

  18. Artificial evolution of coumarin dyes for dye sensitized solar cells.

    Science.gov (United States)

    Venkatraman, Vishwesh; Abburu, Sailesh; Alsberg, Bjørn Kåre

    2015-11-07

    The design and discovery of novel molecular structures with optimal properties has been an ongoing effort for materials scientists. This field has in general been dominated by experiment driven trial-and-error approaches that are often expensive and time-consuming. Here, we investigate if a de novo computational design methodology can be applied to the design of coumarin-based dye sensitizers with improved properties for use in Grätzel solar cells. To address the issue of synthetic accessibility of the designed compounds, a fragment-based assembly is employed, wherein the combination of chemical motifs (derived from the existing databases of structures) is carried out with respect to user-adaptable set of rules. Rather than using computationally intensive density functional theory (DFT)/ab initio methods to screen candidate dyes, we employ quantitative structure-property relationship (QSPR) models (calibrated from empirical data) for rapid estimation of the property of interest, which in this case is the product of short circuit current (Jsc) and open circuit voltage (Voc). Since QSPR models have limited validity, pre-determined applicability domain criteria are used to prevent unacceptable extrapolation. DFT analysis of the top-ranked structures provides supporting evidence of their potential for dye sensitized solar cell applications.

  19. COMPARATIVE STUDY OF TWO DYEING METHODS USING REACTIVE DYE

    Directory of Open Access Journals (Sweden)

    HINOJOSA Belén

    2016-05-01

    Full Text Available Environment preservation is a common worry not only for people but for companies as well. Industry is more and more concern about the necessity of developing new and more respectful processes. Dye is one of the most important processes in the textile industry but it is also considered as no too safe regarding environment issues. This process uses large amounts of water and generates big volumes of wastewater. Following this issue, new regulations and laws emerge to control the waste generated. This leads to the companies and increased costs in terms of wastewater treatments and high water consumption. In this research we compare two systems on garment finishing application, the conventional bath process and the new Ecofinish system that is able to save water and product. To compare these processes, we carried out a reactive dyeing using both systems in order to determine the quality differences in the final product. For this purpose, the samples have been tested to washing and rubbing fastness, according to UNE EN ISO 105 C10 and UNE- EN ISO 105 X12 standards, respectively. This study confirms that this system achieves water savings and reduces the wastewater produced, getting a good dyeing. This process can be considered as an alternative to the conventional one.

  20. Biochemical study of some environmental pollutants dyes Part II: disperse dyes

    International Nuclear Information System (INIS)

    Shakra, S.; Ahmed, F.A.; Fetyan, N.A.

    2005-01-01

    This work was aimed to develop a method for removal of the dyes color from the textile wastewater that is well be much less costly than the other chemical or physical methods used. It therefore included: 1. Preparation of three disperses dyes. 2. Isolation of dyes degradable microorganisms from wastewater effluents and soil after adding 200 ppm of each dye individually. 3. Decolorisation and biodegradation of the dyes in liquid culture of the isolated bacteria (Bacillus thuringiensis). 4. Identification of the probable byproducts by different instruments. 5. Toxicity assessment of the dyes and their biodegraded products

  1. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip.

    Science.gov (United States)

    Xu, Zongli; Langie, Sabine A S; De Boever, Patrick; Taylor, Jack A; Niu, Liang

    2017-01-03

    The Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in epigenome-wide association studies. Both arrays use two fluorescent dyes (Cy3-green/Cy5-red) to measure methylation level at CpG sites. However, performance difference between dyes can result in biased estimates of methylation levels. Here we describe a novel method, called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels. We evaluate the method in several datasets against other widely used dye-bias correction methods. Results on data quality improvement showed that RELIC correction statistically significantly outperforms alternative dye-bias correction methods. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website ( https://www.bioconductor.org/packages/release/bioc/html/ENmix.html ). RELIC is an efficient and robust method to correct for dye-bias in Illumina Methylation BeadChip data. It outperforms other alternative methods and conveniently implemented in R package ENmix to facilitate DNA methylation studies.

  2. Blood extracellular DNA after irradiation

    International Nuclear Information System (INIS)

    Vladimirov, V.G.; Tishchenko, L.I.; Surkova, E.A.; Vasil'eva, I.N.

    1993-01-01

    It has been shown that blood extracellular DNA of irradiated rats largely consists of the low-molecular DNA and its oligomers. Molecular masses of oligomers are multiple to molecular mass of monomer fragment with nucleosome size. The low-molecular DNA has linear form. The average content of GC-pairs in low-molecular DNA is higher than in total rat's DNA (48.5% against 41.5%). The low-molecular DNA is a part of complex containing RNA, acidic proteins and lipids. It is assumed that the formation of low-molecular DNA is a result of Ca/Mg - dependent nuclear endonuclease action

  3. Synthesis, characterization and dyeing behavior of heterocyclic acid dyes and mordent acid dyes on wool and silk fabrics

    Directory of Open Access Journals (Sweden)

    Patel Hitendra M.

    2012-01-01

    Full Text Available Novel heterocyclic acid and mordent acid dyes were synthesized by the coupling of diazonium salt solution of different aromatic amines with 2- butyl-3-(4-hydroxybenzoylbenzofuran. The resulting heterocyclic acid dyes were characterized by spectral techniques, i.e., elemental analysis, IR, 1HNMR, 13C-NMR spectral studies and UV- visible spectroscopy. The dyeing performance of all the heterocyclic acid dyes was evaluated on wool and silk fabrics. The dyeing of chrome pre treated wool and silk fabrics showed better hues on mordented fabrics. Dyeing of wool and silk fabrics resulted in pinkish blue to red shades with very good depth and levelness. The dyed fabrics showed excellent to very good light, washing, perspiration, sublimation and rubbing fastness.

  4. Fate of Colored Smoke Dyes

    Science.gov (United States)

    1992-01-01

    4.13] have been applied to their estimation. This approach has the advantages of sensitivity and of not requiring high purity and known structures...Chrom absorbance detector, and an Alltech Econosil C-18 (10 micrometer) column (4.6 mm X 25 cm with guard column). The mobile phase, HPLC-grade methanol...water partition coefficient or vice versa. The HPLC method is of similar precision and has the advantage that known structure and purity of the dye are

  5. Broad band exciplex dye lasers

    International Nuclear Information System (INIS)

    Dienes, A.; Shank, C.V.; Trozzolo, A.M.

    1975-01-01

    The disclosure is concerned with exciplex dye lasers, i.e., lasers in which the emitting species is a complex formed only from a constituent in an electronically excited state. Noting that an exciplex laser, favorable from the standpoint of broad tunability, results from a broad shift in the peak emission wavelength for the exciplex relative to the unreacted species, a desirable class resulting in such broad shift is described. Preferred classes of laser media utilizing specified resonant molecules are set forth. (auth)

  6. Dataset on analysis of dyeing property of natural dye from Thespesia populnea bark on different fabrics

    Directory of Open Access Journals (Sweden)

    Kuchekar Mohini

    2018-02-01

    Full Text Available The natural dyes separated from plants are of gaining interest as substitutes for synthetic dyes in food and cosmetics. Thespesia populnea (T. populnea is widely grown plant and used in the treatment of various diseases. This study was aimed to separate natural dye from T. populnea bark and analysis of its dyeing property on different fabrics. In this investigation pharmacognostic study was carried out. The pharmacognostic study includes morphological study, microscopical examination, proximate analysis along with the phytochemical study. The dyeing of different fabric was done with a natural dye extracted from T. populnea bark. The fabrics like cotton, butter crep, polymer, chiken, lone, ulene and tarakasa were dye with plant extract. The various evaluation parameters were studied. It includes effect of washing with water, effect of soap, effect of sunlight, effect of alum, effect of Cupric sulphate, microscopical study of fabrics and visual analysis of dyeing by common people were studied. In results, natural dye isolated from T. populnea bark could be used for dyeing fabrics with good fastness properties. The studies reveals that, the dyeing property of fabrics after washing with water and soap, exposed to sunlight does not get affected. It was observed that cotton and tarakasa stains better as compared with other fabrics. It was concluded that the ethanolic extract having good dyeing property. Keywords: Plant, Thespesia populnea, Bark, Natural dye, Fabrics

  7. [1,10]Phenanthroline based cyanine dyes as fluorescent probes for ribonucleic acids in live cells

    Science.gov (United States)

    Kovalska, Vladyslava; Kuperman, Marina; Varzatskii, Oleg; Kryvorotenko, Dmytro; Kinski, Elisa; Schikora, Margot; Janko, Christina; Alexiou, Christoph; Yarmoluk, Sergiy; Mokhir, Andriy

    2017-12-01

    A series of monomethine, trimethine- and styrylcyanine dyes based on a [1,10]phenanthroline moiety was synthesized, characterized and investigated as potential fluorescent probes for nucleic acids in cell free settings and in cells. The dyes were found to be weakly fluorescent in the unbound state, whereas upon the binding to dsDNA or RNA their emission intensity raised up to 50 times (for monomethine benzothiazole derivative FT1 complexed with RNA). The strongest fluorescence intensity in assemblies with dsDNA and RNA was observed for the trimethine benzothiazole derivative FT4. The quantum yield of FT4 fluorescence in its complex with dsDNA was found to be 1.5% and the binding constant (K b) was estimated to be 7.9 × 104 M-1 that is a typical value for intercalating molecules. The FT4 dye was found to be cell membrane permeable. It stains RNA rich components—the nucleoli and most probably the cytoplasmic RNA. FT4 bound to RNAs delivers a very strong fluorescence signal, which makes this easily accessible dye a potentially useful alternative to known RNA stains, e.g. expensive SYTO® 83. The advantage of FT4 is its easy synthetic access including no chromatographic purification steps, which will be reflected in its substantially lower price.

  8. Synthesis and characterization of reactive dye-cassava mesocarp ...

    African Journals Online (AJOL)

    The synthesis of triazine based reactive dyes was carried out. The resultant dyes were characterized by thin layers chromatography, molecular weight, infrared and ultra- violet spectroscopy, and used in dyeing cassava mesocarp to produce dye modified cellulosic substrates. The dyed substrates were tested for dye fixation, ...

  9. Dye removal from textile wastewater using bioadsorbent

    International Nuclear Information System (INIS)

    Gardazi, S.M.H.

    2014-01-01

    Textile industries throughout the world produce huge quantities of dyes and pigments annually. Effluents from textile industries are dye wastewater, and disposal of these wastes to freshwater bodies causes damage to the environment. Among the treatment technologies, adsorption is an attractive and viable option, provided that the sorbent is inexpensive and readily available for use. In this study, a typical basic dye, methylene blue, in wastewater was treated using Melia azedarach sawdust. The effects of contact time, adsorbent amount and particle size were investigated on the removal efficiency of adsorbent for methylene blue. Complete removal of the dye were attained at higher adsorbent dose of 3 g/L with 50 mg/L initial dye concentration. The maximum adsorption was at 240 minutes, whereas more than 90% removal with 105 meu m particle size of 1 g/L adsorbent for same initial dye concentration. The experimental data best fits with 2 Langmuir adsorption isotherm (R= 0.991). (author)

  10. Biological wastewater treatment of azo dyes

    Energy Technology Data Exchange (ETDEWEB)

    Shaul, G.M.; Dempsey, C.R.; Dostal, K.A. (Environmental Protection Agency, Cincinnati, OH (USA))

    1988-09-01

    EPA Water Engineering Research Laboratory, Office of Research and Development, undertook a study to determine the fate of specific water soluble azo dye compounds in the activated sludge process (ASP). The study was approached by dosing the feed to the pilot ASP systems with various water soluble azo dyes and by monitoring each dye compound through the system, analyzing both liquid and sludge samples. The fate of the parent dye compound was assessed via mass balance calculations. These data could determine if the compound was removed by adsorption, apparent biodegradation, or not removed at all. The paper presents results for 18 dye compounds tested from June 1985 through August 1987. The study was conducted at EPAs Test and Evaluation Facility in Cincinnati, Ohio. The objective of this study was to determine the partitioning of water soluble azo dyes in the ASP.

  11. Panchromatic Response in Solid-State Dye-Sensitized Solar Cells Containing Phosphorescent Energy Relay Dyes

    KAUST Repository

    Yum, Jun-Ho; Hardin, Brianâ E.; Moon, Soo-Jin; Baranoff, Etienne; Nà ¼ esch, Frank; McGehee, Michaelâ D.; Grà ¤ tzel, Michael; Nazeeruddin, Mohammadâ K.

    2009-01-01

    Running relay: Incorporating an energyrelay dye (ERD) into the hole transporter of a dye-sensitized solar cell increased power-conversion efficiency by 29% by extending light harvesting into the blue region. In the operating mechanism (see picture

  12. Time dependent – density functional theory characterization of organic dyes for dye-sensitized solar cells

    KAUST Repository

    Hilal, Rifaat; Aziz, Saadullah G.; Osman, Osman I.; Bredas, Jean-Luc

    2017-01-01

    We aim at providing better insight into the parameters that govern the intramolecular charge transfer (ICT) and photo-injection processes in dyes for dye-sensitised solar cells (DSSC). Density functional theory (DFT) and time-dependent DFT (TD

  13. Increased light harvesting in dye-sensitized solar cells with energy relay dyes

    KAUST Repository

    Hardin, Brian E.; Hoke, Eric T.; Armstrong, Paul B.; Yum, Jun-Ho; Comte, Pascal; Torres, Tomá s; Fré chet, Jean M. J.; Nazeeruddin, Md Khaja; Grä tzel, Michael; McGehee, Michael D.

    2009-01-01

    Conventional dye-sensitized solar cells have excellent charge collection efficiencies, high open-circuit voltages and good fill factors. However, dye-sensitized solar cells do not completely absorb all of the photons from the visible and near

  14. Increased light harvesting in dye-sensitized solar cells with energy relay dyes

    KAUST Repository

    Hardin, Brian E.

    2009-06-21

    Conventional dye-sensitized solar cells have excellent charge collection efficiencies, high open-circuit voltages and good fill factors. However, dye-sensitized solar cells do not completely absorb all of the photons from the visible and near-infrared domain and consequently have lower short-circuit photocurrent densities than inorganic photovoltaic devices. Here, we present a new design where high-energy photons are absorbed by highly photoluminescent chromophores unattached to the titania and undergo Förster resonant energy transfer to the sensitizing dye. This novel architecture allows for broader spectral absorption, an increase in dye loading, and relaxes the design requirements for the sensitizing dye. We demonstrate a 26% increase in power conversion efficiency when using an energy relay dye (PTCDI) with an organic sensitizing dye (TT1). We estimate the average excitation transfer efficiency in this system to be at least 47%. This system offers a viable pathway to develop more efficient dye-sensitized solar cells.

  15. 32P-postlabeling assay for carcinogen-DNA adducts: description of beta shielding apparatus and semi-automatic spotting and washing devices that facilitate the handling of multiple samples

    International Nuclear Information System (INIS)

    Reddy, M.V.; Blackburn, G.R.

    1990-01-01

    The utilization of the 32 P-postlabeling assay in combination with TLC for the sensitive detection and estimation of aromatic DNA adducts has been increasing. The procedure consists of 32 P-labeling of carcinogen-adducted 3'-nucleotides in the DNA digests using γ- 32 P ATP and polynucleotide kinase, separation of 32 P-labeled adducts by TLC, and their detection by autoradiography. During both 32 P-labeling and initial phases of TLC, a relatively high amount of γ- 32 P ATP is handled when 30 samples are processed simultaneously. We describe the design of acrylic shielding apparatus, semi-automatic TLC spotting devices, and devices for development and washing of multiple TLC plates, which not only provide substantial protection from exposure to 32 P beta radiation, but also allow quick and easy handling of a large number of samples. Specifically, the equipment includes: (i) a multi-tube carousel rack having 15 wells to hold capless Eppendorf tubes and a rotatable lid with an aperture to access individual tubes; (ii) a pipette shielder; (iii) two semi-automatic spotting devices to apply radioactive solutions to TLC plates; (iv) a multi-plate holder for TLC plates; and (v) a mechanical device for washing multiple TLC plates. Item (i) is small enough to be held in one-hand, vortexed, and centrifuged to mix the solutions in each tube while beta radiation is shielded. Items (iii) to (iv) aid in the automation of the assay. (author)

  16. Hair dye poisoning and the developing world

    Directory of Open Access Journals (Sweden)

    Sampathkumar Krishnaswamy

    2009-01-01

    Full Text Available Hair dye poisoning has been emerging as one of the important causes of intentional self harm in the developing world. Hair dyes contain paraphenylene-diamine and a host of other chemicals that can cause rhabdomyolysis, laryngeal edema, severe metabolic acidosis and acute renal failure. Intervention at the right time has been shown to improve the outcome. In this article, we review the various manifestations, clinical features and treatment modalities for hair dye poisoning.

  17. Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair.

    NARCIS (Netherlands)

    Kraan, TC van der Pouw; Gaalen, van FA; Huizinga, T.W.; Pieterman, E; Breedveld, F.C.; Verweij, C.L.

    2003-01-01

    Rheumatoid arthritis (RA) is a heterogeneous disease. We used cDNA microarray technology to subclassify RA patients and disclose disease pathways in rheumatoid synovium. Hierarchical clustering of gene expression data identified two main groups of tissues (RA-I and RA-II). A total of 121 genes were

  18. Solubilization of Hydrophobic Dyes in Surfactant Solutions

    Directory of Open Access Journals (Sweden)

    Ali Reza Tehrani-Bagha

    2013-02-01

    Full Text Available In this paper, the use of surfactants for solubilization of hydrophobic organic dyes (mainly solvent and disperse dyes has been reviewed. The effect of parameters such as the chemical structures of the surfactant and the dye, addition of salt and of polyelectrolytes, pH, and temperature on dye solubilization has been discussed. Surfactant self-assemble into micelles in aqueous solution and below the concentration where this occurs—the critical micelle concentration (CMC—there is no solubilization. Above the CMC, the amount of solubilized dye increases linearly with the increase in surfactant concentration. It is demonstrated that different surfactants work best for different dyes. In general, nonionic surfactants have higher solubilization power than anionic and cationic surfactants. It is likely that the reason for the good performance of nonionic surfactants is that they allow dyes to be accommodated not only in the inner, hydrocarbon part of the micelle but also in the headgroup shell. It is demonstrated that the location of a dye in a surfactant micelle can be assessed from the absorption spectrum of the dye-containing micellar solution.

  19. Micro-Cavity Fluidic Dye Laser

    DEFF Research Database (Denmark)

    Helbo, Bjarne; Kristensen, Anders; Menon, Aric Kumaran

    2003-01-01

    We have successfully designed, fabricated and characterized a micro-cavity fluidic dye laser with metallic mirrors, which can be integrated with polymer based lab-on-a-chip microsystems without further processing steps. A simple rate-equation model is used to predict the average pumping power...... threshold for lasing as function of cavity-mirror reflectance, laser dye concentration and cavity length. The laser device is characterized using the laser dye Rhodamine 6G dissolved in ethanol. Lasing is observed, and the influence of dye concentration is investigated....

  20. Ultrasonic assisted dyeing: dyeing of acrylic fabrics C.I. Astrazon Basic Red 5BL 200%.

    Science.gov (United States)

    Kamel, M M; Helmy, H M; Mashaly, H M; Kafafy, H H

    2010-01-01

    The dyeing of acrylic fabrics using C.I. Astrazon Basic Red 5BL 200% has been studied with both conventional and ultrasonic techniques. The effect of dye concentration, dye bath pH, ultrasonic power, dyeing time and temperature were studied and the resulting shades obtained by dyeing with both techniques were compared. Colour strength values obtained were found to be higher with ultrasonic than with conventional heating. The results of fastness properties of the dyed fabrics were studied. X-ray and Scanning Electron Microscope SEM were carried out on dyed samples using both methods of dyeing to find out an explanation for the better dyeability of acrylic fabrics with (US) method. Dyeing kinetics of acrylic fabrics using C.I. Astrazon Basic Red 5BL 200% using conventional and ultrasonic conditions were compared. The time/dye-uptake isotherms are revealing the enhanced dye-uptake in the second phase of dyeing. The values of dyeing rate constant, half-time of dyeing and standard affinity and ultrasonic efficiency have been calculated and discussed.

  1. High Excitation Transfer Efficiency from Energy Relay Dyes in Dye-Sensitized Solar Cells

    KAUST Repository

    Hardin, Brian E.; Yum, Jun-Ho; Hoke, Eric T.; Jun, Young Chul; Péchy, Peter; Torres, Tomás; Brongersma, Mark L.; Nazeeruddin, Md. Khaja; Grätzel, Michael; McGehee, Michael D.

    2010-01-01

    The energy relay dye, 4-(Dicyanomethylene)-2-methyl-6-(4- dimethylaminostyryl)-4H-pyran (DCM), was used with a near-infrared sensitizing dye, TT1, to increase the overall power conversion efficiency of a dye-sensitized solar cell (DSC) from 3

  2. Photostability of low cost dye-sensitized solar cells based on natural and synthetic dyes

    Science.gov (United States)

    Abdou, E. M.; Hafez, H. S.; Bakir, E.; Abdel-Mottaleb, M. S. A.

    2013-11-01

    This paper deals with the use of some natural pigments as well as synthetic dyes to act as sensitizers in dye-sensitized solar cells (DSSCs). Anthocyanin dye extracted from rosella (Hibiscus sabdariffa L.) flowers, the commercially available textile dye Remazole Red RB-133 (RR) and merocyanin-like dye based on 7-methyl coumarin are tested. The photostability of the three dyes is investigated under UV-Vis light exposure. The results show a relatively high stability of the three dyes. Moreover, the photostability of the solid dyes is studied over the TiO2 film electrodes. A very low decolorization rates are recorded as; rate constants k = 1.6, 2.1 and 1.9 × 10-3 min-1 for anthocyanin, RR and coumarin dyes, respectively. The stability results favor selecting anthocyanin as a promising sensitizer candidate in DSSCs based on natural products. Dyes-sensitized solar cells are fabricated and their conversion efficiency (η) is 0.27%, 0.14% and 0.001% for the anthocyanin, RR and coumarin dyes, respectively. Moreover, stability tests of the sealed cells based on anthocyanin and RR dyes are done under continuous light exposure of 100 mW cm-2, reveals highly stable DSSCs.

  3. Acid-base indicator properties of dyes from local plants I: Dyes from ...

    African Journals Online (AJOL)

    DR. MIKE HORSFALL

    Acid-base indicator properties of dyes from local plants I: Dyes from Basella alba. (Indian spinach) and ... solution, which change colour immediately after the equivalence point has .... The pH ranges over which the dyes change colour were ...

  4. The copper-pumped dye laser system at Lawrence Livermore National Laboratory

    International Nuclear Information System (INIS)

    Hackel, R.P.; Warner, B.E.

    1993-01-01

    The Lawrence Livermore National Laboratory's (LLNL) Atomic Vapor Laser Isotope Separation (AVLIS) Program has developed a high-average-power, pulsed, tunable, visible laser system. Testing of this hardware is in progress at industrial scale. The LLNL copper-dye laser system is prototypical of a basic module of a uranium-AVLIS plant. The laser demonstration facility (LDF) system consists of copper vapor lasers arranged in oscillator-amplifier chains providing optical pump power to dye-laser master-oscillator-power-amplifier chains. This system is capable of thousands of watts (average) tunable between 550 and 650 mm. The copper laser system at LLNL consists of 12 chains operating continuously. The copper lasers operate at nominally 4.4 kHz, with 50 ns pulse widths and produce 20 W at near the diffraction limit from oscillators and >250 W from each amplifier. Chains consist of an oscillator and three amplifiers and produce >750 W average, with availabilities >95% (i.e., >8,300 h/y). The total copper laser system power averages ∼9,000 W and has operated at over 10,000 W for extended intervals. The 12 copper laser beams are multiplexed and delivered to the dye laser system where they pump multiple dye laser chains. Each dye chain consists of a master oscillator and three or four power amplifiers. The master oscillator operates at nominally 100 mW with a 50 MHz single mode bandwidth. Amplifiers are designed to efficiently amplify the dye beam with low ASE content and high optical quality. Sustained dye chain powers are up to 1,400 W with dye conversion efficiency >50%, ASE content <5%, and wavefront quality correctable to <λ/10 RMS, using deformable mirrors. Since the timing of the copper laser chains can be offset, the dye laser system is capable of repetition rates which are multiples of 4.4 kHz, up to 26 kHz, limited by the dye pumping system. Development of plant-scale copper and dye laser hardware is progressing in off-line facilities

  5. Sorting fluorescent nanocrystals with DNA

    Energy Technology Data Exchange (ETDEWEB)

    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. Aerobic decolourization of two reactive azo dyes under varying ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-02-01

    Feb 1, 2010 ... Azo dyes generally resist aerobic microbial degra- dation, only organisms with specialized azo dye reducing enzymes were found to degrade azo dyes under fully aerobic ... textile mill, in sterile plastic bottles. Isolation of ...

  7. Epstein-Barr virus antibodies in serum and DNA load in saliva are not associated with radiological or clinical disease activity in patients with early multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    René M Gieß

    Full Text Available To investigate the association of Epstein-Barr virus (EBV nuclear antigen-1 (EBNA-1 and viral capsid antigen (VCA immunoglobulin (IgG antibodies in serum as well as EBV DNA load in saliva with radiological and clinical disease activity in patients with clinically isolated syndrome (CIS and early relapsing-remitting MS (RRMS.EBNA-1 and VCA immunoglobulin (IgG antibodies were determined in serum of 100 patients with CIS/early RRMS and 60 healthy controls. EBV DNA load was measured in saliva of 48 patients and 50 controls. Patients underwent clinical assessment with the Expanded Disability Status Scale (EDSS and 3 Tesla magnetic resonance imaging at baseline and after a median of 20 months of follow-up (n = 63 for MRI, n = 71 for EDSS. The association of EBV parameters with occurrence of a second relapse, indicating conversion to clinically definite MS (CDMS, was evaluated over a median of 35 months of follow-up after the first clinical event (n = 89.EBNA-1 IgG antibody frequency (p = 0.00005 and EBNA-1 and VCA IgG antibody levels (p<0.0001 for both were higher in patients than in controls. EBV DNA load in saliva did not differ between groups. Neither EBV antibody levels nor DNA load in saliva were associated with baseline or follow-up number or volume of T2-weighted (T2w or contrast enhancing lesions, number of Barkhof criteria or the EDSS, or with the number of new T2w lesions, T2w lesion volume change or EDSS change on follow-up. Likewise, levels of EBV IgG antibodies in serum and DNA load in saliva were not associated with conversion to CDMS.While these findings confirm the association of EBV infection with early MS, neither EBNA-1 nor VCA IgG antibodies in serum nor EBV DNA load in saliva were associated with radiological or clinical disease activity in patients with CIS/early RRMS. These data are compatible with the concept that EBV may be a trigger for MS acting very early during the development of the disease.

  8. Multicolor fluorescent biosensor for multiplexed detection of DNA.

    Science.gov (United States)

    Hu, Rong; Liu, Tao; Zhang, Xiao-Bing; Huan, Shuang-Yan; Wu, Cuichen; Fu, Ting; Tan, Weihong

    2014-05-20

    Development of efficient methods for highly sensitive and rapid screening of specific oligonucleotide sequences is essential to the early diagnosis of serious diseases. In this work, an aggregated cationic perylene diimide (PDI) derivative was found to efficiently quench the fluorescence emission of a variety of anionic oligonucleotide-labeled fluorophores that emit at wavelengths from the visible to NIR region. This broad-spectrum quencher was then adopted to develop a multicolor biosensor via a label-free approach for multiplexed fluorescent detection of DNA. The aggregated perylene derivative exhibits a very high quenching efficiency on all ssDNA-labeled dyes associated with biosensor detection, having efficiency values of 98.3 ± 0.9%, 97 ± 1.1%, and 98.2 ± 0.6% for FAM, TAMRA, and Cy5, respectively. An exonuclease-assisted autocatalytic target recycling amplification was also integrated into the sensing system. High quenching efficiency combined with autocatalytic target recycling amplification afforded the biosensor with high sensitivity toward target DNA, resulting in a detection limit of 20 pM, which is about 50-fold lower than that of traditional unamplified homogeneous fluorescent assay methods. The quencher did not interfere with the catalytic activity of nuclease, and the biosensor could be manipulated in either preaddition or postaddition manner with similar sensitivity. Moreover, the proposed sensing system allows for simultaneous and multicolor analysis of several oligonucleotides in homogeneous solution, demonstrating its potential application in the rapid screening of multiple biotargets.

  9. Dye Sensitized Solar Cell, DSSC

    Directory of Open Access Journals (Sweden)

    Pongsatorn Amornpitoksuk

    2003-07-01

    Full Text Available A dye sensitized solar cell is a new type of solar cell. The operating system of this solar cell type is similar to plant’s photosynthesis process. The sensitizer is available for absorption light and transfer electrons to nanocrystalline metal oxide semiconductor. The ruthenium(II complexes with polypyridyl ligands are usually used as the sensitizers in solar cell. At the present time, the complex of [Ru(2,2',2'’-(COOH3- terpy(NCS3] is the most efficient sensitizer. The total photon to current conversion efficiency was approximately 10% at AM = 1.5.

  10. DNA typing for HLA-DPB1*02 and -DPB1*04 in multiple sclerosis and juvenile rheumatoid arthritis

    DEFF Research Database (Denmark)

    Fugger, L; Ryder, L P; Morling, N

    1990-01-01

    DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes (SSOP) has recently been reported. The amplification step may be specific for the HLA-DPB locus, or it may be specific for one or a group of HLA-DPB alleles, thus increasing the discriminatory...... power of the system. We report the combined use of group-specific DNA in vitro amplification followed by SSOP in typing for DPB1*02 and DPB1*04 variants. The method was used to type for these variants in 96 randomly selected, healthy Danes, in 37 patients with pauciarticular juvenile rheumatoid...... based on the cellularly defined HLA-DP types of the patients and the frequencies of the DPB1*02 and DPB1*04 variants among healthy Danes....

  11. Quantitative detection of epstein-barr virus DNA in cerebrospinal fluid and blood samples of patients with relapsing-remitting multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Clementina E Cocuzza

    Full Text Available The presence of Epstein-Barr Virus (EBV DNA in cerebrospinal fluid (CSF and peripheral blood (PB samples collected from 55 patients with clinical and radiologically-active relapsing-remitting MS (RRMS and 51 subjects with other neurological diseases was determined using standardized commercially available kits for viral nucleic acid extraction and quantitative EBV DNA detection. Both cell-free and cell-associated CSF and PB fractions were analyzed, to distinguish latent from lytic EBV infection. EBV DNA was detected in 5.5% and 18.2% of cell-free and cell-associated CSF fractions of patients with RRMS as compared to 7.8% and 7.8% of controls; plasma and peripheral blood mononuclear cells (PBMC positivity rates were 7.3% and 47.3% versus 5.8% and 31.4%, respectively. No significant difference in median EBV viral loads of positive samples was found between RRMS and control patients in all tested samples. Absence of statistically significant differences in EBV positivity rates between RRMS and control patients, despite the use of highly sensitive standardized methods, points to the lack of association between EBV and MS disease activity.

  12. Multicolour probes for sequence-specific DNA detection based on graphene oxide.

    Science.gov (United States)

    Zhu, Qing; Xiang, Dongshan; Zhang, Cuiling; Ji, Xinghu; He, Zhike

    2013-09-21

    The bifunctionality of graphene oxide (GO) which can highly adsorb single-stranded DNA (ssDNA) and effectively quench the emission of organic dyes is reasonably utilized in a multiplexed DNA detection system, achieving sensitive and selective detection of HIV, VV and EV, respectively.

  13. A single thiazole orange molecule forms an exciplex in a DNA i-motif.

    Science.gov (United States)

    Xu, Baochang; Wu, Xiangyang; Yeow, Edwin K L; Shao, Fangwei

    2014-06-18

    A fluorescent exciplex of thiazole orange (TO) is formed in a single-dye conjugated DNA i-motif. The exciplex fluorescence exhibits a large Stokes shift, high quantum yield, robust response to pH oscillation and little structural disturbance to the DNA quadruplex, which can be used to monitor the folding of high-order DNA structures.

  14. Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity.

    Science.gov (United States)

    Sindbert, Simon; Kalinin, Stanislav; Nguyen, Hien; Kienzler, Andrea; Clima, Lilia; Bannwarth, Willi; Appel, Bettina; Müller, Sabine; Seidel, Claus A M

    2011-03-02

    In Förster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 Å in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 Å is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 Å). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A

  15. Characteristics of dye Rhoeo spathacea in dye sensitizer solar cell (DSSC)

    Science.gov (United States)

    Sumardiasih, Sri; Obina, Wilfrida M.; Cari; Supriyanto, Agus; Septiawan, Trio Y.; Khairuddin

    2017-01-01

    Dye-sensitized solar cell (DSSC) is a device that converts solar energy into electrical energy. The magnitude of the efficiency of DSSC is mainly based on the amount of dye absorbed by the surface of TiO2. In this work, used natural dye extracted from leaves Rhoeo spathacea. The dye partially used to immerse of TiO2 as working electrodes, and the rest are directly mixed TiO2 paste to obtain dye titanium dioxide.The paste TiO2 and dye titanium dioxide coated onto the fluorine-doped tin oxide (FTO) glass plate by spin coating method. The absorbance spectra of the dye, dye titanium dioxide and TiO2 were obtained by UV-Vis spectroscopy. The conductivity of the dye, dye titanium dioxide, and TiO2 was measured by two point probe El-Kahfi 100. The DSSC based on dye titanium dioxide that stirring for 5 hours the highest efficiency of 0,0520 % whereas those based on TiO2 immersed for 36 hours showed achieved 0,0501 % obtained from I-V characterization.

  16. Characteristics of dye Rhoeo spathacea in dye sensitizer solar cell (DSSC)

    International Nuclear Information System (INIS)

    Sumardiasih, Sri; Obina, Wilfrida M.; Cari; Supriyanto, Agus; Septiawan, Trio Y.; Khairuddin

    2017-01-01

    Dye-sensitized solar cell (DSSC) is a device that converts solar energy into electrical energy. The magnitude of the efficiency of DSSC is mainly based on the amount of dye absorbed by the surface of TiO 2 . In this work, used natural dye extracted from leaves Rhoeo spathacea. The dye partially used to immerse of TiO 2 as working electrodes, and the rest are directly mixed TiO 2 paste to obtain dye titanium dioxide.The paste TiO 2 and dye titanium dioxide coated onto the fluorine-doped tin oxide (FTO) glass plate by spin coating method. The absorbance spectra of the dye, dye titanium dioxide and TiO 2 were obtained by UV-Vis spectroscopy. The conductivity of the dye, dye titanium dioxide, and TiO 2 was measured by two point probe El-Kahfi 100. The DSSC based on dye titanium dioxide that stirring for 5 hours the highest efficiency of 0,0520 % whereas those based on TiO 2 immersed for 36 hours showed achieved 0,0501 % obtained from I-V characterization. (paper)

  17. Theoretical study of indoline dyes for dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Ham, Ho Wan; Kim, Young Sik

    2010-01-01

    Indoline dye sensitizers were designed and studied theoretically to increase molar extinction coefficients in the visible to near infrared region for solar-cell devices. To gain insight into dye sensitizers' structural, electronic, and optical properties, DFT/TDDFT calculations were performed on a series of dye sensitizers derived from the D149. The good agreement between the experimental and TDDFT calculated absorption spectra of the D149 sensitizer allowed us to provide a detailed assessment of the main spectral features of a series of dye sensitizers. Increase in the conjugation length resulted in a more red-shifted spectral response and less positive oxidation potential than that of the D149. The dye with the dimethylfluorene group showed stronger absorption bands due to a large dipole moment. The calculated dipoles for the dye series correlate well with the observed strong absorption bands of the electronic spectra. These results provided useful clues for the molecular engineering of efficient organic dye sensitizers.

  18. High Excitation Transfer Efficiency from Energy Relay Dyes in Dye-Sensitized Solar Cells

    KAUST Repository

    Hardin, Brian E.

    2010-08-11

    The energy relay dye, 4-(Dicyanomethylene)-2-methyl-6-(4- dimethylaminostyryl)-4H-pyran (DCM), was used with a near-infrared sensitizing dye, TT1, to increase the overall power conversion efficiency of a dye-sensitized solar cell (DSC) from 3.5% to 4.5%. The unattached DCM dyes exhibit an average excitation transfer efficiency (EÌ?TE) of 96% inside TT1-covered, mesostructured TiO2 films. Further performance increases were limited by the solubility of DCM in an acetonitrile based electrolyte. This demonstration shows that energy relay dyes can be efficiently implemented in optimized dye-sensitized solar cells, but also highlights the need to design highly soluble energy relay dyes with high molar extinction coefficients. © 2010 American Chemical Society.

  19. Low-threshold conical microcavity dye lasers

    DEFF Research Database (Denmark)

    Grossmann, Tobias; Schleede, Simone; Hauser, Mario

    2010-01-01

    element simulations confirm that lasing occurs in whispering gallery modes which corresponds well to the measured multimode laser-emission. The effect of dye concentration on lasing threshold and lasing wavelength is investigated and can be explained using a standard dye laser model....

  20. Molecular structure-adsorption study on current textile dyes.

    Science.gov (United States)

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models.

  1. DNA Polymerases Drive DNA Sequencing-by-Synthesis Technologies: Both Past and Present

    Directory of Open Access Journals (Sweden)

    Cheng-Yao eChen

    2014-06-01

    Full Text Available Next-generation sequencing (NGS technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. E. coli DNA polymerase I proteolytic (Klenow fragment was originally utilized in Sanger's dideoxy chain terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ⱷ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ⱷ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.

  2. Tunability of optofluidic distributed feedback dye lasers

    DEFF Research Database (Denmark)

    Gersborg-Hansen, Morten; Kristensen, Anders

    2007-01-01

    We investigate the tunability of optofluidic distributed feedback (DFB) dye lasers. The lasers rely on light-confinement in a nano-structured polymer film where an array of nanofluidic channels constitutes a third order Bragg grating DFB laser resonator with a central phase-shift. The lasers...... are operated by filling the DFB laser resonator with a dye solution by capillary action and optical pumping with a frequency doubled Nd: YAG laser. The low reflection order of the DFB laser resonator yields low out-of-plane scattering losses as well as a large free spectral range (FSR), and low threshold...... fluences down to similar to 7 mu J/mm2 are observed. The large FSR facilitates wavelength tuning over the full gain spectrum of the chosen laser dye and we demonstrate 45 nm tunability using a single laser dye by changing the grating period and dye solution refractive index. The lasers are straight...

  3. Biodegradation of carcinogenic textile azo dyes using bacterial isolates of mangrove sediment

    Directory of Open Access Journals (Sweden)

    Guru Prasad Srinivasan

    2014-02-01

    Full Text Available Objective: To evaluate the biodegrading property against carcinogenic azo dyes using bacterial isolates of mangrove sediment. Methods: The bacterial isolates were subjected to submerged fermentation and their growth kinetics were studied. The potential strain was characterized using 16S rDNA sequencing. Results: In the present study, dye degrading bacterial colonies were isolated from the mangrove sediment samples of Parangipettai estuarine area, Tamil Nadu. Of the 30 morphologically different strains isolated, 5 showed antagonistic property. The growth kinetics of the two strains, P1 and G1, which showed potent activity were calculated. One particular isolate (P1 showing promising dye degrading potential in the submerged fermentation was further characterized. The strain was identified as Paenibacillus sp. by 16S rDNA sequencing. Conclusions: This study reveals the less explored microflora of mangrove sediments. The novel strain may further be analyzed and used in the treatment of effluent from dye industry so as to reduce the impact of carcinogenic contaminants.

  4. Quantification of protein concentration using UV absorbance and Coomassie dyes.

    Science.gov (United States)

    Noble, James E

    2014-01-01

    The measurement of a solubilized protein concentration in solution is an important assay in biochemistry research and development labs for applications ranging from enzymatic studies to providing data for biopharmaceutical lot release. Spectrophotometric protein quantification assays are methods that use UV and visible spectroscopy to rapidly determine the concentration of protein, relative to a standard, or using an assigned extinction coefficient. Where multiple samples need measurement, and/or the sample volume and concentration is limited, preparations of the Coomassie dye commonly known as the Bradford assay can be used. © 2014 Elsevier Inc. All rights reserved.

  5. Identification of new sensitive biomarkers for the in vivo response to interferon-beta treatment in multiple sclerosis using DNA-array evaluation

    DEFF Research Database (Denmark)

    Sellebjerg, F.; Krakauer, M.; Hesse, D.

    2009-01-01

    Neutralizing antibodies (NAbs) occur in a proportion of multiple sclerosis (MS) patients treated with interferon (IFN)-beta. NAbs impair the effect of treatment. The biological effect of IFN-beta can be measured as the induction of the myxovirus resistance protein A (MxA) molecule. However, other...

  6. A putative non-hr origin of DNA replication in the HindIII-K fragment of Autographa californica multiple nucleocapsid nuclear polyhedrosis virus

    NARCIS (Netherlands)

    Kool, M.; Goldbach, R. W.; Vlak, J. M.

    1994-01-01

    In addition to the seven known homologous regions (hrs) of Autographa californica multiple nucleocapsid polyhedrosis virus (AcMNPV) the HindIII-K fragment was also found to carry a putative ori, although this fragment does not contain an hr. Deletion analysis showed that this ori contains several

  7. Fabrication and characterization of mixed dye: Natural and synthetic organic dye

    Science.gov (United States)

    Richhariya, Geetam; Kumar, Anil

    2018-05-01

    Mixed dye from hibiscus sabdariffa and eosin Y was employed in the fabrication of dye sensitized solar cell (DSSC). Nanostructured mesoporous film was prepared from the titanium dioxide (TiO2). The energy conversion efficiency of hibiscus, eosin Y and mixed dye was obtained as 0.41%, 1.53% and 2.02% respectively. Mixed DSSC has shown improvement in the performance of the cell as compared to hibiscus and eosin Y dye due to addition of synthetic organic dye. This illustrates the effect of synthetic organic dyes in performance enhancement of natural dyes. It has been credited to the improved absorption of light mainly in higher energy state (λ = 440-560 nm) when two dyes were employed simultaneously as was obvious from the absorption spectra of dyes adsorbed onto TiO2 electrode. The cell with TiO2 electrode sensitized by mixed dye gives short circuit current density (Jsc) = 4.01 mA/cm2, open circuit voltage (Voc) = 0.67 V, fill factor (FF) = 0.60 and energy conversion efficiency (η) of 2.02%.

  8. Chemical modifications and reactions in DNA nanostructures

    DEFF Research Database (Denmark)

    Gothelf, Kurt Vesterager

    2017-01-01

    such as hydrocarbons or steroids have been introduced to change the surface properties of DNA origami structures, either to protect the DNA nanostructure or to dock it into membranes and other hydrophobic surfaces. DNA nanostructures have also been used to control covalent chemical reactions. This article provides......DNA nanotechnology has the power to form self-assembled and well-defined nanostructures, such as DNA origami, where the relative positions of each atom are known with subnanometer precision. Our ability to synthesize oligonucleotides with chemical modifications in almost any desired position...... provides rich opportunity to incorporate molecules, biomolecules, and a variety of nanomaterials in specific positions on DNA nanostructures. Several standard modifications for oligonucleotides are available commercially, such as dyes, biotin, and chemical handles, and such modified oligonucleotides can...

  9. Cuprolinic Blue: a specific dye for single-stranded RNA in the presence of magnesium chloride. I. Fundamental aspects

    NARCIS (Netherlands)

    Tas, J.; MENDELSON, D.; NOORDEN, C. J. F.

    1983-01-01

    Qualitative and quantitative aspects of the cationic dye Cuprolinic Blue were investigated with model films of polyacrylamide gel in which RNA, DNA and other biological polyanionic compounds had been incorporated. In the presence of 1 M MgCl2, Curpolinic Blue was found to bind specifically to

  10. Ultrasound-assisted dyeing of cellulose acetate.

    Science.gov (United States)

    Udrescu, C; Ferrero, F; Periolatto, M

    2014-07-01

    The possibility of reducing the use of auxiliaries in conventional cellulose acetate dyeing with Disperse Red 50 using ultrasound technique was studied as an alternative to the standard procedure. Dyeing of cellulose acetate yarn was carried out by using either mechanical agitation alone, with and without auxiliaries, or coupling mechanical and ultrasound agitation in the bath where the temperature range was maintained between 60 and 80 °C. The best results of dyeing kinetics were obtained with ultrasound coupled with mechanical agitation without auxiliaries (90% of bath exhaustion value at 80 °C). Hence the corresponding half dyeing times, absorption rate constants according to Cegarra-Puente modified equation and ultrasound efficiency were calculated confirming the synergic effect of sonication on the dyeing kinetics. Moreover the apparent activation energies were also evaluated and the positive effect of ultrasound added to mechanical agitation was evidenced by the lower value (48 kJ/mol) in comparison with 112 and 169 kJ/mol for mechanical stirring alone with auxiliaries and without, respectively. Finally, the fastness tests gave good values for samples dyed with ultrasound technique even without auxiliaries. Moreover color measurements on dyed yarns showed that the color yield obtained by ultrasound-assisted dyeing at 80 °C of cellulose acetate without using additional chemicals into the dye bath reached the same value yielded by mechanical agitation, but with remarkably shorter time. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Photochemistry of triarylmethane dyes bound to proteins

    Science.gov (United States)

    Indig, Guilherme L.

    1996-04-01

    Triarylmethanes represent a class of cationic dyes whose potential as photosensitizers for use in photodynamic therapy of neoplastic diseases has never been comprehensively evaluated. Here, the laser-induced photodecomposition of three triarylmethane dyes, crystal violet, ethyl violet, and malachite green, non-covalently bound to bovine serum albumin (a model biological target) was investigated. Upon laser excitation at 532 nm, the bleaching of the corresponding dye-protein molecular complexes follows spectroscopic patterns that suggest the formation of reduced forms of the dyes as major reaction photoproducts. That implies that an electron or hydrogen atom transfer from the protein to the dye's moiety within the guest-host complex is the first step of the photobleaching process. Since the availability of dissolved molecular oxygen was not identified as a limiting factor for the phototransformations to occur, these dyes can be seen as potential phototherapeutic agents for use in hypoxic areas of tumors. These triarylmethane dyes strongly absorb at relatively long wavelengths (absorption maximum around 600 nm; (epsilon) max approximately equals 105 M-1 cm-1), and only minor changes in their absorption characteristics are observed upon binding to the protein. However the binding event leads to a remarkable increase in their fluorescence quantum yield and photoreactivity.

  12. In vivo effects of UV radiation on multiple endpoints and expression profiles of DNA repair and heat shock protein (Hsp) genes in the cycloid copepod Paracyclopina nana

    Energy Technology Data Exchange (ETDEWEB)

    Won, Eun-Ji; Han, Jeonghoon [Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Lee, Yeonjung; Kumar, K. Suresh; Shin, Kyung-Hoon [Department of Marine Sciences and Convergent Technology, College of Science and Technology, Hanyang University, Ansan 426-791 (Korea, Republic of); Lee, Su-Jae [Department of Life Sciences, College of Natural Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of); Park, Heum Gi, E-mail: hgpark@gwnu.ac.kr [Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702 (Korea, Republic of); Lee, Jae-Seong, E-mail: jslee2@skku.edu [Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2015-08-15

    Highlights: • UV-B radiation induced a significant reduction of the re-brooding rate of ovigerous females. • A dose-dependent decrease in food ingestion and the rate of assimilation to the body upon UV radiation. • Expression of base excision repair-associated and hsp chaperoning genes was significantly increased upon UV radiation in P. nana. - Abstract: To evaluate the effects of ultraviolet (UV) radiation on energy acquisition and consumption, the copepod Paracyclopina nana was irradiated with several doses (0–3 kJ/m{sup 2}) of UV. After UV radiation, we measured the re-brooding success, growth pattern of newly hatched nauplii, ingestion rate, and assimilation of diet. In addition, we checked the modulated patterns of DNA repair and heat shock protein (hsp) chaperoning genes of P. nana. UV-B radiation induced a significant reduction (7–87%) of the re-brooding rate of ovigerous females, indicating that UV-induced egg sac damage is closely correlated with a reduction in the hatching rate of UV-irradiated ovigerous female offspring. Using chlorophyll a and stable carbon isotope incubation experiments, we found a dose-dependent decrease (P < 0.05) in food ingestion and the rate of assimilation to the body in response to UV radiation, implying that P. nana has an underlying ability to shift its balanced-energy status from growth and reproduction to DNA repair and adaptation. Also, expression of P. nana base excision repair (BER)-associated genes and hsp chaperoning genes was significantly increased in response to UV radiation in P. nana. These findings indicate that even 1 kJ/m{sup 2} of UV radiation induces a reduction in reproduction and growth patterns, alters the physiological balance and inhibits the ability to cope with UV-induced damage in P. nana.

  13. In vivo effects of UV radiation on multiple endpoints and expression profiles of DNA repair and heat shock protein (Hsp) genes in the cycloid copepod Paracyclopina nana

    International Nuclear Information System (INIS)

    Won, Eun-Ji; Han, Jeonghoon; Lee, Yeonjung; Kumar, K. Suresh; Shin, Kyung-Hoon; Lee, Su-Jae; Park, Heum Gi; Lee, Jae-Seong

    2015-01-01

    Highlights: • UV-B radiation induced a significant reduction of the re-brooding rate of ovigerous females. • A dose-dependent decrease in food ingestion and the rate of assimilation to the body upon UV radiation. • Expression of base excision repair-associated and hsp chaperoning genes was significantly increased upon UV radiation in P. nana. - Abstract: To evaluate the effects of ultraviolet (UV) radiation on energy acquisition and consumption, the copepod Paracyclopina nana was irradiated with several doses (0–3 kJ/m 2 ) of UV. After UV radiation, we measured the re-brooding success, growth pattern of newly hatched nauplii, ingestion rate, and assimilation of diet. In addition, we checked the modulated patterns of DNA repair and heat shock protein (hsp) chaperoning genes of P. nana. UV-B radiation induced a significant reduction (7–87%) of the re-brooding rate of ovigerous females, indicating that UV-induced egg sac damage is closely correlated with a reduction in the hatching rate of UV-irradiated ovigerous female offspring. Using chlorophyll a and stable carbon isotope incubation experiments, we found a dose-dependent decrease (P < 0.05) in food ingestion and the rate of assimilation to the body in response to UV radiation, implying that P. nana has an underlying ability to shift its balanced-energy status from growth and reproduction to DNA repair and adaptation. Also, expression of P. nana base excision repair (BER)-associated genes and hsp chaperoning genes was significantly increased in response to UV radiation in P. nana. These findings indicate that even 1 kJ/m 2 of UV radiation induces a reduction in reproduction and growth patterns, alters the physiological balance and inhibits the ability to cope with UV-induced damage in P. nana

  14. Bleaching and diffusion dynamics in optofluidic dye lasers

    DEFF Research Database (Denmark)

    Gersborg-Hansen, Morten; Balslev, Søren; Mortensen, Asger

    2007-01-01

    The authors have investigated the bleaching dynamics that occur in optofluidic dye lasers where the liquid laser dye in a microfluidic channel is locally bleached due to optical pumping. They find that for microfluidic devices, the dye bleaching may be compensated through diffusion of dye molecules...

  15. Supramolecular hair dyes: a new application of cocrystallization

    DEFF Research Database (Denmark)

    Delori, Amit; Urquhart, Andrew; Oswald, Iain D. H.

    2016-01-01

    The manuscript presents the first report of hair dyes of various colors formed by cocrystallization. Unlike the most popular oxidative hair dye (OHD) products, these dyes are NH3 free and do not require H2O2 as a color developer. The importance of these new hair dyes products is further enhanced...

  16. Contact allergy to common ingredients in hair dyes

    DEFF Research Database (Denmark)

    Søsted, Heidi; Rustemeyer, Thomas; Gonçalo, Margarida

    2013-01-01

    p-Phenylenediamine (PPD) is the primary patch test screening agent for hair dye contact allergy, and approximately 100 different hair dye chemicals are allowed.......p-Phenylenediamine (PPD) is the primary patch test screening agent for hair dye contact allergy, and approximately 100 different hair dye chemicals are allowed....

  17. Identification of Colored Dyes that are Resistant to Fading on Exposure to Ethylene Oxide; Use with Indicating FTA™ Sample Collection Cards

    Directory of Open Access Journals (Sweden)

    Nina Moran

    2016-01-01

    Full Text Available Regulatory Standards and Forensic Communities are expressing an expectation for HID products to be certified as “DNA-free.” Recently, “DNA-free” status was described for HID-related products using ethylene oxide (EtO; this gas reduces the presence of amplifiable DNA and causes minimal interference to downstream HID-analytical methods. During sample collection, indicating cards, for example, Indicating FTA™ (GE Healthcare Life Sciences, UK, are used to collect and store buccal cell DNA. These cards contain a dye which changes color on application of a colorless sample. Generating “DNA-free” indicating cards using EtO should not impact the dyes' ability to indicate sample location or the efficacy of the card in downstream HID-analytical methods. This study was initiated to identify alternative dyes to those currently used with sample indicating collection cards. The most promising, dyes when applied to cellulose papers exhibited a uniform color distribution and excellent sample indicating properties even when mixed with chemicals associated with FTA™. When dyed cellulose papers were exposed to EtO, ultraviolet radiation, elevated temperature, and humidity, negligible fading or discoloration was observed. The presence of these dyes on cellulose papers did not interfere with direct short tandem repeat (STR profiling. Allelic concordance, first pass success rate, and mean peak heights were comparable to samples applied to Indicating FTA. Biological samples applied to EtO-treated dyed cellulose papers and stored >1 month produced full STR profiles of sufficient quality to allow submission to DNA databases, confirming negligible interference from EtO treatment. These alternative sample indicating dyes resist EtO-mediated fading while fulfilling the Forensic Community's expectation for “DNA-free” with negligible impact on collection card performance.

  18. Quirks of dye nomenclature. 5. Rhodamines.

    Science.gov (United States)

    Cooksey, C J

    2016-01-01

    Rhodamines were first produced in the late 19(th) century, when they constituted a new class of synthetic dyes. These compounds since have been used to color many things including cosmetics, inks, textiles, and in some countries, food products. Certain rhodamine dyes also have been used to stain biological specimens and currently are widely used as fluorescent probes for mitochondria in living cells. The early history and current biological applications are sketched briefly and an account of the ambiguities, complications and confusions concerning dye identification and nomenclature are discussed.

  19. Simulations of longitudinally pumped dye laser amplifier

    International Nuclear Information System (INIS)

    Takehisa, Kiwamu; Takemori, Satoshi

    1995-01-01

    Simulations of a copper laser pumped dye laser amplifier and new designs of the longitudinally pumped dye laser amplifier are presented. The simulations take the consideration of the amplified spontaneous emission (ASE). The new designs utilize a center-hole reflector instead of a dichroic mirror. The simulation results indicate that the poor spatial overlap between the pump beam and the dye beam in the transverse pumping not only reduces the laser output power, but also generates ASE strongly. The results also indicate that the longitudinal pumping is as efficient as the transverse pumping. (author)

  20. Hypersensitivity to contrast media and dyes.

    Science.gov (United States)

    Brockow, Knut; Sánchez-Borges, Mario

    2014-08-01

    This article updates current knowledge on hypersensitivity reactions to diagnostic contrast media and dyes. After application of a single iodinated radiocontrast medium (RCM), gadolinium-based contrast medium, fluorescein, or a blue dye, a hypersensitivity reaction is not a common finding; however, because of the high and still increasing frequency of those procedures, patients who have experienced severe reactions are nevertheless frequently encountered in allergy departments. Evidence on allergologic testing and management is best for iodinated RCM, limited for blue dyes, and insufficient for fluorescein. Skin tests can be helpful in the diagnosis of patients with hypersensitivity reactions to these compounds. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Single Molecule Screening of Disease DNA Without Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ji-Young [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA

  2. Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response

    Energy Technology Data Exchange (ETDEWEB)

    Crnolatac, Ivo; Rogan, Iva; Majić, Boris; Tomić, Sanja [Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb (Croatia); Deligeorgiev, Todor [Faculty of Chemistry and Pharmacy, University of Sofia (Bulgaria); Horvat, Gordan [Department of Physical Chemistry, Faculty of Science/Chemistry, Horvatovac 102A, HR-10000 Zagreb (Croatia); Makuc, Damjan; Plavec, Janez [Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana (Slovenia); EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, Ljubljana (Slovenia); Pescitelli, Gennaro [Department of Chemistry, University of Pisa, Via Moruzzi 13, Pisa (Italy); Piantanida, Ivo, E-mail: pianta@irb.hr [Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb (Croatia)

    2016-10-12

    Two small molecules showed intriguing properties of analytical multipurpose probes, whereby one chromophore gives different signal for many different DNA/RNA by application of several highly sensitive spectroscopic methods. Dyes revealed pronounced fluorescence ratiomeric differentiation between ds-AU-RNA, AT-DNA and GC-DNA in approximate order 10:8:1. Particularly interesting, dyes showed specific fluorimetric response for poly rA even at 10-fold excess of any other ss-RNA, and moreover such emission selectivity is preserved in multicomponent ss-RNA mixtures. The dyes also showed specific chiral recognition of poly rU in respect to the other ss-RNA by induced CD (ICD) pattern in visible range (400–500 nm), which was attributed to the dye-side-chain contribution to binding (confirmed by absence of any ICD band for reference compound lacking side-chain). Most intriguingly, minor difference in the side-chain attached to dye chromophore resulted in opposite sign of dye-ICD pattern, whereby differences in NMR NOESY contacts and proton chemical shifts between two dye/oligo rU complexes combined with MD simulations and CD calculations attributed observed bisignate ICD to the dimeric dye aggregate within oligo rU. - Highlights: • Novel dyes emit fluorescence only for poly rA even at high excess of all other ss-RNA. • Fluorescence response for AT-DNA is 8 times stronger than for GC-DNA. • Florescence induced by ds-RNA is 20% stronger that emission induced by ds-DNA. • Intrinsically non-chiral, dyes show strong and characteristic ICD response for poly rU.

  3. DFT Studies on the electronic structures of indoline dyes for dye-sensitized solar cells

    Directory of Open Access Journals (Sweden)

    JIE XU

    2010-02-01

    Full Text Available A series of indoline dyes with promising efficiency for dye-sensitized solar cells (DSSCs were studied using the density functional theory at the B3LYP/6-31g (d level. The ground-state geometries, electronic structures and absorption spectra of these dyes are reported. The calculated results indicate that the energy levels of the HOMOs and LUMOs of these dyes are advantageous for electron injection. Their intense and broad absorption bands as well as favorable excited-state energy levels are key factor for their outstanding efficiencies in DSSCs.

  4. Dyeing behaviour of gamma irradiated cotton fabric using Lawson dye extracted from henna leaves (Lawsonia inermis)

    International Nuclear Information System (INIS)

    Rehman, Fazal-ur; Adeel, Shahid; Qaiser, Summia; Ahmad Bhatti, Ijaz; Shahid, Muhammad; Zuber, Mohammad

    2012-01-01

    Dyeing behavior of gamma irradiated cotton fabric using Lawson dye extracted from henna leaves has been investigated. Cotton and dye powder are irradiated to different absorbed doses of 2, 4, 6, 8 and 10 kGy using Cs-137 gamma irradiator. The dyeing parameters such as dyeing time, electrolyte (salt) concentration and mordant concentrations using copper and iron as mordants are optimized. Dyeing is performed using un-irradiated and irradiated cotton with dye solutions and their color strength values are evaluated in CIE Lab system using Spectraflash –SF650. Methods suggested by International Standard Organization (ISO) have been employed to investigate the colourfastness properties such as colourfastness to light, washing and rubbing of irradiated dyed fabric. It is found that gamma ray treatment of cotton dyed with extracts of henna leaves has significantly improved the color strength as well as enhanced the rating of fastness properties. - Highlights: ► The optimum absorbed dose obtained for surface modification of cotton (RC) is 8 kGy. ► Irradiation has enhanced antioxidant, anti bacterial and hemolytic activities. ► Optimum dyeing conditions are 60 min dyeing time and 8 g/L salt concentration. ► At optimum conditions, color strength and fastness properties are enhanced.

  5. Industrial scale salt-free reactive dyeing of cationized cotton fabric with different reactive dye chemistry.

    Science.gov (United States)

    Nallathambi, Arivithamani; Venkateshwarapuram Rengaswami, Giri Dev

    2017-10-15

    Dyeing of knitted cotton goods in the industry has been mostly with reactive dyes. Handling of salt laden coloured effluent arising out of dyeing process is one of the prime concerns of the industry. Cationization of cotton is one of the effective alternative to overcome the above problem. But for cationization to be successful at industrial scale it has to be carried out by exhaust process and should be adoptable for the various dye chemistries currently practiced in the industry. Hence, in the present work, industrial level exhaust method of cationization process was carried out with concentration of 40g/L and 80g/L. The fabrics were dyed with dyes of three different dye chemistry and assessed for its dyeing performance without the addition of salt. Dye shades ranging from medium to extra dark shades were produced without the addition of salt. This study will provide industries the recipe that can be adopted for cationized cotton fabric for the widely used reactive dyes at industrial level. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Dye-sensitized solar cells using natural dyes as sensitizers from Malaysia local fruit `Buah Mertajam'

    Science.gov (United States)

    Hambali, N. A. M. Ahmad; Roshidah, N.; Hashim, M. Norhafiz; Mohamad, I. S.; Saad, N. Hidayah; Norizan, M. N.

    2015-05-01

    We experimentally demonstrate the high conversion efficiency, low cost, green technology and easy to fabricate dye-sensitized solar cells (DSSCs) using natural anthocyanin dyes as sensitizers. The DSSCs was fabricated by using natural anthocyanin dyes which were extracted from different parts of the plants inclusive `Buah Mertajam', `Buah Keriang Dot', `Bunga Geti', Hibiscus, Red Spinach and Henna. The natural anthocyanin dyes that found in flower, leaves and fruits were extracted by the simple procedures. This anthocyanin dye is used to replace the expensive chemical synthetic dyes due to its ability to effectively attach into the surface of Titanium dioxide (TiO2). A natural anthocyanin dyes molecule adsorbs to each particle of the TiO2 and acts as the absorber of the visible light. A natural anthocyanin dye from Buah Mertajam shows the best performance with the conversion efficiency of 5.948% and fill factor of 0.708 followed by natural anthocyanin dyes from `Buah Keriang Dot', `Bunga Geti', Hibiscus, Red Spinach and Henna. Buah Mertajam or scientifically known as eriglossum rubiginosum is a local Malaysia fruit.

  7. Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species

    Directory of Open Access Journals (Sweden)

    Kotewong Rattanawadee

    2010-11-01

    Full Text Available Abstract Background Many species of marine shrimp in the Family Penaeidae, viz. Penaeus (Litopenaeus vannamei, Penaeus monodon, Penaeus (Fenneropenaeus chinensis, and Penaeus (Marsupenaeus japonicus, are animals of economic importance in the aquaculture industry. Yet information about their DNA and protein sequences is lacking. In order to predict their collective proteome, we combined over 270,000 available EST and cDNA sequences from the 4 shrimp species with all protein sequences of Drosophila melanogaster and Caenorhabditis elegans. EST data from 4 other crustaceans, the crab Carcinus maenas, the lobster Homarus americanus (Decapoda, the water flea Daphnia pulex, and the brine shrimp Artemia franciscana were also used. Findings Similarity searches from EST collections of the 4 shrimp species matched 64% of the protein sequences of the fruit fly, but only 45% of nematode proteins, indicating that the shrimp proteome content is more similar to that of an insect than a nematode. Combined results with 4 additional non-shrimp crustaceans increased matching to 78% of fruit fly and 56% of nematode proteins, suggesting that present shrimp EST collections still lack sequences for many conserved crustacean proteins. Analysis of matching data revealed the presence of 4 EST groups from shrimp, namely sequences for proteins that are both fruit fly-like and nematode-like, fruit fly-like only, nematode-like only, and non-matching. Gene ontology profiles of proteins for the 3 matching EST groups were analyzed. For non-matching ESTs, a small fraction matched protein sequences from other species in the UniProt database, including other crustacean-specific proteins. Conclusions Shrimp ESTs indicated that the shrimp proteome is comprised of sub-populations of proteins similar to those common to both insect and nematode models, those present specifically in either model, or neither. Combining small EST collections from related species to compensate for their

  8. Development of new near-infrared and leuco-dye optical systems for forensic and crime fighting applications

    Science.gov (United States)

    Patonay, Gabor; Strekowski, Lucjan; Salon, Jozef; Medou-Ovono, Martial; Krutak, James J.; Leggitt, Jeffrey; Seubert, Heather; Craig, Rhonda

    2004-12-01

    New chemistry for leuco fluorescin and leuco rhodamine for latent bloodstain and fingerprint detection has been developed in our laboratories. The use of these leuco dyes results in excellent contrast for several hours. The FBI's Evidence Response Team and DNA I unit collaborated with Georgia State University to validate the new fluorescin chemistry for use in the field. In addition, several new NIR dyes have been developed in our laboratories that can be used to detect different chemical residues, e.g., pepper spray, latent fingerprint, latent blood, metal ions, or other trace evidence during crime scene investigations. Proof of principle experiments showed that NIR dyes reacting with such residues can be activated with appropriately filtered semiconductor lasers and LEDs to emit NIR fluorescence that can be observed using optimally filtered night vision intensifiers or pocket scopes, digital cameras, CCD and CMOS cameras, or other NIR detection systems. The main advantage of NIR detection is that the color of the background has very little influence on detection and that there are very few materials that would interfere by exhibiting NIR fluorescence. The use of pocket scopes permits sensitive and convenient detection. Once the residues are located, digital images of the fluorescence can be recorded and samples obtained for further analyses. NIR dyes do not interfere with subsequent follow-up or confirmation methods such as DNA or LC/MS analysis. Near-infrared absorbing dyes will be summarized along with detection mechanisms.

  9. Polymerization of novel methacrylated anthraquinone dyes

    Directory of Open Access Journals (Sweden)

    Christian Dollendorf

    2013-02-01

    Full Text Available A new series of polymerizable methacrylated anthraquinone dyes has been synthesized by nucleophilic aromatic substitution reactions and subsequent methacrylation. Thereby, green 5,8-bis(4-(2-methacryloxyethylphenylamino-1,4-dihydroxyanthraquinone (2, blue 1,4-bis(4-((2-methacryloxyethyloxyphenylaminoanthraquinone (6 and red 1-((2-methacryloxy-1,1-dimethylethylaminoanthraquinone (12, as well as 1-((1,3-dimethacryloxy-2-methylpropan-2-ylaminoanthraquinone (15 were obtained. By mixing of these brilliant dyes in different ratios and concentrations, a broad color spectrum can be generated. After methacrylation, the monomeric dyes can be covalently emplaced into several copolymers. Due to two polymerizable functionalities, they can act as cross-linking agents. Thus, diffusion out of the polymer can be avoided, which increases the physiological compatibility and makes the dyes promising compounds for medical applications, such as iris implants.

  10. Computer control of pulsed tunable dye lasers

    International Nuclear Information System (INIS)

    Thattey, S.S.; Dongare, A.S.; Suri, B.M.; Nair, L.G.

    1992-01-01

    Pulsed tunable dye lasers are being used extensively for spectroscopic and photo-chemical experiments, and a system for acquisition and spectral analysis of a volume of data generated will be quite useful. The development of a system for wavelength tuning and control of tunable dye lasers and an acquisition system for spectral data generated in experiments with these lasers are described. With this system, it is possible to control the tuning of three lasers, and acquire data in four channels, simultaneously. It is possible to arrive at the desired dye laser wavelength with a reproducibility of ± 0.012 cm -1 , which is within the absorption width (atomic interaction) caused by pulsed dye lasers of linewidth 0.08 cm -1 . The spectroscopic data generated can be analyzed for spectral identification within absolute accuracy ± 0.012 cm -1 . (author). 6 refs., 11 figs

  11. Sub–100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA

    Science.gov (United States)

    Woehrstein, Johannes B.; Strauss, Maximilian T.; Ong, Luvena L.; Wei, Bryan; Zhang, David Y.; Jungmann, Ralf; Yin, Peng

    2017-01-01

    Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness. To address this challenge, we introduce metafluorophores, which are constructed as DNA nanostructure–based fluorescent probes with digitally tunable optical properties. Each metafluorophore is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact sub–100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 × 60 nm2, substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and photostability and demonstrated a palette of 124 virtual colors. Using these probes as fluorescent barcodes, we implemented an assay for multiplexed quantification of nucleic acids. Additionally, we demonstrated the triggered in situ self-assembly of fluorescent DNA nanostructures with prescribed brightness upon initial hybridization to a nucleic acid target. PMID:28691083

  12. Green dyeing process of modified cotton fibres using natural dyes extracted from Tamarix aphylla (L.) Karst. leaves.

    Science.gov (United States)

    Baaka, Noureddine; Mahfoudhi, Adel; Haddar, Wafa; Mhenni, Mohamed Farouk; Mighri, Zine

    2017-01-01

    This research work involves an eco-friendly dyeing process of modified cotton with the aqueous extract of Tamarix aphylla leaves. During this process, the dyeing step was carried out on modified cotton by several cationising agents in order to improve its dyeability. The influence of the main dyeing conditions (dye bath pH, dyeing time, dyeing temperature, salt addition) on the performances of this dyeing process were studied. The dyeing performances of this process were appreciated by measuring the colour yield (K/S) and the fastness properties of the dyed samples. The effect of mordant type with different mordanting methods on dyeing quality was also studied. The results showed that mordanting gave deeper shades and enhanced fastness properties. In addition, environmental indicators (BOD 5 , COD and COD/BOD 5 ) were used to describe potential improvements in the biodegradability of the dyebath wastewater. Further, HPLC was used to identify the major phenolic compounds in the extracted dye.

  13. Modeling the efficiency of Förster resonant energy transfer from energy relay dyes in dye-sensitized solar cells

    KAUST Repository

    Hoke, Eric T.

    2010-02-11

    Förster resonant energy transfer can improve the spectral breadth, absorption and energy conversion efficiency of dye sensitized solar cells. In this design, unattached relay dyes absorb the high energy photons and transfer the excitation to sensitizing dye molecules by Förster resonant energy transfer. We use an analytic theory to calculate the excitation transfer efficiency from the relay dye to the sensitizing dye accounting for dynamic quenching and relay dye diffusion. We present calculations for pores of cylindrical and spherical geometry and examine the effects of the Förster radius, the pore size, sensitizing dye surface concentration, collisional quenching rate, and relay dye lifetime. We find that the excitation transfer efficiency can easily exceed 90% for appropriately chosen dyes and propose two different strategies for selecting dyes to achieve record power conversion efficiencies. © 2010 Optical Society of America.

  14. HPV18 Persistence Impairs Basal and DNA Ligand-Mediated IFN-β and IFN-λ1 Production through Transcriptional Repression of Multiple Downstream Effectors of Pattern Recognition Receptor Signaling.

    Science.gov (United States)

    Albertini, Silvia; Lo Cigno, Irene; Calati, Federica; De Andrea, Marco; Borgogna, Cinzia; Dell'Oste, Valentina; Landolfo, Santo; Gariglio, Marisa

    2018-03-15

    Although it is clear that high-risk human papillomaviruses (HPVs) can selectively infect keratinocytes and persist in the host, it still remains to be unequivocally determined whether they can escape antiviral innate immunity by interfering with pattern recognition receptor (PRR) signaling. In this study, we have assessed the innate immune response in monolayer and organotypic raft cultures of NIKS cells harboring multiple copies of episomal HPV18 (NIKSmcHPV18), which fully recapitulates the persistent state of infection. We show for the first time, to our knowledge, that NIKSmcHPV18, as well as HeLa cells (a cervical carcinoma-derived cell line harboring integrated HPV18 DNA), display marked downregulation of several PRRs, as well as other PRR downstream effectors, such as the adaptor protein stimulator of IFN genes and the transcription factors IRF1 and 7. Importantly, we provide evidence that downregulation of stimulator of IFN genes, cyclic GMP-AMP synthase, and retinoic acid-inducible gene I mRNA levels occurs at the transcriptional level through a novel epigenetic silencing mechanism, as documented by the accumulation of repressive heterochromatin markers seen at the promoter region of these genes. Furthermore, stimulation of NIKSmcHPV18 cells with salmon sperm DNA or poly(deoxyadenylic-deoxythymidylic) acid, two potent inducers of PRR signaling, only partially restored PRR protein expression. Accordingly, the production of IFN-β and IFN-λ 1 was significantly reduced in comparison with the parental NIKS cells, indicating that HPV18 exerts its immunosuppressive activity through downregulation of PRR signaling. Altogether, our findings indicate that high-risk human papillomaviruses have evolved broad-spectrum mechanisms that allow simultaneous depletion of multiple effectors of the innate immunity network, thereby creating an unreactive cellular milieu suitable for viral persistence. Copyright © 2018 by The American Association of Immunologists, Inc.

  15. Amino Acid-Assisted Incorporation of Dye Molecules within Calcite Crystals.

    Science.gov (United States)

    Marzec, Bartosz; Green, David C; Holden, Mark A; Coté, Alexander S; Ihli, Johannes; Khalid, Saba; Kulak, Alexander; Walker, Daniel; Tang, Chiu; Duffy, Dorothy M; Kim, Yi-Yeoun; Meldrum, Fiona C

    2018-05-23

    Biomineralisation processes invariably occur in the presence of multiple organic additives, which act in combination to give exceptional control over structures and properties. However, few synthetic studies have investigated the cooperative effects of soluble additives. This work addresses this challenge and focuses on the combined effects of amino acids and coloured dye molecules. The experiments demonstrate that strongly coloured calcite crystals only form in the presence of Brilliant Blue R (BBR) and four of the seventeen soluble amino acids, as compared with almost colourless crystals using the dye alone. The active amino acids are identified as those which themselves effectively occlude in calcite, suggesting a mechanism where they can act as chaperones for individual molecules or even aggregates of dyes molecules. These results provide new insight into crystal-additive interactions and suggest a novel strategy for generating materials with target properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Multiple phosphorylation sites at the C-terminus regulate nuclear import of HCMV DNA polymerase processivity factor ppUL44

    International Nuclear Information System (INIS)

    Alvisi, Gualtiero; Marin, Oriano; Pari, Gregory; Mancini, Manuela; Avanzi, Simone; Loregian, Arianna; Jans, David A.; Ripalti, Alessandro

    2011-01-01

    The processivity factor of human cytomegalovirus DNA polymerase, phosphoprotein ppUL44, is essential for viral replication. During viral infection ppUL44 is phosphorylated by the viral kinase pUL97, but neither the target residues on ppUL44 nor the effect of phosphorylation on ppUL44's activity are known. We report here that ppUL44 is phosphorylated when transiently expressed in mammalian cells and coimmunoprecipitates with cellular kinases. Of three potential phosphorylation sites (S413, S415, S418) located upstream of ppUL44's nuclear localization signal (NLS) and one (T427) within the NLS itself, protein kinase CK2 (CK2) specifically phosphorylates S413, to trigger a cascade of phosphorylation of S418 and S415 by CK1 and CK2, respectively. Negative charge at the CK2/CK1 target serine residues facilitates optimal nuclear accumulation of ppUL44, whereas negative charge on T427, a potential cyclin-dependent 1 phosphorylation site, strongly decreases nuclear accumulation. Thus, nuclear transport of ppUL44 is finely tuned during viral infection through complex phosphorylation events.

  17. DNA fingerprinting of Shiga-toxin producing Escherichia coli O157 based on Multiple-Locus Variable-Number Tandem-Repeats Analysis (MLVA

    Directory of Open Access Journals (Sweden)

    Vardund Traute

    2003-12-01

    Full Text Available Abstract Background The ability to react early to possible outbreaks of Escherichia coli O157:H7 and to trace possible sources relies on the availability of highly discriminatory and reliable techniques. The development of methods that are fast and has the potential for complete automation is needed for this important pathogen. Methods In all 73 isolates of shiga-toxin producing E. coli O157 (STEC were used in this study. The two available fully sequenced STEC genomes were scanned for tandem repeated stretches of DNA, which were evaluated as polymorphic markers for isolate identification. Results The 73 E. coli isolates displayed 47 distinct patterns and the MLVA assay was capable of high discrimination between the E. coli O157 strains. The assay was fast and all the steps can be automated. Conclusion The findings demonstrate a novel high discriminatory molecular typing method for the important pathogen E. coli O157 that is fast, robust and offers many advantages compared to current methods.

  18. Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa.

    Science.gov (United States)

    Li, Lin-Feng; Häkkinen, Markku; Yuan, Yong-Ming; Hao, Gang; Ge, Xue-Jun

    2010-10-01

    Musaceae is a small paleotropical family. Three genera have been recognised within this family although the generic delimitations remain controversial. Most species of the family (around 65 species) have been placed under the genus Musa and its infrageneric classification has long been disputed. In this study, we obtained nuclear ribosomal ITS and chloroplast (atpB-rbcL, rps16, and trnL-F) DNA sequences of 36 species (42 accessions of ingroups representing three genera) together with 10 accessions of ingroups retrieved from GenBank database and 4 accessions of outgroups, to construct the phylogeny of the family, with a special reference to the infrageneric classification of the genus Musa. Our phylogenetic analyses elaborated previous results in supporting the monophyly of the family and suggested that Musella and Ensete may be congeneric or at least closely related, but refuted the previous infrageneric classification of Musa. None of the five sections of Musa previously defined based on morphology was recovered as monophyletic group in the molecular phylogeny. Two infrageneric clades were identified, which corresponded well to the basic chromosome numbers of x=11 and 10/9/7, respectively: the former clade comprises species from the sections Musa and Rhodochlamys while the latter contains sections of Callimusa, Australimusa, and Ingentimusa. Copyright 2010 Elsevier Inc. All rights reserved.

  19. Development of species-specific rDNA probes for Giardia by multiple fluorescent in situ hybridization combined with immunocytochemical identification of cyst wall antigens.

    Science.gov (United States)

    Erlandsen, Stanley L; Jarroll, Edward; Wallis, Peter; van Keulen, Harry

    2005-08-01

    In this study, we describe the development of fluorescent oligonucleotide probes to variable regions in the small subunit of 16S rRNA in three distinct Giardia species. Sense and antisense probes (17-22 mer) to variable regions 1, 3, and 8 were labeled with digoxygenin or selected fluorochomes (FluorX, Cy3, or Cy5). Optimal results were obtained with fluorochome-labeled oligonucleotides for detection of rRNA in Giardia cysts. Specificity of fluorescent in situ hybridization (FISH) was shown using RNase digestion and high stringency to diminish the hybridization signal, and oligonucleotide probes for rRNA in Giardia lamblia, Giardia muris, and Giardia ardeae were shown to specifically stain rRNA only within cysts or trophozoites of those species. The fluorescent oligonucleotide specific for rRNA in human isolates of Giardia was positive for ten different strains. A method for simultaneous FISH detection of cysts using fluorescent antibody (genotype marker) and two oligonucleotide probes (species marker) permitted visualization of G. lamblia and G. muris cysts in the same preparation. Testing of an environmental water sample revealed the presence of FISH-positive G. lamblia cysts with a specific rDNA probe for rRNA, while negative cysts were presumed to be of animal or bird origin.

  20. Phytoremediation in education: textile dye teaching experiments.

    Science.gov (United States)

    Ibbini, Jwan H; Davis, Lawrence C; Erickson, Larry E

    2009-07-01

    Phytoremediation, the use of plants to clean up contaminated soil and water, has a wide range of applications and advantages, and can be extended to scientific education. Phytoremediation of textile dyes can be used as a scientific experiment or demonstration in teaching laboratories of middle school, high school and college students. In the experiments that we developed, students were involved in a hands-on activity where they were able to learn about phytoremediation concepts. Experiments were set up with 20-40 mg L(-1) dye solutions of different colors. Students can be involved in the set up process and may be involved in the experimental design. In its simplest forms, they use two-week-old sunflower seedlings and place them into a test tube of known volume of dye solution. Color change and/or dye disappearance can be monitored by visual comparison or with a spectrophotometer. Intensity and extent of the lab work depends on student's educational level, and time constraints. Among the many dyes tested, Evan's Blue proved to be the most readily decolorized azo dye. Results could be observed within 1-2 hours. From our experience, dye phytoremediation experiments are suitable and easy to understand by both college and middle school students. These experiments help visual learners, as students compare the color of the dye solution before and after the plant application. In general, simple phytoremediation experiments of this kind can be introduced in many classes including biology, biochemistry and ecological engineering. This paper presents success stories of teaching phytoremediation to middle school and college students.

  1. Stability of the elderberry dye in vodkas

    International Nuclear Information System (INIS)

    Pizlo, A.; Jankowska, D.

    2001-01-01

    The effect of light, pH, strength of vodkas and by-products on Sambucus nigra pigments stability was tested in this paper. The elderberry dye was unstable in vodkas during light action in general. It was stated that low strength of vodkas and high pH effected an increase of the vodkas colour stability. The presence of vitamin C caused discolouring effect on elderberry dye but chockeberry distillate effected an increase of the vodkas colour stability

  2. Decolorization of six synthetic dyes by fungi

    OpenAIRE

    Hartikainen, E. Samuel; Miettinen, Otto; Hatakka, Annele; Kähkönen, Mika A.

    2016-01-01

    To find out ability of fourteen basidiomycetes and four ascomycetes strains to grow in the presence of synthetic colour dyes and to degrade them, fungi were cultivated on the malt agar plates containing 0.5 g kg-1 dye, either Remazol Brilliant Blue R, Remazol Brilliant Yellow GL, Remazol Brilliant Orange 3 R, Reactive Blue 4, Remazol Brilliant Red F3B or Reactive Black 5. Fungi representing basidiomycetes were Phlebia radiata (FBCC 43), Tremella encephala (FBCC 1145), Dichomitus squalens (FBC...

  3. Radiolysis of anthraquinone dyes in aqueous solutions

    International Nuclear Information System (INIS)

    Vysotskaya, N.A.; Bortun, L.N.; Ogurtsov, N.A.; Migdalovich, E.A.; Revina, A.A.; Volodko, V.V.; AN SSSR, Moscow. Inst. Ehlektrokhimii)

    1986-01-01

    The commercial anthraquinone dyes (Dark Blue, Light Blue, Green) in aqueous solutions were shown to be decoloured and degrade under the action of ionizing radiation. The degree of decolouration and degradation of aromatic rings was found to increase in presence of oxygen. Hydroxyl radicals were shown to play the key role in the degradation of the dyes under irradiation. The radiolysis intermediate products were studied using the pulse radiolysis technique. (author)

  4. Ultrasensitive FRET-based DNA sensor using PNA/DNA hybridization.

    Science.gov (United States)

    Yang, Lan-Hee; Ahn, Dong June; Koo, Eunhae

    2016-12-01

    In the diagnosis of genetic diseases, rapid and highly sensitive DNA detection is crucial. Therefore, many strategies for detecting target DNA have been developed, including electrical, optical, and mechanical methods. Herein, a highly sensitive FRET based sensor was developed by using PNA (Peptide Nucleic Acid) probe and QD, in which red color QDs are hybridized with capture probes, reporter probes and target DNAs by EDC-NHS coupling. The hybridized probe with target DNA gives off fluorescent signal due to the energy transfer from QD to Cy5 dye in the reporter probe. Compared to the conventional DNA sensor using DNA probes, the DNA sensor using PNA probes shows higher FRET factor and efficiency due to the higher reactivity between PNA and target DNA. In addition, to elicit the effect of the distance between the donor and the acceptor, we have investigated two types of the reporter probes having Cy5 dyes attached at the different positions of the reporter probes. Results show that the shorter the distance between QDs and Cy5s, the stronger the signal intensity. Furthermore, based on the fluorescence microscopy images using microcapillary chips, the FRET signal is enhanced to be up to 276% times stronger than the signal obtained using the cuvette by the fluorescence spectrometer. These results suggest that the PNA probe system conjugated with QDs can be used as ultrasensitive DNA nanosensors. Copyright © 2016. Published by Elsevier B.V.

  5. First Principle Modelling of Materials and Processes in Dye-Sensitized Photoanodes for Solar Energy and Solar Fuels

    Directory of Open Access Journals (Sweden)

    Mariachiara Pastore

    2017-01-01

    Full Text Available In the context of solar energy exploitation, dye-sensitized solar cells and dye-sensitized photoelectrosynthetic cells offer the promise of low-cost sunlight conversion and storage, respectively. In this perspective we discuss the main successes and limitations of modern computational methodologies, ranging from hybrid and long-range corrected density functionals, GW approaches and multi-reference perturbation theories, in describing the electronic and optical properties of isolated components and complex interfaces relevant to these devices. While computational modelling has had a crucial role in the development of the dye-sensitized solar cells technology, the theoretical characterization of the interface structure and interfacial processes in water splitting devices is still at its infancy, especially concerning the electron and hole transfer phenomena. Quantitative analysis of interfacial charge separation and recombination reactions in multiple metal-oxide/dye/catalyst heterointerfaces, thus, undoubtedly represents the compelling challenge in the field of modern computational material science.

  6. A multilevel reuse system with source separation process for printing and dyeing wastewater treatment: A case study.

    Science.gov (United States)

    Wang, Rui; Jin, Xin; Wang, Ziyuan; Gu, Wantao; Wei, Zhechao; Huang, Yuanjie; Qiu, Zhuang; Jin, Pengkang

    2018-01-01

    This paper proposes a new system of multilevel reuse with source separation in printing and dyeing wastewater (PDWW) treatment in order to dramatically improve the water reuse rate to 35%. By analysing the characteristics of the sources and concentrations of pollutants produced in different printing and dyeing processes, special, highly, and less contaminated wastewaters (SCW, HCW, and LCW, respectively) were collected and treated separately. Specially, a large quantity of LCW was sequentially reused at multiple levels to meet the water quality requirements for different production processes. Based on this concept, a multilevel reuse system with a source separation process was established in a typical printing and dyeing enterprise. The water reuse rate increased dramatically to 62%, and the reclaimed water was reused in different printing and dyeing processes based on the water quality. This study provides promising leads in water management for wastewater reclamation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Treatment of dyeing drainage by radiation

    International Nuclear Information System (INIS)

    Shimokawa, Toshinari; Sawai, Takeshi

    1985-01-01

    Decolorization of artificial dyeing drainage and sewage by radiation treatment. Artifical dyeing drainage was prepared from water, polyvinyl alcohol, starch, urea and several kinds of inorganic salts, and artificial sewage, from water, peptone, broth, urea and several kinds of inorganic salts. The above mentioned sample liquors of artificial dyeing drainage and sewage were exposed to γ-radiation of 5 kCi of 60 Co source by aerating through a ball filter. Absorption spectra, total organic carbon (TOC) and chemical oxygen demand (COD) were determined after irradiation to evaluate radiation treatment effect. With the experimental data obtained, it was clarified that absorbance, COD and TOC was decreased with the increase of absorbed dose. Decoloring was made effectively and about 95 % of bleaching ratio was obtained at 5 kGy of radiation. COD was decreased also by irradiation rather slower decreasing rate than that of decolorization, and TOC decrease was very slow at the initial stage of radiation but 40 % of TOC was decomposed by 10 kGy radiation. Dye of chemically stable structure was found more resistant to radiation decolorization. Decomposition efficiency was found less for dyes in the artificial sewage but secondary treated sewage showed no adverse effect. With the obtained understandings, a tentative scheme was planned for the radiation decolorization of dyeing drainage after aeration treatment. (Takagi, S.)

  8. Degradation of textile dyes by cyanobacteria.

    Science.gov (United States)

    Dellamatrice, Priscila Maria; Silva-Stenico, Maria Estela; Moraes, Luiz Alberto Beraldo de; Fiore, Marli Fátima; Monteiro, Regina Teresa Rosim

    Dyes are recalcitrant compounds that resist conventional biological treatments. The degradation of three textile dyes (Indigo, RBBR and Sulphur Black), and the dye-containing liquid effluent and solid waste from the Municipal Treatment Station, Americana, São Paulo, Brazil, by the cyanobacteria Anabaena flos-aquae UTCC64, Phormidium autumnale UTEX1580 and Synechococcus sp. PCC7942 was evaluated. The dye degradation efficiency of the cyanobacteria was compared with anaerobic and anaerobic-aerobic systems in terms of discolouration and toxicity evaluations. The discoloration was evaluated by absorption spectroscopy. Toxicity was measured using the organisms Hydra attenuata, the alga Selenastrum capricornutum and lettuce seeds. The three cyanobacteria showed the potential to remediate textile effluent by removing the colour and reducing the toxicity. However, the growth of cyanobacteria on sludge was slow and discoloration was not efficient. The cyanobacteria P. autumnale UTEX1580 was the only strain that completely degraded the indigo dye. An evaluation of the mutagenicity potential was performed by use of the micronucleus assay using Allium sp. No mutagenicity was observed after the treatment. Two metabolites were produced during the degradation, anthranilic acid and isatin, but toxicity did not increase after the treatment. The cyanobacteria showed the ability to degrade the dyes present in a textile effluent; therefore, they can be used in a tertiary treatment of effluents with recalcitrant compounds. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  9. Adsorption of dyes onto activated carbon cloth: using QSPRs as tools to approach adsorption mechanisms.

    Science.gov (United States)

    Metivier-Pignon, Hélène; Faur, Catherine; Le Cloirec, Pierre

    2007-01-01

    The present study aimed to investigate the adsorption of dyes onto activated carbon cloths. Kinetics and isotherms were studied based on results of batch reactors to constitute databases for the adsorption rates and capacities of 22 commercial dyes. Added to a qualitative analysis of experimental results, quantitative structure property relationships (QSPRs) were used to determine the structural features that influence most adsorption processes. QSPRs consisted of multiple linear regressions correlating adsorption parameters with molecular connectivity indices (MCIs) as molecular descriptors. Results related to adsorption kinetics showed that the size of molecules was the significant feature, the high order MCIs involved in QSPRs indicating the influence of a critical size on adsorption rate. Improved statistical fits were obtained when the database was divided according to the chemical classes of dyes. As regards to adsorption isotherms, their particular form led to the use of saturation capacity as the adsorption parameter. By contrast with adsorption kinetics, molecular overcrowding seemed to be of less influence on adsorption equilibrium. In this case, MCIs included in the QSPR were more related to details of the molecular structure. The robustness of the QSPR assessed for azo dyes was studied for the other dyes. Although the small size of the database limited predictive ability, features relevant to the influence of the database composition on QSPRs have been highlighted.

  10. Excited-state properties from ground-state DFT descriptors: A QSPR approach for dyes.

    Science.gov (United States)

    Fayet, Guillaume; Jacquemin, Denis; Wathelet, Valérie; Perpète, Eric A; Rotureau, Patricia; Adamo, Carlo

    2010-02-26

    This work presents a quantitative structure-property relationship (QSPR)-based approach allowing an accurate prediction of the excited-state properties of organic dyes (anthraquinones and azobenzenes) from ground-state molecular descriptors, obtained within the (conceptual) density functional theory (DFT) framework. The ab initio computation of the descriptors was achieved at several levels of theory, so that the influence of the basis set size as well as of the modeling of environmental effects could be statistically quantified. It turns out that, for the entire data set, a statistically-robust four-variable multiple linear regression based on PCM-PBE0/6-31G calculations delivers a R(adj)(2) of 0.93 associated to predictive errors allowing for rapid and efficient dye design. All the selected descriptors are independent of the dye's family, an advantage over previously designed QSPR schemes. On top of that, the obtained accuracy is comparable to the one of the today's reference methods while exceeding the one of hardness-based fittings. QSPR relationships specific to both families of dyes have also been built up. This work paves the way towards reliable and computationally affordable color design for organic dyes. Copyright 2009 Elsevier Inc. All rights reserved.

  11. USEBILITY OF HYDROGELS IN ADSORPTION TECHNOLOGHY FOR REMOVAL OF HEAVY METAL AND DYE

    Directory of Open Access Journals (Sweden)

    AÇIKEL Safiye Meriç

    2016-05-01

    Full Text Available Heavy metals and Dyes are very toxic and nonbiodegradable in waste waters to cause adverse health effects in human body and to induce irreversible pollution. Adsorption offers many potential advantages for removal of toxic heavy metals being flexibility in design and operation, high-quality treated effluent, reversible nature for multiple uses, and many commercially available adsorbent materials, such as activated carbon, zeolite, clay, sawdust, bark, biomass, lignin, chitosan and other polymer adsorbents. Compared to conventional adsorbent materials above, hydrogelbased adsorbents recently have attracted special attention to their highly potential for effective removal of heavy metals and dyes. Hydrogels are named “Hydrophilic Polymer” because of care for water. Hydrogels is not solved in water; however they have been swollen to their balance volume. Because of this swell behavior, they can adsorb big quantity of water in this structure. So they can term of “three sized polymers” due to protect their existing shape [9]. Hydrogels with porous structures and chemically-responsive functional groups, enable to readily capture metal ions and dyes from wastewater. Hydrogels with porous structures and chemically-responsive functional groups, enable to readily capture metal ions and dyes from wastewater. In adsorption applications, hydrogels are used in water purification, heavy metal/dying removing, controlled fertilizer released, ion exchange applications, chromatographic applications, dilute extractions, waste water treatments. This article general inform about usage of hydrogels in Dye and Heavy Metal adsorption.

  12. Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA using boric acid-functionalized nano-microsphere fluorescent probes.

    Science.gov (United States)

    Chen, Hua-Yan; Wei, Jing-Ru; Pan, Jiong-Xiu; Zhang, Wei; Dang, Fu-Quan; Zhang, Zhi-Qi; Zhang, Jing

    2017-05-15

    5-hydroxymethylcytosine (5hmC) is the sixth base of DNA. It is involved in active DNA demethylation and can be a marker of diseases such as cancer. In this study, we developed a simple and sensitive 2-(4-boronophenyl)quinoline-4-carboxylic acid modified poly (glycidyl methacrylate (PBAQA-PGMA) fluorescent probe to detect the 5hmC content of genomic DNA based on T4 β-glucosyltransferase-catalyzed glucosylation of 5hmC. The fluorescence-enhanced intensity recorded from the DNA sample was proportional to its 5-hydroxymethylcytosine content and could be quantified by fluorescence spectrophotometry. The developed probe showed good detection sensitivity and selectivity and a good linear relationship between the fluorescence intensity and the concentration of 5 hmC within a 0-100nM range. Compared with other fluorescence detection methods, this method not only could determine trace amounts of 5 hmC from genomic DNA but also could eliminate the interference of fluorescent dyes and the need for purification. It also could avoid multiple labeling. Because the PBAQA-PGMA probe could enrich the content of glycosyl-5-hydroxymethyl-2-deoxycytidine from a complex ground substance, it will broaden the linear detection range and improve sensitivity. The limit of detection was calculated to be 0.167nM after enrichment. Furthermore, the method was successfully used to detect 5-hydroxymethylcytosine from mouse tissues. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Chlorine disinfection of dye wastewater: Implications for a commercial azo dye mixture

    Energy Technology Data Exchange (ETDEWEB)

    Vacchi, Francine Inforcato; Albuquerque, Anjaina Fernandes; Vendemiatti, Josiane Aparecida; Morales, Daniel Alexandre [Faculdade de Tecnologia, Universidade Estadual de Campinas, Limeira, SP, 13484-332 (Brazil); Ormond, Alexandra B.; Freeman, Harold S. [Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, NC 27695-8301 (United States); Zocolo, Guilherme Juliao; Zanoni, Maria Valnice Boldrin [Departamento de Quimica Analitica, Universidade Estadual Paulista Julio de Mesquita Filho, Instituto de Quimica de Araraquara, Araraquara, SP 14801-970 (Brazil); Umbuzeiro, Gisela, E-mail: giselau@ft.unicamp.br [Faculdade de Tecnologia, Universidade Estadual de Campinas, Limeira, SP, 13484-332 (Brazil)

    2013-01-01

    Azo dyes, the most widely used family of synthetic dyes, are often employed as colorants in areas such as textiles, plastics, foods/drugs/cosmetics, and electronics. Following their use in industrial applications, azo dyes have been found in effluents and various receiving waters. Chemical treatment of effluents containing azo dyes includes disinfection using chlorine, which can generate compounds of varying eco/genotoxicity. Among the widely known commercial azo dyes for synthetic fibers is C.I. Disperse Red 1. While this dye is known to exist as a complex mixture, reports of eco/genotoxicity involve the purified form. Bearing in mind the potential for adverse synergistic effects arising from exposures to chemical mixtures, the aim of the present study was to characterize the components of commercial Disperse Red 1 and its chlorine-mediated decoloration products and to evaluate their ecotoxicity and mutagenicity. In conducting the present study, Disperse Red 1 was treated with chlorine gas, and the solution obtained was analyzed with the aid of LC-ESI-MS/MS to identify the components present, and then evaluated for ecotoxicity and mutagenicity, using Daphnia similis and Salmonella/microsome assays, respectively. The results of this study indicated that chlorination of Disperse Red 1 produced four chlorinated aromatic compounds as the main products and that the degradation products were more ecotoxic than the parent dye. These results suggest that a disinfection process using chlorine should be avoided for effluents containing hydrophobic azo dyes such commercial Disperse Red 1. -- Highlights: Black-Right-Pointing-Pointer Aqueous solutions of Disperse Red 1 were treated with chlorine. Black-Right-Pointing-Pointer The chlorination products of Disperse Red 1 were identified using LC-ESI-MS/MS. Black-Right-Pointing-Pointer Daphnia and Salmonella/microsome were employed for eco/genotoxicity testing. Black-Right-Pointing-Pointer The chlorinated dye was more mutagenic

  14. Optical properties of natural dyes on the dye-sensitized solar cells (DSSC) performance

    International Nuclear Information System (INIS)

    Pratiwi, D. D.; Nurosyid, F.; Supriyanto, A.; Suryana, R.

    2016-01-01

    This study reported several natural dyes for application in dye-sensitized solar cells (DSSC). This study aims was to determine the effect of optical absorption properties of natural dyes on efficiency of DSSC. The sandwich structure of DSSC consist of TiO 2 as working electrode, carbon layer as counter electrode, natural dyes as photosensitizer, and electrolyte as electron transfer media. The natural dyes used in this experiment were extracted from dragon fruit anthocyanin, mangosteen peels anthocyanin, and red cabbage anthocyanin. The absorbance of dyes solutions and the adsorption of the dye on the surface of TiO 2 were characterized using UV-Vis spectrophotometer, the quantum efficiency versus wavelength was characterized using incident photon-to-current efficiency (IPCE) measurement system, and the efficiency of DSSC was calculated using I-V meter. UV-Vis characteristic curves showed that wavelength absorption of anthocyanin dye of red cabbage was 450 - 580 nm, anthocyanin of mangosteen peels was 400 - 480 nm, and anthocyanin of dragon fruit was 400 - 650 nm. Absorption spectra of the dye adsorption on the surface of TiO 2 which was resulted in the highest absorbance of red cabbage anthocyanin. IPCE characteristic curves with anthocyanin dye of red cabbage, mangosteen peels anthocyanin, and dragon fruit anthocyanin resulted quantum efficiency of 0.058%; 0.047%; and 0.043%, respectively at wavelength maximum about 430 nm. I-V characteristic curves with anthocyanin dye of red cabbage, mangosteen peels anthocyanin, and dragon fruit anthocyanin resulted efficiency of 0.054%; 0.042%; and 0.024%, respectively. (paper)

  15. Chlorine disinfection of dye wastewater: Implications for a commercial azo dye mixture

    International Nuclear Information System (INIS)

    Vacchi, Francine Inforçato; Albuquerque, Anjaina Fernandes; Vendemiatti, Josiane Aparecida; Morales, Daniel Alexandre; Ormond, Alexandra B.; Freeman, Harold S.; Zocolo, Guilherme Julião; Zanoni, Maria Valnice Boldrin; Umbuzeiro, Gisela

    2013-01-01

    Azo dyes, the most widely used family of synthetic dyes, are often employed as colorants in areas such as textiles, plastics, foods/drugs/cosmetics, and electronics. Following their use in industrial applications, azo dyes have been found in effluents and various receiving waters. Chemical treatment of effluents containing azo dyes includes disinfection using chlorine, which can generate compounds of varying eco/genotoxicity. Among the widely known commercial azo dyes for synthetic fibers is C.I. Disperse Red 1. While this dye is known to exist as a complex mixture, reports of eco/genotoxicity involve the purified form. Bearing in mind the potential for adverse synergistic effects arising from exposures to chemical mixtures, the aim of the present study was to characterize the components of commercial Disperse Red 1 and its chlorine-mediated decoloration products and to evaluate their ecotoxicity and mutagenicity. In conducting the present study, Disperse Red 1 was treated with chlorine gas, and the solution obtained was analyzed with the aid of LC–ESI-MS/MS to identify the components present, and then evaluated for ecotoxicity and mutagenicity, using Daphnia similis and Salmonella/microsome assays, respectively. The results of this study indicated that chlorination of Disperse Red 1 produced four chlorinated aromatic compounds as the main products and that the degradation products were more ecotoxic than the parent dye. These results suggest that a disinfection process using chlorine should be avoided for effluents containing hydrophobic azo dyes such commercial Disperse Red 1. -- Highlights: ► Aqueous solutions of Disperse Red 1 were treated with chlorine. ► The chlorination products of Disperse Red 1 were identified using LC–ESI-MS/MS. ► Daphnia and Salmonella/microsome were employed for eco/genotoxicity testing. ► The chlorinated dye was more mutagenic than the dye itself. ► Chlorination should be avoided in effluents containing azo-dyes.

  16. A comparative study on the interaction of phenazinium dyes with low pH induced protonated structure and B-form structure of naturally occurring deoxyribonucleic acid

    International Nuclear Information System (INIS)

    Pradhan, Ankur Bikash; Das, Shubhajit; Haque, Lucy; Bhuiya, Sutanwi; Das, Suman

    2016-01-01

    The interaction of two phenazinium dyes namely Phenosafranine (PSF) and Safranin T (ST) with right-handed B-form and left-handed protonated form of Calf Thymus (CT) DNA was investigated using different spectroscopic techniques. Both the dyes have been shown to bind strongly to the right-handed B-form of DNA by the mechanism intercalation as revealed from fluorescence quenching, circular dichroism (CD) and viscosity measurement. From circular dichroic studies it was evidenced that both of them convert the low pH induced left-handed protonated form of DNA back to the bound right-handed form. Scatchard analysis showed that both the dyes bound strongly to B-form of DNA in a non-cooperative manner. In case of protonated form, there was sequential conversion of the polynucleotide from left-handed to the bound right-handed conformation. Our results suggest that the binding environment of the dyes in the two forms of DNA is similar and our data predict that PSF is more effective in the conversion than ST. Experimental data enabled the calculation of the number of base pairs of protonated-form that adopted a right-handed conformation for each bound dye. Our data revealed that PSF is more effective in the conversion compard to that of ST. These results are attributed to greater steric crowd in ST compared to PSF which restricts the former to intercalate between DNA base pairs. The results of these studies allow a better understanding of dye-polymorphic nucleic acid interactions at a molecular level.

  17. Glacial vicariance in the Pacific Northwest: evidence from a lodgepole pine mitochondrial DNA minisatellite for multiple genetically distinct and widely separated refugia.

    Science.gov (United States)

    Godbout, Julie; Fazekas, Aron; Newton, Craig H; Yeh, Francis C; Bousquet, Jean

    2008-05-01

    The Canadian side of the Pacific Northwest was almost entirely covered by ice during the last glacial maximum, which has induced vicariance and genetic population structure for several plant and animal taxa. Lodgepole pine (Pinus contorta Dougl. ex. Loud.) has a wide latitudinal and longitudinal distribution in the Pacific Northwest. Our main objective was to identify relictual signatures of glacial vicariance in the population structure of the species and search for evidence of distinct glacial refugia in the Pacific Northwest. A maternally inherited mitochondrial DNA minisatellite-like marker was used to decipher haplotype diversity in 91 populations of lodgepole pine located across the natural range. Overall population differentiation was sizeable (G(ST) = 0.365 and R(ST) = 0.568). Four relatively homogeneous groups of populations, possibly representative of as many genetically distinct glacial populations, were identified for the two main subspecies, ssp. latifolia and ssp. contorta. For ssp. contorta, one glacial lineage is suggested to have been located at high latitudes and possibly off the coast of mainland British Columbia (BC), while the other is considered to have been located south of the ice sheet along the Pacific coast. For ssp. latifolia, two genetically distinct glacial populations probably occurred south of the ice sheet: in the area bounded by the Cascades and Rocky Mountains ranges, and on the eastern side of the Rockies. A possible fifth refugium located in the Yukon may have also been present for ssp. latifolia. Zones of contact between these ancestral lineages were also apparent in interior and northern BC. These results indicate the role of the Queen Charlotte Islands and the Alexander Archipelago as a refugial zone for some Pacific Northwest species and the vicariant role played by the Cascades and the American Rocky Mountains during glaciation.

  18. Rehydrating dye sensitized solar cells

    Directory of Open Access Journals (Sweden)

    Christian Hellert

    2017-05-01

    Full Text Available Dye sensitized solar cells (DSSCs are silicon free, simply producible solar cells. Longevity, however, is a longstanding problem for DSSCs. Due to liquid electrolytes being commonly used, evaporation of the electrolyte causes a dramatic drop in electric output as cells continue to be used unmaintained. Stopping evaporation has been tried in different ways in the past, albeit with differing degrees of success. In a recent project, a different route was chosen, exploring ways of revitalizing DSSCs after varying periods of usage. For this, we focused on rehydration of the cells using distilled water as well as the electrolyte contained in the cells. The results show a significant influence of these rehydration procedures on the solar cell efficiency. In possible applications of DSSCs in tents etc., morning dew may thus be used for rehydration of solar cells. Refillable DSSCs can also be used in tropical climates or specific types of farms and greenhouses where high humidity serves the purpose of rehydrating DSSCs.

  19. DYEING COTTON WITH EISENIA BICYCLIS AS NATURAL DYE USING DIFFERENT BIOMORDANTS

    Directory of Open Access Journals (Sweden)

    BONET Mª Ángeles

    2015-05-01

    Full Text Available Natural dyes are known for their use in coloring of food substrate, leather as well as natural protein fibers like wool, silk and cotton as major areas of application since pre-historic times. Nowadays, there has been revival of the growing interest on the application of natural dyes on natural fibers due to worldwide environmental consciousness. Some researchers focus their studies on the improvement of these dyes using mordants. Most works use metallic mordants like aluminum or iron are used, but some of them are hazardous. In this work we used a biomordant to solve environmental problems caused by metallic mordants. The effects of chitosan weight molecular in mordanting on the dyeing characteristics and the UV protection property were examined in this study. Chitosan mordanted Eisenia Bicyclis dyed cotton showed better dyeing characteristic and higher UV protection property compared with undyed cotton fabric. To analyze the differences of the dyeing, reflection spectrophotometer was used, evaluating the results of CIELAB color difference values and the strength color (in terms of K/S value. We conclude that the type of chitosan used affect the dyeing efficiency and the UV protection, showing different behavior between dye sample using chitosan with low or medium molecular weight.

  20. Organic dye for highly efficient solid-state dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt-Mende, L.; Bach, U.; Humphry-Baker, R.; Ito, S.; Graetzel, M. [Institut des Sciences et Ingenierie Chimiques (ISIC), Laboratoire de Photonique et Interfaces (LPI), Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Horiuchi, T.; Miura, H. [Technology Research Laboratory, Corporate Research Center, Mitsubishi Paper Mills Limited, 46, Wadai, Tsukuba City, Ibaraki 300-4247 (Japan); Uchida, S. [Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 1-1 Katahira 2-chome, Aoba-ku, Sendai 980-8577 (Japan)

    2005-04-04

    The feasibility of solid-state dye-sensitized solar cells as a low-cost alternative to amorphous silicon cells is demonstrated. Such a cell with a record efficiency of over 4 % under simulated sunlight is reported, made possible by using a new organic metal-free indoline dye as the sensitizer with high absorption coefficient. (Abstract Copyright [2005], Wiley Periodicals, Inc.)

  1. Isolation and screening of azo dye decolorizing bacterial isolates from dye-contaminated textile wastewater

    Directory of Open Access Journals (Sweden)

    Shahid Mahmood

    2011-04-01

    Full Text Available Azo dyes are released into wastewater streams without any pretreatment and pollute water and soilenvironments. To prevent contamination of our vulnerable resources, removal of these dye pollutants is of greatimportance. For this purpose, wastewater samples were collected from dye-contaminated sites of Faisalabad. About200 bacterial isolates were isolated through enrichment and then tested for their potential to remove RemazolBlack-B azo dye in liquid medium. Five bacterial isolates capable of degrading Remazol Black-B azo dye efficientlywere screened through experimentation on modified mineral salt medium. Isolate SS1 (collected from wastewater ofSupreme Textile Industry was able to completely remove the Remazol Black-B dye from the liquid medium in 18 h.Further, the isolate showed the best performance at the dye concentration of 100 mg L-1 medium (pH 7 and attemperature 35oC. Similarly, yeast extract proved to be the best carbon source for decolorization purpose. Theresults imply that the isolate SS1 could be used for the removal of the reactive dyes from textile effluents.

  2. Optical fiber taste sensors using potential sensitive dye coatings. Makuden'i kanjusei shikisomaku wo mochiita hikari fiber mikaku sensor

    Energy Technology Data Exchange (ETDEWEB)

    Yamakawa, S.; Yamaguchi, A. (Toyama National College of Maritime Technology, Toyama (Japan))

    1992-12-20

    The present paper proposes a new taste recognition system using optical response patterns from multi-channel optical fiber sensors having potential sensitive dye coatings. It was found that the sensors give large changes in optical absorption spectra of the dyes when they are immersed in various taste solutions. Consequently, it was shown that the sensors can be used as a taste sensor. Six dyes, which give large changes in dye absorption, were selected from twenty dyes and used for six-channel optical fiber taste sensors array. The absorption spectra change data were processed by multiple discriminant analysis and neural networks using back-propagation algorithm. From the analytical results, it was demonstrated that salty (NaCl), bitter (quinidine), sweet (sucrose), sour (HCl), and umami (sodium glutamate) substances can be recognized from each other by using the optical taste sensor system. 11 refs., 8 figs., 2 tabs.

  3. Bioremediation of coractive blue dye by using Pseudomonas spp. isolated from the textile dye wastewater

    Science.gov (United States)

    Sunar, N. M.; Mon, Z. K.; Rahim, N. A.; Leman, A. M.; Airish, N. A. M.; Khalid, A.; Ali, R.; Zaidi, E.; Azhar, A. T. S.

    2018-04-01

    Wastewater released from the textile industry contains variety substances, mainly dyes that contains a high concentration of color and organic. In this study the potential for bacterial decolorization of coractive blue dye was examined that isolated from textile wastewater. The optimum conditions were determined for pH, temperature and initial concentration of the dye. The bacteria isolated was Pseudomonas spp. The selected bacterium shows high decolorization in static condition at an optimum of pH 7.0. The Pseudomonas spp. could decolorize coractive blue dye by 70% within 24 h under static condition, with the optimum of pH 7.0. Decolorization was confirmed by using UV-VIS spectrophotometer. This present study suggests the potential of Pseudomonas spp. as an approach in sustainable bioremediation that provide an efficient method for decolorizing coractive blue dye.

  4. Raman spectroscopy for DNA quantification in cell nucleus.

    Science.gov (United States)

    Okotrub, K A; Surovtsev, N V; Semeshin, V F; Omelyanchuk, L V

    2015-01-01

    Here we demonstrate the feasibility of a novel approach to quantify DNA in cell nuclei. This approach is based on spectroscopy analysis of Raman light scattering, and avoids the problem of nonstoichiometric binding of dyes to DNA, as it directly measures the signal from DNA. Quantitative analysis of nuclear DNA contribution to Raman spectrum could be reliably performed using intensity of a phosphate mode at 1096 cm(-1) . When compared to the known DNA standards from cells of different animals, our results matched those values at error of 10%. We therefore suggest that this approach will be useful to expand the list of DNA standards, to properly adjust the duration of hydrolysis in Feulgen staining, to assay the applicability of fuchsines for DNA quantification, as well as to measure DNA content in cells with complex hydrolysis patterns, when Feulgen densitometry is inappropriate. © 2014 International Society for Advancement of Cytometry.

  5. Quantification of DNA damage by single-cell electrophoresis

    International Nuclear Information System (INIS)

    Ikushima, Takaji

    1990-01-01

    A simple technique of micro-agarose gel electrophoresis has been developed to quantify DNA damage in individual cells. Cells are embedded in agarose gel on microscope slides, lysed by detergents and then electrophoresed for a short time under neutral or alkaline condition. In irradiated cells, DNA migrates from the nucleus toward the anode, displaying commet-like pattern by staining with DNA-specific fluorescence dye. DNA damage is evaluated by measuring the distance of DNA migration. The technique was applied for measuring DNA damage in single cells exposed to 60 Co γ-rays, or to KUR radiation in the presence or absence of 10 B-enriched boric acid. The enhanced production of double-stranded DNA breaks by 10 B(n,α) 7 Li reaction was demonstrated here. The significant increase in the length of DNA migration was observed in single cells exposed to such a low dose as 20 cGy after alkaline micro electrophoresis. (author)

  6. Synchronization of DNA array replication kinetics

    Science.gov (United States)

    Manturov, Alexey O.; Grigoryev, Anton V.

    2016-04-01

    In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

  7. Chromed Leather Dyeing Peculiarities when Deliming with Peracetic Acid

    OpenAIRE

    Kęstutis BELEŠKA; Virgilijus VALEIKA; Justa ŠIRVAITYTĖ; Violeta VALEIKIENĖ

    2013-01-01

    The research was aimed to investigate the influence of deliming with peracetic acid on leather dyeing kinetics. Hydrophobic C.I. Acid Red 213 and hydrophilic C.I. Acid Red 423 dyes were used. Sorption of dye depends on hydrophobicity/hydrophility of dye and dyeing temperature. Equilibrium of process is reached faster using hydrophobic C.I. Acid Red 213 at 45 ºC. However, both control and experimental leather fibres adsorb more hydrophilic dye C.I. Acid Red 423 and this fact does not depend on...

  8. The effect of dendrimer on cotton dyeability with direct dyes

    Directory of Open Access Journals (Sweden)

    Khakzar Bafrooei F.

    2014-01-01

    Full Text Available Pretreatment of cotton fabric with poly(propylene imine dendrimer enhanced its colour strength using C.I. Direct Red 81 and C.I. Direct Blue 78. Application of this dendrimer and the direct dye simultaneously on cotton fabric by the exhaust and the continuous dyeing method were studied; slight improvements in the dyeing results were obtained. Pretreatment of the cotton fabric with dendrimer in an emulsion form using the pad-dry method followed by continuous dyeing markedly increased the colour strength. In addition, level dyeing was obtained, and no negative effects on the fastness properties of the dyes used were observed.

  9. Diffusion dynamics in micro-fluidic dye lasers

    DEFF Research Database (Denmark)

    Gersborg-Hansen, Morten; Balslev, Søren; Mortensen, Niels Asger

    2007-01-01

    We have investigated the bleaching dynamics that occur in opto-fluidic dye lasers, where the liquid laser dye in a channel is locally bleached due to optical pumping. Our studies suggest that for micro-fluidic devices, the dye bleaching may be compensated through diffusion of dye molecules alone....... By relying on diffusion rather than convection to generate the necessary dye replenishment, our observation potentially allows for a significant simplification of opto-fluidic dye laser device layouts, omitting the need for cumbersome and costly external fluidic handling or on-chip micro-fluidic pumping...

  10. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  11. Biofunctionalization of zinc oxide nanowires for DNA sensory applications

    Directory of Open Access Journals (Sweden)

    Rudolph Bettina

    2011-01-01

    Full Text Available Abstract We report on the biofunctionalization of zinc oxide nanowires for the attachment of DNA target molecules on the nanowire surface. With the organosilane glycidyloxypropyltrimethoxysilane acting as a bifunctional linker, amino-modified capture molecule oligonucleotides have been immobilized on the nanowire surface. The dye-marked DNA molecules were detected via fluorescence microscopy, and our results reveal a successful attachment of DNA capture molecules onto the nanowire surface. The electrical field effect induced by the negatively charged attached DNA molecules should be able to control the electrical properties of the nanowires and gives way to a ZnO nanowire-based biosensing device.

  12. Physical and chemical investigations on natural dyes

    Science.gov (United States)

    Acquaviva, S.; D'Anna, E.; de Giorgi, M. L.; Della Patria, A.; Baraldi, P.

    2010-09-01

    Natural dyes have been used extensively in the past for many purposes, such us to colour fibers and to produce inks, watercolours and paints, but their use declined rapidly after the discovery of synthetic colours. Nowadays we witness a renewed interest, as natural dyes are neither toxic nor polluting. In this work, physical and chemical properties of four selected dyes, namely red (Madder), yellow (Weld and Turmeric) and blue (Woad) colours, produced by means of traditional techniques at the Museo dei Colori Naturali (Lamoli, Italy), have been investigated. The chromatic properties have been studied through the reflectance spectroscopy, a non-invasive technique for the characterisation of chromaticity. Reflection spectra both from powders and egg-yolk tempera models have been acquired to provide the typical features of the dyes in the UV-vis spectral range. Moreover, to assess the feasibility of laser cleaning procedures, tempera layers were investigated after irradiation with an excimer laser. Micro Raman spectroscopy, Scanning Electron Microscopy and Energy Dispersive X-Ray analyses have complemented the survey, returning compositional and morphological information as well. Efforts have been made to give scientific feedback to the production processes and to support the research activity in the restoration of the artworks where these dyes were employed.

  13. My journey to DNA repair.

    Science.gov (United States)

    Lindahl, Tomas

    2013-02-01

    I completed my medical studies at the Karolinska Institute in Stockholm but have always been devoted to basic research. My longstanding interest is to understand fundamental DNA repair mechanisms in the fields of cancer therapy, inherited human genetic disorders and ancient DNA. I initially measured DNA decay, including rates of base loss and cytosine deamination. I have discovered several important DNA repair proteins and determined their mechanisms of action. The discovery of uracil-DNA glycosylase defined a new category of repair enzymes with each specialized for different types of DNA damage. The base excision repair pathway was first reconstituted with human proteins in my group. Cell-free analysis for mammalian nucleotide excision repair of DNA was also developed in my laboratory. I found multiple distinct DNA ligases in mammalian cells, and led the first genetic and biochemical work on DNA ligases I, III and IV. I discovered the mammalian exonucleases DNase III (TREX1) and IV (FEN1). Interestingly, expression of TREX1 was altered in some human autoimmune diseases. I also showed that the mutagenic DNA adduct O(6)-methylguanine (O(6)mG) is repaired without removing the guanine from DNA, identifying a surprising mechanism by which the methyl group is transferred to a residue in the repair protein itself. A further novel process of DNA repair discovered by my research group is the action of AlkB as an iron-dependent enzyme carrying out oxidative demethylation. Copyright © 2013. Production and hosting by Elsevier Ltd.

  14. Chromed Leather Dyeing Peculiarities when Deliming with Peracetic Acid

    Directory of Open Access Journals (Sweden)

    Kęstutis BELEŠKA

    2013-05-01

    Full Text Available The research was aimed to investigate the influence of deliming with peracetic acid on leather dyeing kinetics. Hydrophobic C.I. Acid Red 213 and hydrophilic C.I. Acid Red 423 dyes were used. Sorption of dye depends on hydrophobicity/hydrophility of dye and dyeing temperature. Equilibrium of process is reached faster using hydrophobic C.I. Acid Red 213 at 45 ºC. However, both control and experimental leather fibres adsorb more hydrophilic dye C.I. Acid Red 423 and this fact does not depend on temperature. The diffusion coefficient of dye C.I. Acid Red 423 calculated according to Weisz model is higher when dyeing conventional leather. The change of deliming method has influence on chromed leather dyeing but this influence is not significant. The adsorption ability of control leather fibres at 30 ºC and 45 ºC is higher using both dyes as compared to the dyeing the experimental one. The increase of dyeing temperature increases the adsorption ability independently on the sort of leather fibres. Such dependence of the adsorption ability on the temperature shows that hydrophobic action and van der Waals forces prevail between dye and fibres during dyeing process. The Gibbs energy changes show that adsorption of both dyes by leather fibres independently on their sort is a spontaneous process. The affinity of both dyes to conventional leather fibres is higher comparing with experimental one. The change of enthalpy is positive in all cases, and it means that the driving force of the dyeing is the change of entropy.DOI: http://dx.doi.org/10.5755/j01.ms.19.2.4431

  15. Radiation Degradation of some Commercial Dyes in Wastewater

    International Nuclear Information System (INIS)

    Dessouki, A.M.; Abdel-Aal, S.E.

    1999-01-01

    The degradation Kinetic due to irradiation of aqueous solutions of some commercial dyes, (Reactive Blue Brilliant, Reactive Yellow and Basic Blue 9 Dye (Methylene Blue 2 B), was studied. Factors affecting radiolysis of the dye such as dye concentration, irradiation dose, dose rate and ph of the solutions were studied. The effects of different additives such as nitrogen oxygen, hydrogen peroxide and sodium hypochlorite on the degradation process were investigated. The effect of irradiation dose on the different dye solutions at various concentrations, showed that the Reactive Yellow G. was very sensitive to gamma radiation. The effect of the ph of the dye solutions proved to very according type of the dye. Synergistic treatment of the dye solutions by irradiation and conventional method showed that saturation of the dye solutions with nitrogen did not enhance the radiation degradation of the dyes, while addition of oxygen resulted in a remarkable enhancement of the degradation of the dyes. Also, the addition of sodium hypochlorite (5%) and the oxidation by hydrogen peroxide resulted in more radiation degradation, Also, adsorption of the dyes onto Ga and some ion exchangers showed that Ga has the highest adsorption capacity. Radiation degradation of the toxic dye pollutants and their removal from wastewater down to concentrations not exceeding the maximum permissible concentration (Mpc) according to international standards, proved to be better than conventional methods of purification alone

  16. Quantum dot-dye hybrid systems for energy transfer applications

    International Nuclear Information System (INIS)

    Ren, Ting

    2010-01-01

    In this thesis, we focus on the preparation of energy transfer-based quantum dot (QD)-dye hybrid systems. Two kinds of QD-dye hybrid systems have been successfully synthesized: QD-silica-dye and QD-dye hybrid systems. In the QD-silica-dye hybrid system, multishell CdSe/CdS/ZnS QDs were adsorbed onto monodisperse Stoeber silica particles with an outer silica shell of thickness 2-24 nm containing organic dye molecules (Texas Red). The thickness of this dye layer has a strong effect on the total sensitized acceptor emission, which is explained by the increase in the number of dye molecules homogeneously distributed within the silica shell, in combination with an enhanced surface adsorption of QDs with increasing dye amount. Our conclusions were underlined by comparison of the experimental results with Monte-Carlo simulations, and by control experiments confirming attractive interactions between QDs and Texas Red freely dissolved in solution. New QD-dye hybrid system consisting of multishell QDs and organic perylene dyes have been synthesized. We developed a versatile approach to assemble extraordinarily stable QD-dye hybrids, which uses dicarboxylate anchors to bind rylene dyes to QD. This system yields a good basis to study the energy transfer between QD and dye because of its simple and compact design: there is no third kind of molecule linking QD and dye; no spacer; and the affinity of the functional group to the QD surface is strong. The FRET signal was measured for these complexes as a function of both dye to QD ratio and center-to-center distance between QD and dye by controlling number of covered ZnS layers. Data showed that fluorescence resonance energy transfer (FRET) was the dominant mechanism of the energy transfer in our QD-dye hybrid system. FRET efficiency can be controlled by not only adjusting the number of dyes on the QD surface or the QD to dye distance, but also properly choosing different dye and QD components. Due to the strong stability, our QD-dye

  17. Quantum dot-dye hybrid systems for energy transfer applications

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Ting

    2010-07-01

    In this thesis, we focus on the preparation of energy transfer-based quantum dot (QD)-dye hybrid systems. Two kinds of QD-dye hybrid systems have been successfully synthesized: QD-silica-dye and QD-dye hybrid systems. In the QD-silica-dye hybrid system, multishell CdSe/CdS/ZnS QDs were adsorbed onto monodisperse Stoeber silica particles with an outer silica shell of thickness 2-24 nm containing organic dye molecules (Texas Red). The thickness of this dye layer has a strong effect on the total sensitized acceptor emission, which is explained by the increase in the number of dye molecules homogeneously distributed within the silica shell, in combination with an enhanced surface adsorption of QDs with increasing dye amount. Our conclusions were underlined by comparison of the experimental results with Monte-Carlo simulations, and by control experiments confirming attractive interactions between QDs and Texas Red freely dissolved in solution. New QD-dye hybrid system consisting of multishell QDs and organic perylene dyes have been synthesized. We developed a versatile approach to assemble extraordinarily stable QD-dye hybrids, which uses dicarboxylate anchors to bind rylene dyes to QD. This system yields a good basis to study the energy transfer between QD and dye because of its simple and compact design: there is no third kind of molecule linking QD and dye; no spacer; and the affinity of the functional group to the QD surface is strong. The FRET signal was measured for these complexes as a function of both dye to QD ratio and center-to-center distance between QD and dye by controlling number of covered ZnS layers. Data showed that fluorescence resonance energy transfer (FRET) was the dominant mechanism of the energy transfer in our QD-dye hybrid system. FRET efficiency can be controlled by not only adjusting the number of dyes on the QD surface or the QD to dye distance, but also properly choosing different dye and QD components. Due to the strong stability, our QD-dye

  18. Effect of Mixing Dyes and Solvent in Electrolyte Toward Characterization of Dye Sensitized Solar Cell Using Natural Dyes as The Sensitizer

    Science.gov (United States)

    Puspitasari, Nurrisma; Nurul Amalia, Silviyanti S.; Yudoyono, Gatut; Endarko

    2017-07-01

    Dye Sensitized Solar Cell (DSSC) using natural dyes (chlorophyll, curcumin from turmeric extract, and anthocyanin from mangosteen extract) have been successfully fabricated for determining the effect of variation natural dyes, mixing dyes and acetonitrile in electrolyte toward characterization of DSSC. DSSC consists of five parts namely ITO (Indium Tin Oxide) as a substrate; TiO2 as semiconductor materials; natural dyes as an electron donor; electrolyte as electron transfer; and carbon as a catalyst that can convert light energy into electric energy. Two types of gel electrolyte based on PEG that mixed with liquid electrolyte have utilized for analyzing the lifetime of DSSC. Type I used distilled water as a solvent whilst type II used acetonitrile as a solvent with addition of concentration of KI and iodine. The main purpose of study was to investigate influence of solvent in electrolyte, variation of natural dyes and mixing dyes toward an efficiency that resulted by DSSC. The result showed that electrolyte type II is generally better than type I with efficiency 0,0556 and 0,0456 %, respectively. An efficiency values which resulted from a variation of mixed three natural dyes showed the greatest efficiency compared to mixed two natural dyes and one dye, with an efficiency value can be achieved at 0,0194 % for chlorophyll; 0,111 % for turmeric; 0,0105 % for mangosteen; 0,0244% (mangosteen and chlorophyll); 0,0117 % (turmeric and mangosteen); 0,0158 % (turmeric and chlorophyll); and 0.0566 % (mixed three natural dyes).

  19. Colorimetric Nucleic Acid Detection on Paper Microchip Using Loop Mediated Isothermal Amplification and Crystal Violet Dye.

    Science.gov (United States)

    Roy, Sharmili; Mohd-Naim, Noor Faizah; Safavieh, Mohammadali; Ahmed, Minhaz Uddin

    2017-11-22

    Nucleic acid detection is of paramount importance in monitoring of microbial pathogens in food safety and infectious disease diagnostic applications. To address these challenges, a rapid, cost-effective label-free technique for nucleic acid detection with minimal instrumentations is highly desired. Here, we present paper microchip to detect and quantify nucleic acid using colorimetric sensing modality. The extracted DNA from food samples of meat as well as microbial pathogens was amplified utilizing loop-mediated isothermal amplification (LAMP). LAMP amplicon was then detected and quantified on a paper microchip fabricated in a cellulose paper and a small wax chamber utilizing crystal violet dye. The affinity of crystal violet dye toward dsDNA and positive signal were identified by changing the color from colorless to purple. Using this method, detection of Sus scrofa (porcine) and Bacillus subtilis (bacteria) DNA was possible at concentrations as low as 1 pg/μL (3.43 × 10 -1 copies/μL) and 10 pg/μL (2.2 × 10 3 copies/μL), respectively. This strategy can be adapted for detection of other DNA samples, with potential for development of a new breed of simple and inexpensive paper microchip at the point-of-need.

  20. Synthesis, characterization and dyeing assessment of novel acid azo dyes and mordent acid azo dyes based on 2-hydroxy-4-methoxybenzophenone on wool and silk fabrics

    Directory of Open Access Journals (Sweden)

    DHIRUBHAI J. DESAI

    2010-05-01

    Full Text Available Novel acid mono azo and mordent acid mono azo dyes were synthesised by the coupling of diazonium salt solution of different aromatic amines with 2-hydroxy-4-methoxybenzophenone. The resulting dyes were characterized by spectral techniques, i.e., elemental analysis, IR, 1H-NMR and UV–visible spectroscopy. The dyeing performance of all the dyes was evaluated on wool and silk fabrics. The dyeing of chrome pre-treated wool and silk fabrics showed better hues on mordented fabrics. Dyeing of wool and silk fabrics resulted in pinkish blue to red shades with very good depth and levelness. The dyed fabrics showed excellent to very good light, washing, perspiration, sublimation and rubbing fastness. The results of antibacterial studies of chrome pre-treated fabrics revealed that the toxicity of mordented dyes against Escherichia coli, Staphylococcus aureus, Salmonella typhi, Bacillus subtilis bacteria was fairly good.

  1. Mesoporous multi-shelled ZnO microspheres for the scattering layer of dye sensitized solar cell with a high efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Weiwei; Mei, Chao; Zeng, Xianghua, E-mail: xhzeng@yzu.edu.cn; Wu, Guoqing; Shen, Xiaoshuang [College of Physics Science and Technology and Institute of Optoelectronic Technology, Yangzhou University, Yangzhou 225002 (China); Chang, Shuai [Beijing Key Laboratory of Nanophotonics and Ultrafine Optoelectronic Systems, School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081 (China)

    2016-03-14

    Both light scattering and dye adsorbing are important for the power conversion efficiency PCE performance of dye sensitized solar cell (DSSC). Nanostructured scattering layers with a large specific surface area are regarded as an efficient way to improve the PCE by increasing dye adsorbing, but excess adsorbed dye will hinder light scattering and light penetration. Thus, how to balance the dye adsorbing and light penetration is a key problem to improve the PCE performance. Here, multiple-shelled ZnO microspheres with a mesoporous surface are fabricated by a hydrothermal method and are used as scattering layers on the TiO{sub 2} photoanode of the DSSC in the presence of N719 dye and iodine–based electrolyte, and the results reveal that the DSSCs based on triple shelled ZnO microsphere with a mesoporous surface exhibit an enhanced PCE of 7.66%, which is 13.0% higher than those without the scattering layers (6.78%), indicating that multiple-shelled microspheres with a mesoporous surface can ensure enough light scattering between the shells, and a favorable concentration of the adsorbed dye can improve the light penetration. These results may provide a promising pathway to obtain the high efficient DSSCs.

  2. Plasma dye coating as straightforward and widely applicable procedure for dye immobilization on polymeric materials.

    Science.gov (United States)

    De Smet, Lieselot; Vancoillie, Gertjan; Minshall, Peter; Lava, Kathleen; Steyaert, Iline; Schoolaert, Ella; Van De Walle, Elke; Dubruel, Peter; De Clerck, Karen; Hoogenboom, Richard

    2018-03-16

    Here, we introduce a novel concept for the fabrication of colored materials with significantly reduced dye leaching through covalent immobilization of the desired dye using plasma-generated surface radicals. This plasma dye coating (PDC) procedure immobilizes a pre-adsorbed layer of a dye functionalized with a radical sensitive group on the surface through radical addition caused by a short plasma treatment. The non-specific nature of the plasma-generated surface radicals allows for a wide variety of dyes including azobenzenes and sulfonphthaleins, functionalized with radical sensitive groups to avoid significant dye degradation, to be combined with various materials including PP, PE, PA6, cellulose, and PTFE. The wide applicability, low consumption of dye, relatively short procedure time, and the possibility of continuous PDC using an atmospheric plasma reactor make this procedure economically interesting for various applications ranging from simple coloring of a material to the fabrication of chromic sensor fabrics as demonstrated by preparing a range of halochromic materials.

  3. In-situ Decolorization of Residual Dye Effluent in Textile Jet Dyeing Machine by Ozone

    Directory of Open Access Journals (Sweden)

    Irfan Ahmed Shaikh

    2014-12-01

    Full Text Available In this study, a new idea of decolourization was investigated in which residual dyeing effluent from textile dyeing process was treated using O3 in the same machine where it was generated. The novelty comes from the idea of doing dyeing and treatment simultaneously. At the completion of dyeing process, O3 gas was injected directly into the machine to remove colour and COD from the wastewater. To evaluate the effectiveness of new method, pilot-scale studies were performed, and decolourization of residual dyeing effluents containing C.I. Reactive Orange 7, C.I. Reactive Blue 19, and C.I. Reactive Black 5 was carried out in specially built textile jet dyeing machine. The results showed that almost 100% colour removal and 90% COD reduction were achieved when process conditions such as pH, dye concentration (mg/L, ozone production rate (g/hr, and temperature were optimized. The study concludes that new method has a great potential to eliminate the need of a separate end-of-the-pipe wastewater treatment system, thus offering an on-site and cost-effective solution.

  4. Quirks of dye nomenclature. 6. Malachite green.

    Science.gov (United States)

    Cooksey, C J

    2016-08-01

    Malachite green was discovered independently by two researchers in Germany in the 19(th) century and found immediate employment as a dye and a pigment. Subsequently, other uses, such as staining biological specimens, emerged. A much later application was the control of fungal and protozoan infections in fish, for which the dye remains popular, although illegal in many countries owing to a variety of toxicity problems. In solution, malachite green can exist as five different species depending on the pH. The location of the positive charge of the colored cation on a carbon atom or a nitrogen atom is still debated. The original names of this dye, and their origins, are briefly surveyed.

  5. Somatic mutations, allele loss, and DNA methylation of the Cub and Sushi Multiple Domains 1 (CSMD1 gene reveals association with early age of diagnosis in colorectal cancer patients.

    Directory of Open Access Journals (Sweden)

    Austin Y Shull

    Full Text Available The Cub and Sushi Multiple Domains 1 (CSMD1 gene, located on the short arm of chromosome 8, codes for a type I transmembrane protein whose function is currently unknown. CSMD1 expression is frequently lost in many epithelial cancers. Our goal was to characterize the relationships between CSMD1 somatic mutations, allele imbalance, DNA methylation, and the clinical characteristics in colorectal cancer patients.We sequenced the CSMD1 coding regions in 54 colorectal tumors using the 454FLX pyrosequencing platform to interrogate 72 amplicons covering the entire coding sequence. We used heterozygous SNP allele ratios at multiple CSMD1 loci to determine allelic balance and infer loss of heterozygosity. Finally, we performed methylation-specific PCR on 76 colorectal tumors to determine DNA methylation status for CSMD1 and known methylation targets ALX4, RUNX3, NEUROG1, and CDKN2A.Using 454FLX sequencing and confirming with Sanger sequencing, 16 CSMD1 somatic mutations were identified in 6 of the 54 colorectal tumors (11%. The nonsynonymous to synonymous mutation ratio of the 16 somatic mutations was 15:1, a ratio significantly higher than the expected 2:1 ratio (p = 0.014. This ratio indicates a presence of positive selection for mutations in the CSMD1 protein sequence. CSMD1 allelic imbalance was present in 19 of 37 informative cases (56%. Patients with allelic imbalance and CSMD1 mutations were significantly younger (average age, 41 years than those without somatic mutations (average age, 68 years. The majority of tumors were methylated at one or more CpG loci within the CSMD1 coding sequence, and CSMD1 methylation significantly correlated with two known methylation targets ALX4 and RUNX3. C:G>T:A substitutions were significantly overrepresented (47%, suggesting extensive cytosine methylation predisposing to somatic mutations.Deep amplicon sequencing and methylation-specific PCR reveal that CSMD1 alterations can correlate with earlier clinical

  6. DETECTION OF DNA DAMAGE USING A FIBEROPTIC BIOSENSOR

    Science.gov (United States)

    A rapid and sensitive fiber optic biosensor assay for radiation-induced DNA damage is reported. For this assay, a biotin-labeled capture oligonucleotide (38 mer) was immobilized to an avidin-coated quartz fiber. Hybridization of a dye-labeled complementary sequence was observed...

  7. Effectiveness of dye sensitised solar cell under low light condition using wide band dye

    Energy Technology Data Exchange (ETDEWEB)

    Sahmer, Ahmad Zahrin, E-mail: ahmadzsahmer@gmail.com; Mohamed, Norani Muti, E-mail: noranimuti-mohamed@petronas.com.my; Zaine, Siti Nur Azella, E-mail: ct.azella@gmail.com [Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tronoh, Perak (Malaysia)

    2015-07-22

    Dye sensistised solar cell (DSC) based on nanocrystalline TiO{sub 2} has the potential to be used in indoor consumer power application. In realizing this, the DSC must be optimized to generate power under low lighting condition and under wider visible light range. The use of wide band dye N749 which has a wider spectrum sensitivity increases the photon conversion to electron between the visible light spectrums of 390nm to 700nm. This paper reports the study on the effectiveness of the dye solar cell with N749 dye under low light condition in generating usable power which can be used for indoor consumer application. The DSC was fabricated using fluorine doped tin oxide (FTO) glass with screen printing method and the deposited TiO{sub 2} film was sintered at 500°C. The TiO{sub 2} coated FTO glass was then soaked in the N749 dye, assembled into test cell, and tested under the standard test condition at irradiance of 1000 W/m{sup 2} with AM1.5 solar soaker. The use of the 43T mesh for the dual pass screen printing TiO{sub 2} paste gives a uniform TiO{sub 2} film layer of 16 µm. The low light condition was simulated using 1/3 filtered irradiance with the solar soaker. The fabricated DSC test cell with the N749 dye was found to have a higher efficiency of 6.491% under low light condition compared to the N719 dye. Under the standard test condition at 1 sun the N749 test cell efficiency is 4.55%. The increases in efficiency is attributed to the wider spectral capture of photon of the DSC with N749 dye. Furthermore, the use of N749 dye is more effective under low light condition as the V{sub OC} decrement is less significant compared to the latter.

  8. Excimer Pumped Pulsed Tunable Dye Laser

    Science.gov (United States)

    Littman, Michael G.

    1988-06-01

    It has been recently shown and reported for the first time at this meeting, that Excimer pumping of a single-mode, short-cavity, grazing-incidence, longitudinally-pumped pulsed dye laser is feasible. In this paper the key concepts upon which this latest development is based are presented and are in a somewhat unusual form. This manuscript describes five specific dye laser examples. The five examples represent a progression from the simplest type of dye laser to the single-mode version mentioned above. The examples thus serve as a tutorial introduction to potential users of dye lasers. The article is organized into five sections or STEPS, each of which describes a different pulsed dye laser. Since the subtle points about dye lasers are best appreciated only after one actually attempts to build a working model, a PROCEDURES category is included in which details about the construction of the particular form of laser are given. As one reads through this category, think of it as looking over the shoulder of the laser builder. The NOTES category which follows is a brief but essential discussion explaining why various components and procedures are used, as well as how laser performance specifications are obtained. This subsection can he viewed as a discussion with the laser builder concerning the reasons for specific actions and choices made in the assembly of the example laser. The last category contains COMMENTS which provide additional related information pertaining to the example laser that goes beyond the earlier annotated discussion. If you like, these are the narrator's comments. At the end of the article, after the five sequential forms of the laser have been presented, there is a brief summation.

  9. Photophysical and laser characteristics of pyrromethene 567 dye ...

    Indian Academy of Sciences (India)

    Narrow-band laser performance of alcohol solutions of pyrromethene 567 ... curves of each dye solution were obtained by scanning the wavelength of the dye ... solutions, using ethanol and methanol solvents, are summarized in table 1.

  10. Novel Tunable Dye Laser for Lidar Detection, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — A tunable dye laser for Lidar detection will be fabricated based on the innovative dye-doped Holographic Polymer Dispersed Liquid Crystals (HPDLC) technology. The...

  11. Determination of 8 Synthetic Food Dyes by Solid Phase Extraction ...

    African Journals Online (AJOL)

    Keywords: Synthetic colors, Food, Fruit flavored drinks, Solid phase extraction, RP-HPLC. Tropical Journal of ..... food dyes by thin-layer chromatography-fast atom bombardment ... food dyes in soft drinks containing natural pigments by.

  12. Unconsumed precursors and couplers after formation of oxidative hair dyes

    DEFF Research Database (Denmark)

    Rastogi, Suresh Chandra; Søsted, Heidi; Johansen, Jeanne Duus

    2006-01-01

    Contact allergy to hair dye ingredients, especially precursors and couplers, is a well-known entity among consumers having hair colouring done at home or at a hairdresser. The aim of the present investigation was to estimate consumer exposure to some selected precursors (p-phenylenediamine, toluene......-2,5-diamine) and couplers (3-aminophenol, 4-aminophenol, resorcinol) of oxidative hair dyes during and after hair dyeing. Concentrations of unconsumed precursors and couplers in 8 hair dye formulations for non-professional use were investigated, under the conditions reflecting hair dyeing. Oxidative...... hair dye formation in the absence of hair was investigated using 6 products, and 2 products were used for experimental hair dyeing. In both presence and absence of hair, significant amounts of unconsumed precursors and couplers remained in the hair dye formulations after final colour development. Thus...

  13. Optofluidic third order distributed feedback dye laser

    DEFF Research Database (Denmark)

    Gersborg-Hansen, Morten; Kristensen, Anders

    2006-01-01

    which has a refractive index lower than that of the polymer. In combination with a third order DFB grating, formed by the array of nanofluidic channels, this yields a low threshold for lasing. The laser is straightforward to integrate on lab-on-a-chip microsystems where coherent, tunable light......This letter describes the design and operation of a polymer-based third order distributed feedback (DFB) microfluidic dye laser. The device relies on light confinement in a nanostructured polymer film where an array of nanofluidic channels is filled by capillary action with a liquid dye solution...

  14. Dye linked conjugated homopolymers: using conjugated polymer electroluminescence to optically pump porphyrin-dye emission

    DEFF Research Database (Denmark)

    Nielsen, K.T.; Spanggaard, H.; Krebs, Frederik C

    2004-01-01

    . Electroluminescent devices of the homopolymer itself and of the zinc-porphyrin containing polymer were prepared and the nature of the electroluminescence was characterized. The homopolymer segments were found to optically pump the emission of the zinc-porphyrin dye moities. The homopolymer exhibits blue......Zinc-porphyrin dye molecules were incorporated into the backbone of a conjugated polymer material by a method, which allowed for the incorporation of only one zinc-porphyrin dye molecule into the backbone of each conjugated polymer molecule. The electronic properties of the homopolymer were...

  15. Monogenic diseases of DNA repair

    DEFF Research Database (Denmark)

    Keijzers, Guido; Bakula, Daniela; Scheibye-Knudsen, Morten

    2017-01-01

    Maintaining the stability of the genome is essential for all organisms, and it is not surprising that damage to DNA has been proposed as an explanation for multiple chronic diseases.1-5 Conserving a pristine genome is therefore of central importance to our health. To overcome the genotoxic stress...... of a growing number of human diseases. Notably, many of these monogenic DNA-repair disorders display features of accelerated aging, supporting the notion that genome maintenance is a key factor for organismal longevity. This review focuses on the physiological consequences of loss of DNA repair, particularly...... in the context of monogenic DNA-repair diseases....

  16. Design and construction of liquid lasers using organic dyes

    International Nuclear Information System (INIS)

    Hariri, Akbar.

    1984-01-01

    Organic dye solution show great promise of obtaining tunable coherent light over the uv, visible and near infrared portion of spectrum. In this paper we describe various pumping schemes of dye molecules. Design, construction and performance of a pulsed dye laser, transversely pumped by a nitrogen laser and wall-ablation flash lamp-pumped dye lasers are the particular examples which are presented in detail

  17. Studies on the use of power ultrasound in leather dyeing.

    Science.gov (United States)

    Sivakumar, Venkatasubramanian; Rao, Paruchuri Gangadhar

    2003-03-01

    Uses of power ultrasound for acceleration/performing the chemical as well as physical processes are gaining importance. In conventional leather processing, the diffusion of chemicals through the pores of the skin/hide is achieved by the mechanical agitation caused by the paddle or drumming action. In this work, the use of power ultrasound in the dyeing of leather has been studied with the aim to improve the exhaustion of dye for a given processing time, to reduce the dyeing time and to improve the quality of dyed leather. The effect of power ultrasound in the dyeing of full chrome cow crust leather in a stationary condition is compared with dyeing in the absence of ultrasound as a control experiment both in a stationary as well as conventional drumming condition. An ultrasonic cleaner (150 W and 33 kHz) was used for the experiments. Actual power dissipated into the system was calculated from the calorimetric measurement. Experiments were carried out with variation in type of dye, amount of dye offer, temperature and time. The results show that there is a significant improvement in the percentage exhaustion of dye due to the presence of ultrasound, when compared to dyeing in absence of ultrasound. Experiments on equilibrium dye uptake carried out with or without ultrasound suggest that ultrasound help to improve the kinetics of leather dyeing. The results indicate that leathers dyed in presence of ultrasound have higher colour values, better dye penetration and fastness properties compared to control leathers. The physical testing results show that strength properties of the dyed leathers are not affected due to the application of ultrasound under the given process conditions. Apparent diffusion coefficient during the initial stage of dyeing process, both in presence and in absence of ultrasound was calculated. The values show that ultrasound helps in improving the apparent diffusion coefficient more for the difficult dyeing conditions such as in the case of metal

  18. What cost mitochondria? The maintenance of functional mitochondrial DNA within and across generations

    NARCIS (Netherlands)

    Aanen, D.K.; Spelbrink, J.N.; Beekman, M.

    2014-01-01

    The peculiar biology of mitochondrial DNA (mtDNA) potentially has detrimental consequences for organismal health and lifespan. Typically, eukaryotic cells contain multiple mitochondria, each with multiple mtDNA genomes. The high copy number of mtDNA implies that selection on mtDNA functionality is

  19. Simultaneous G-Quadruplex DNA Logic.

    Science.gov (United States)

    Bader, Antoine; Cockroft, Scott L

    2018-04-03

    A fundamental principle of digital computer operation is Boolean logic, where inputs and outputs are described by binary integer voltages. Similarly, inputs and outputs may be processed on the molecular level as exemplified by synthetic circuits that exploit the programmability of DNA base-pairing. Unlike modern computers, which execute large numbers of logic gates in parallel, most implementations of molecular logic have been limited to single computing tasks, or sensing applications. This work reports three G-quadruplex-based logic gates that operate simultaneously in a single reaction vessel. The gates respond to unique Boolean DNA inputs by undergoing topological conversion from duplex to G-quadruplex states that were resolved using a thioflavin T dye and gel electrophoresis. The modular, addressable, and label-free approach could be incorporated into DNA-based sensors, or used for resolving and debugging parallel processes in DNA computing applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Modeling the efficiency of Förster resonant energy transfer from energy relay dyes in dye-sensitized solar cells

    KAUST Repository

    Hoke, Eric T.; Hardin, Brian E.; McGehee, Michael D.

    2010-01-01

    Förster resonant energy transfer can improve the spectral breadth, absorption and energy conversion efficiency of dye sensitized solar cells. In this design, unattached relay dyes absorb the high energy photons and transfer the excitation

  1. PHYSICO-CHEMICAL STUDIES OF DISAZO DYES DERIVED ...

    African Journals Online (AJOL)

    DJFLEX

    with disazo disperse dyes on synthetic polymer-fibres. (Venkataraman, 1974; Otutu et al., 2008). In this present study, the physico-chemical studies of disazo dyes derived from p-aminophenol recently prepared by our research group is described. We also described the kinetics of the dyes on nylon 6 fibre. In another study.

  2. Decolorization of reactive dyes under batch anaerobic condition by ...

    African Journals Online (AJOL)

    However, decolorization was lower for the dye of RB 49 than other two dyes in all concentrations despite 72 h incubation period by mixed anaerobic culture. All of the three dyes correlated with 1st order reaction kinetic with respect to decolorization kinetics. The results of the study demonstrated that high decolorization was ...

  3. Dye-sensitized photopolymerization of N,N ...

    Indian Academy of Sciences (India)

    Unknown

    and a primary radical derived from the reducing agent. This radical initiates the vinyl polymerization. (scheme 1). In scheme 1, D is the dye, 1D the first excited singlet state, 3D the triplet state, DH. • the semi- quinone dye, DH2 the leuco dye, RH the reducing agent and R. • the initiating radical. Similar schemes. 1D → 3D,.

  4. Integrated and sequential anaerobic/aerobic biodegradation of azo dyes

    NARCIS (Netherlands)

    Tan, N.G.C.

    2001-01-01

    Azo dyes constitute a major class of environmental pollutants accounting for 60 to 70% of all dyes and pigments used. These compounds are characterized by aromatic moieties linked together with azo groups (-N=N-). The release of azo dyes into the environment is a concern due to coloration

  5. Biotreatment of anthraquinone dye Drimarene Blue K 2 RL | Siddiqui ...

    African Journals Online (AJOL)

    Drimarene Blue (Db) K2RL is a reactive anthraquinone dye, used extensively in textile industry, due to poor adsorbability to textile fiber; it has a higher exhaustion rate in wastewater. The dye is toxic, carcinogenic, mutagenic and resistant to degradation. Decolorization of this dye was studied in two different systems.

  6. Column studies for biosorption of dyes from aqueous solutions on ...

    African Journals Online (AJOL)

    Biosorption is becoming a promising alternative to replace or supplement the present dye removal processes from dye wastewaters. Based on the results of batch studies on biosorption of the dyes on powdered fungal biomass, Aspergillus niger, an immobilised fungal biomass was used in column studies for removal of four ...

  7. Near-infrared dyes and upconverting phosphors as biomolecule labels and probes

    Science.gov (United States)

    Patonay, Gabor; Strekowski, Lucjan; Nguyen, Diem-Ngoc; Seok, Kim Jun

    2007-02-01

    Near-Infrared (NIR) absorbing chromophores have been used in analytical and bioanalytical chemistry extensively, including for determination of properties of biomolecules, DNA sequencing, immunoassays, capillary electrophoresis (CE) separations, etc. The major analytical advantages of these dyes are low background interference and high molar absorptivities. NIR dyes have additional advantages due to their sensitivity to microenvironmental changes. Spectral changes induced by the microenvironment are not desirable if the labels are used as a simple reporting group, e.g., during a biorecognition reaction. For these applications upconverting phosphors seem to be a better choice. There are several difficulties in utilizing upconverting phosphors as reporting labels. These are: large physical size, no reactive groups and insolubility in aqueous systems. This presentation will discuss how these difficulties can be overcome for bioanalytical and forensic applications. During these studies we also have investigated how to reduce physical size of the phosphor by simple grinding without losing activity and how to attach reactive moiety to the phosphor to covalently bind to the biomolecule of interest. It has to be emphasized that the described approach is not suitable for medical applications and the results of this research are not applicable in medical applications. For bioanalytical and forensic applications upconverting phosphors used as reporting labels have several advantages. They are excited with lasers that are red shifted respective to phosphorescence, resulting in no light scatter issues during detection. Also some phosphors are excited using eye safe lasers. In addition energy transfer to NIR dyes is possible, allowing detection schemes using donor-acceptor pairs. Data is presented to illustrate the feasibility of this phenomenon. If microenvironmental sensitivity is required, then specially designed NIR dyes can be used as acceptor labels. Several novel dyes

  8. Dye Sensitized Solar Cells for Economically Viable Photovoltaic Systems.

    Science.gov (United States)

    Jung, Hyun Suk; Lee, Jung-Kun

    2013-05-16

    TiO2 nanoparticle-based dye sensitized solar cells (DSSCs) have attracted a significant level of scientific and technological interest for their potential as economically viable photovoltaic devices. While DSSCs have multiple benefits such as material abundance, a short energy payback period, constant power output, and compatibility with flexible applications, there are still several challenges that hold back large scale commercialization. Critical factors determining the future of DSSCs involve energy conversion efficiency, long-term stability, and production cost. Continuous advancement of their long-term stability suggests that state-of-the-art DSSCs will operate for over 20 years without a significant decrease in performance. Nevertheless, key questions remain in regards to energy conversion efficiency improvements and material cost reduction. In this Perspective, the present state of the field and the ongoing efforts to address the requirements of DSSCs are summarized with views on the future of DSSCs.

  9. Development of Carbocyanine Dyes for PRMT Inhibition and Imaging

    Science.gov (United States)

    Sinha, Sarmistha Halder; Owens, Eric A.; Feng, You; Yang, Yutao; Xie, Yan; Tu, Yaping; Henary, Maged; Zheng, Yujun George

    2014-01-01

    Summary Protein arginine methylation regulates multiple biological processes. Deregulation of protein arginine methyltransferase (PRMT) activities has been observed in many disease phenotypes. Small molecule probes that target PRMTs with strong affinity and selectivity can be used as valuable tools to dissect biological mechanisms of arginine methylation and establish the role of PRMT proteins in a disease process. In this work, we report synthesis and evaluation of a class of carbocyanine compounds containing indolium, benz[e]indolium or benz[c,d]indolium heterocyclic moieties that bind to the predominant arginine methyltransferase PRMT1 and inhibit its methyltransferase activity at low micromolar potencies. In particular, the developed molecules have long wavelength colorimetric and fluorometric photoactivities, which can be used for optical and near-infrared fluorescence imaging in cells or biological tissues. Together, these new chemical probes have potential application in PRMT studies both as enzyme inhibitors and as fluorescent dyes for microscope imaging. PMID:22749641

  10. Dye-sensitized solar cells with natural dyes extracted from achiote seeds

    Energy Technology Data Exchange (ETDEWEB)

    Gomez-Ortiz, N.M.; Vazquez-Maldonado, I.A.; Azamar-Barrios, J.A.; Oskam, G. [Departamento de Fisica Aplicada, CINVESTAV-IPN, Merida, Yuc. 97310 (Mexico); Perez-Espadas, A.R.; Mena-Rejon, G.J. [Laboratorio de Quimica Organica de Investigacion, Facultad de Quimica, Universidad Autonoma de Yucatan, Merida, Yuc. 97150 (Mexico)

    2010-01-15

    We have explored the application of natural dyes extracted from the seeds of the achiote shrub (Bixa orellana L.) in dye-sensitized solar cells (DSCs). The main pigments are bixin and norbixin, which were obtained by separation and purification from the dark-red extract (annatto). The dyes were characterized using {sup 1}H-NMR, FTIR spectroscopy, and UV-Vis spectrophotometry. Solar cells were prepared using TiO{sub 2} and ZnO nanostructured, mesoporous films and the annatto, bixin, and norbixin as sensitizers. The best results were obtained with bixin-sensitized TiO{sub 2} solar cells with efficiencies of up to 0.53%, illustrating the importance of purification of dyes from natural extracts. (author)

  11. Development auxiliaries for dyeing polyester with disperse dyes at low temperatures

    Science.gov (United States)

    Carrion-Fite, F. J.; Radei, S.

    2017-10-01

    High-molecular weight organic compounds known as carriers are widely used to expedite polyester dyeing at atmospheric pressure at 100 °C. However, carriers are usually poorly biodegradable and can partially plasticize fibres. Also, dyeing at temperatures above 100 °C in the absence of a carrier entails using expensive equipment. In this work, we developed an alternative method for dyeing polyester at temperatures below 100 °C that reduces energy expenses, dispenses with the need to invest in new equipment and avoids the undesirable effects of non-biodegradable carriers. The method uses disperse dyes in a microemulsion containing a low proportion of a non-toxic organic solvent and either of two alternative development auxiliaries (coumarin and o-vanillin) that is prepared with the aid of ultrasound.

  12. Electrophoresis-base dye adsorption into titanium dioxide film for dye sensitized solar cell application

    International Nuclear Information System (INIS)

    Ratno Nuryadi; Zico Alaia Akbar Junior; Lia Aprilia

    2010-01-01

    Dye Sensitized Solar Cell (DSSC) is one of renewable energy sources which has demanded a substitute non renewable energy sources. The most important factor influencing DSSC performance is dye adsorption into semiconductor nano-porous TiO 2 particles. The purpose of this work is to study the effect of dye eosin Y adsorption on DSSC characteristics by an electrophoresis method. As result, Open Circuit Voltage (V oc ) of DSSC increases as the applied voltage of electrophoresis increases. It is also found that the eosin Y absorbance at wavelength of around 500 nm increases when the electrophoresis voltage is increased. These results indicate that electrophoresis process plays an important role in dye adsorption. (author)

  13. Plasmonic properties and enhanced fluorescence of gold and dye-doped silica nanoparticle aggregates

    Science.gov (United States)

    Green, Nathaniel Scott

    The development of metal-enhanced fluorescence has prompted a great interest in augmenting the photophysical properties of fluorescent molecules with noble metal nanostructures. Our research efforts, outlined in this dissertation, focus on augmenting properties of fluorophores by conjugation with gold nanostructures. The project goals are split into two separate efforts; the enhancement in brightness of fluorophores and long distance non-radiative energy transfer between fluorophores. We believe that interacting dye-doped silica nanoparticles with gold nanoparticles can facilitate both of these phenomena. Our primary research interest is focused on optimizing brightness, as this goal should open a path to studying the second goal of non-radiative energy transfer. The two major challenges to this are constructing suitable nanomaterials and functionalizing them to promote plasmonically active complexes. The synthesis of dye-doped layered silica nanoparticles allows for control over the discrete location of the dye and a substrate that can be surface functionalized. Controlling the exact location of the dye is important to create a silica spacer, which promotes productive interactions with metal nanostructures. Furthermore, the synthesis of silica nanoparticles allows for various fluorophores to be studied in similar environments (removing solvent and other chemo-sensitive issues). Functionalizing the surface of silica nanoparticles allows control over the degree of silica and gold nanoparticle aggregation in solution. Heteroaggregation in solution is useful for producing well-aggregated clusters of many gold around a single silica nanoparticle. The dye-doped surface functionalized silica nanoparticles can than be mixed efficiently with gold nanomaterials. Aggregating multiple gold nanospheres around a single dye-doped silica nanoparticle can dramatically increase the fluorescent brightness of the sample via metal-enhanced fluorescence due to increase plasmonic

  14. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  15. Dye-sensitised solar cell (artificial photosynthesis)

    CSIR Research Space (South Africa)

    Le Roux, Lukas J

    2006-02-01

    Full Text Available is the nano- crystalline TiO2dye- sensitised solar cell (DSC), in conjunction with several new concepts, such as nanotechnology and molecular devices. An efficient and low-cost cell can be produced by using simple materials. The production process generates...

  16. Advanced oxidation of acid and reactive dyes

    DEFF Research Database (Denmark)

    Arslan-Alaton, I.; Gursoy, B.H.; Schmidt, Jens Ejbye

    2008-01-01

    M) for 10:hsp sp="0.25" min Fenton treatment at pH 3, resulting in reduced chemical oxygen demand and dissolved organic carbon removal efficiencies; only acetate was detected as a stable dye oxidation end product. During anaerobic digestion, 100, 29% and no inhibition in methane production was observed...

  17. Photochromic dye-sensitized solar cells

    Directory of Open Access Journals (Sweden)

    Noah M. Johnson

    2015-11-01

    Full Text Available We report the fabrication and characterization of photochromic dye sensitized solar cells that possess the ability to change color depending on external lighting conditions. This device can be used as a “smart” window shade that tints, collects the sun's energy, and blocks sunlight when the sun shines, and is completely transparent at night.

  18. Removal of Triphenylmethane Dyes by Bacterial Consortium

    Directory of Open Access Journals (Sweden)

    Jihane Cheriaa

    2012-01-01

    Full Text Available A new consortium of four bacterial isolates (Agrobacterium radiobacter; Bacillus spp.; Sphingomonas paucimobilis, and Aeromonas hydrophila-(CM-4 was used to degrade and to decolorize triphenylmethane dyes. All bacteria were isolated from activated sludge extracted from a wastewater treatment station of a dyeing industry plant. Individual bacterial isolates exhibited a remarkable color-removal capability against crystal violet (50 mg/L and malachite green (50 mg/L dyes within 24 h. Interestingly, the microbial consortium CM-4 shows a high decolorizing percentage for crystal violet and malachite green, respectively, 91% and 99% within 2 h. The rate of chemical oxygen demand (COD removal increases after 24 h, reaching 61.5% and 84.2% for crystal violet and malachite green, respectively. UV-Visible absorption spectra, FTIR analysis and the inspection of bacterial cells growth indicated that color removal by the CM-4 was due to biodegradation. Evaluation of mutagenicity by using Salmonella typhimurium test strains, TA98 and TA100 studies revealed that the degradation of crystal violet and malachite green by CM-4 did not lead to mutagenic products. Altogether, these results demonstrated the usefulness of the bacterial consortium in the treatment of the textile dyes.

  19. Expeditious, mechanochemical synthesis of BODIPY dyes

    Directory of Open Access Journals (Sweden)

    Laramie P. Jameson

    2013-04-01

    Full Text Available BODIPY dyes have been synthesized under solvent-free or essentially solvent-free conditions, within about 5 minutes in an open-to-air setup by using a pestle and mortar, with yields that are comparable to those obtained via traditional routes that typically require reaction times of several hours to days.

  20. Magnetically modified spent grain for dye removal

    Czech Academy of Sciences Publication Activity Database

    Šafařík, Ivo; Horská, Kateřina; Šafaříková, Miroslava

    2011-01-01

    Roč. 53, č. 1 (2011), s. 78-80 ISSN 0733-5210 R&D Projects: GA MŠk OC09052; GA MPO 2A-1TP1/094 Institutional research plan: CEZ:AV0Z60870520 Keywords : Spent grain * Magnetic fluid * Adsorption * Dyes Subject RIV: GM - Food Processing Impact factor: 2.073, year: 2011

  1. Dye-sensitised solar cell (artificial photosynthesis)

    CSIR Research Space (South Africa)

    Le Roux, Lukas J

    2005-07-01

    Full Text Available A novel system that harnesses solar energy is the nano-crystalline TiO dye-sensitised solar cell (DSC), in conjunction with several new concepts, such as nanotechnology and molecular devices. An efficient and low-cost cell can be produced by using...

  2. Holograms made with a pulsed dye laser

    International Nuclear Information System (INIS)

    Fernandez-Guasti, M.; Iturbe-Castillo, D.; Silva-Perez, A.; Gil-Villegas, A.; Gonzalez-Torres, H.; Lopez-Guerrero, R.

    1989-01-01

    We report the obtention of holograms with a nitrogen pumped dye laser, whose source is inherently pulsed. We review the advantages and posibilities of holograms of moving objects which are impossible to make with CW lasers. The lasers used in these experiments were designed and built in the quantum optics laboratory at the Universidad Autonoma Metropolitana-Iztapalapa. (Author)

  3. Electrochemistry and dye-sensitized solar cells

    Czech Academy of Sciences Publication Activity Database

    Kavan, Ladislav

    2017-01-01

    Roč. 2, č. 1 (2017), s. 88-98 ISSN 2451-9103 R&D Projects: GA ČR GA13-07724S Institutional support: RVO:61388955 Keywords : electrochemistry * dye-sensitized cells * photoelectrode Subject RIV: CG - Electrochemistry OBOR OECD: Electrochemistry (dry cells, batteries, fuel cells, corrosion metals, electrolysis)

  4. Pulse radiolysis of anthraquinone dye aqueous solution

    International Nuclear Information System (INIS)

    Perkowski, J.; Gebicki, J.L.; Lubis, R.; Mayer, J.

    1988-01-01

    Pulse radiolysis of argon flushed aqueous solutions of 10 -5 -10 -4 mol dm -3 anthraquinone dye (C.I. Acid Blue 62) gives rise to the transients originated from the reactions of e - aq , OH and H. The rate constants of these reactions are determined. (author)

  5. Nanoimprinted polymer photonic crystal dye lasers

    DEFF Research Database (Denmark)

    Christiansen, Mads Brøkner; Smith, Cameron; Buss, Thomas

    2010-01-01

    Optically pumped polymer photonic crystal band-edge dye lasers are presented. The photonic crystal is a rectangular lattice providing laser feedback as well as an optical resonance for the pump light. The lasers are defined in a thin film of photodefinable Ormocore hybrid polymer, doped...

  6. Traditional Dyeing--An Educational Approach

    Science.gov (United States)

    Alves, H.; Manhita, A.; Dias, C. Barrocas; Ferreira, T.

    2014-01-01

    This paper describes a mini-project developed with 10th grade Portuguese students where, by using an experimental activity involving the use of natural dyes to colour wool, students acquired a better understanding of the concepts and relationship between the colour, the electromagnetic spectrum, and chemical bonding. As demonstrated by the results…

  7. Effect of dye extracting solvents and sensitization time on photovoltaic performance of natural dye sensitized solar cells

    Directory of Open Access Journals (Sweden)

    Md. Khalid Hossain

    Full Text Available In this study, natural dye sensitizer based solar cells were successfully fabricated and photovoltaic performance was measured. Sensitizer (turmeric sources, dye extraction process, and photoanode sensitization time of the fabricated cells were analyzed and optimized. Dry turmeric, verdant turmeric, and powder turmeric were used as dye sources. Five distinct types of solvents were used for extraction of natural dye from turmeric. Dyes were characterized by UV–Vis spectrophotometric analysis. The extracted turmeric dye was used as a sensitizer in the dye sensitized solar cell’s (DSSC photoanode assembly. Nano-crystalline TiO2 was used as a film coating semiconductor material of the photoanode. TiO2 films on ITO glass substrate were prepared by simple doctor blade technique. The influence of the different parameters VOC, JSC, power density, FF, and η% on the photovoltaic characteristics of DSSCs was analyzed. The best energy conversion performance was obtained for 2 h adsorption time of dye on TiO2 nano-porous surface with ethanol extracted dye from dry turmeric. Keywords: DSSC, Natural dye, TiO2 photoanode, Dye extracting solvent, Dye-adsorption time

  8. Application of natural dyes in textile industry and the treatment of dye solutions using electrolytic techniques

    OpenAIRE

    Abouamer, Karima Massaud

    2008-01-01

    This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University, 25/02/2008. Anodic oxidation of a commercial dye, methylene blue (MB), from aqueous solutions using an electrochemical cell is reported. Data are provided on the effects of eight different types of supporting electrolytes, concentration of electrolytes, initial dye concentration, current and electrolytic time on the percentage removal of methylene blue. Anodic oxidation was found to be effect...

  9. Dye-sensitized solar cell using natural dyes extracted from spinach and ipomoea

    Energy Technology Data Exchange (ETDEWEB)

    Chang, H., E-mail: f10381@ntut.edu.t [Department of Mechanical Engineering, National Taipei University of Technology, No. 1. Sec. 3, Chung-Hsiao E. Rd., Taipei 10608, Taiwan (China); Wu, H.M. [Department of Materials Engineering, Tatung University, No. 40, Sec. 3, Jhongshan N. Rd. Jhongshan District, Taipei City 104, Taiwan (China); Chen, T.L. [Department of Industrial Design, National Taipei University of Technology, No. 1, Sec. 3, Chung-Hsiao E. Rd., Taipei 10608, Taiwan (China); Huang, K.D. [Department of Vehicle Engineering, National Taipei University of Technology, No. 1, Sec. 3, Chung-Hsiao E. Rd., Taipei 10608, Taiwan (China); Jwo, C.S. [Department of Energy and Air-Conditioning Refrigeration Engineering, National Taipei University of Technology, No. 1, Sec. 3, Chung-Hsiao E. Rd., Taipei 10608, Taiwan (China); Lo, Y.J. [Department of Mechanical Engineering, National Taipei University of Technology, No. 1. Sec. 3, Chung-Hsiao E. Rd., Taipei 10608, Taiwan (China)

    2010-04-16

    This study used spinach extract, ipomoea leaf extract and their mixed extracts as the natural dyes for a dye-sensitized solar cell (DSSC). Spinach and ipomoea leaves were first placed separately in ethanol and the chlorophyll of these two kinds of plants was extracted to serve as the natural dyes for using in DSSCs. In addition, the self-developed nanofluid synthesis system prepared a TiO{sub 2} nanofluid with an average particle size of 50 nm. Electrophoresis deposition was performed to let the TiO{sub 2} deposit nanoparticles on the indium tin oxide (ITO) conductive glass, forming a TiO{sub 2} thin film with the thickness of 11.61 {mu}m. This TiO{sub 2} thin film underwent sintering at 450 {sup o}C to enhance the compactness of thin film. Finally, the sintered TiO{sub 2} thin film was immersed in the natural dye solutions extracted from spinach and ipomoea leaves, completing the production of the anode of DSSC. This study then further inspected the fill factor, photoelectric conversion efficiency and incident photon current efficiency of the encapsulated DSSC. According to the experimental results of current-voltage curve, the photoelectric conversion efficiency of the DSSCs prepared by natural dyes from ipomoea leaf extract is 0.318% under extraction temperature of 50 {sup o}C and pH value of extraction fluid at 1.0. This paper also investigated the influence of the temperature in the extraction process of this kind of natural dye and the influence of pH value of the dye solution on the UV-VIS patterns absorption spectra of the prepared natural dye solutions, and the influence of these two factors on the photoelectric conversion efficiency of DSSC.

  10. Immobilized laccase mediated dye decolorization and transformation pathway of azo dye acid red 27

    OpenAIRE

    Chhabra, Meenu; Mishra, Saroj; Sreekrishnan, Trichur Ramaswamy

    2015-01-01

    Background Laccases have good potential as bioremediating agents and can be used continuously in the immobilized form like many other enzymes. Methods In the present study, laccase from Cyathus bulleri was immobilized by entrapment in Poly Vinyl Alcohol (PVA) beads cross-linked with either nitrate or boric acid. Immobilized laccase was used for dye decolorization in both batch and continuous mode employing a packed bed column. The products of degradation of dye Acid Red 27 were identified by ...

  11. Pond dyes are Culex mosquito oviposition attractants

    Directory of Open Access Journals (Sweden)

    Natali Ortiz Perea

    2017-05-01

    Full Text Available Background British mosquito population distribution, abundance, species composition and potential for mosquito disease transmission are intimately linked to the physical environment. The presence of ponds and water storage can significantly increase the density of particular mosquito species in the garden. Culex pipiens is the mosquito most commonly found in UK gardens and a potential vector of West Nile Virus WNV, although the current risk of transmission is low. However any factors that significantly change the distribution and population of C. pipiens are likely to impact subsequent risk of disease transmission. Pond dyes are used to control algal growth and improve aesthetics of still water reflecting surrounding planting. However, it is well documented that females of some species of mosquito prefer to lay eggs in dark water and/or containers of different colours and we predict that dyed ponds will be attractive to Culex mosquitoes. Methods Black pond dye was used in oviposition choice tests using wild-caught gravid C. pipiens. Larvae from wild-caught C. pipiens were also reared in the pond dye to determine whether it had any impact on survival. An emergence trap caught any adults that emerged from the water. Water butts (80 L were positioned around university glasshouses and woodland and treated with black pond dye or left undyed. Weekly sampling over a six month period through summer and autumn was performed to quantified numbers of larvae and pupae in each treatment and habitat. Results Gravid female Culex mosquitoes preferred to lay eggs in dyed water. This was highly significant in tests conducted under laboratory conditions and in a semi-field choice test. Despite this, survivorship in black dyed water was significantly reduced compared to undyed water. Seasonal analysis of wild larval and pupal numbers in two habitats with and without dye showed no impact of dye but a significant impact of season and habitat. Mosquitoes were more

  12. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    Science.gov (United States)

    Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S

    2013-06-25

    A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.

  13. Triphenylamine based organic dyes for dye sensitized solar cells: A theoretical approach

    Energy Technology Data Exchange (ETDEWEB)

    Mohankumar, V.; Pandian, Muthu Senthil; Ramasamy, P., E-mail: ramasamyp@ssn.edu.in [SSN Research Centre, SSN College of Engineering, Chennai-603110, Tamilnadu (India)

    2016-05-23

    The geometry, electronic structure and absorption spectra for newly designed triphenylamine based organic dyes were investigated by density functional theory (DFT) and time dependent density functional theory (TD-DFT) with the Becke 3-Parameter-Lee-Yang-parr(B3LYP) functional, where the 6-31G(d,p) basis set was employed. All calculations were performed using the Gaussian 09 software package. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. Ultraviolet–visible (UV–vis) spectrum was simulated by TD-DFT in gas phase. The calculation shows that all of the dyes can potentially be good sensitizers for DSSC. The LUMOs are just above the conduction band of TiO{sub 2} and their HOMOs are under the reduction potential energy of the electrolytes (I{sup −}/I{sub 3}{sup −}) which can facilitate electron transfer from the excited dye to TiO{sub 2} and charge regeneration process after photo oxidation respectively. The simulated absorption spectrum of dyes match with solar spectrum. Frontier molecular orbital results show that among all the three dyes, the “dye 3” can be used as potential sensitizer for DSSC.

  14. Mediator-assisted decolorization and detoxification of textile dyes/dye mixture by Cyathus bulleri laccase.

    Science.gov (United States)

    Chhabra, Meenu; Mishra, Saroj; Sreekrishnan, T R

    2008-12-01

    Laccase from basidiomycete fungus Cyathus bulleri was evaluated for its ability to decolorize a number of reactive and acidic dyes in the presence of natural and synthetic mediators. The extent of decolorization was monitored at different mediator/dye concentrations and incubation time. Among the synthetic mediators, 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) was effective at low mediator/dye ratios and resulted in 80-95% decolorization at rates that varied from 226 +/- 4 nmol min(-1) mg(-1) for Reactive Orange 1 to 1,333 +/- 15 nmol min(-1) mg(-1) for Reactive Red 198. Other synthetic mediators like 1-hydroxybenzotriazole and violuric acid showed both concentration- and time-dependent increases in percent decolorization. Natural mediators like vanillin, on the other hand, were found to be less effective on all the dyes except Reactive Orange 1. Computed rates of decolorization were about twofold lower than that with ABTS. The laccase-ABTS system also led to nearly 80% decolorization for the simulated dye mixture. No clear correlation between laccase activity on the mediator and its ability to decolorize dyes was found, but pH had a significant effect: Optimum pH for decolorization coincided with the optimum pH for mediator oxidation. The treated samples were also evaluated for toxicity in model microbial systems. The laccase-mediator system appears promising for treatment of textile wastewaters.

  15. Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays.

    Science.gov (United States)

    Hou, Sen; Sun, Lili; Wieczorek, Stefan A; Kalwarczyk, Tomasz; Kaminski, Tomasz S; Holyst, Robert

    2014-01-15

    Fluorescent double-stranded DNA (dsDNA) molecules labeled at both ends are commonly produced by annealing of complementary single-stranded DNA (ssDNA) molecules, labeled with fluorescent dyes at the same (3' or 5') end. Because the labeling efficiency of ssDNA is smaller than 100%, the resulting dsDNA have two, one or are without a dye. Existing methods are insufficient to measure the percentage of the doubly-labeled dsDNA component in the fluorescent DNA sample and it is even difficult to distinguish the doubly-labeled DNA component from the singly-labeled component. Accurate measurement of the percentage of such doubly labeled dsDNA component is a critical prerequisite for quantitative biochemical measurements, which has puzzled scientists for decades. We established a fluorescence correlation spectroscopy (FCS) system to measure the percentage of doubly labeled dsDNA (PDL) in the total fluorescent dsDNA pool. The method is based on comparative analysis of the given sample and a reference dsDNA sample prepared by adding certain amount of unlabeled ssDNA into the original ssDNA solution. From FCS autocorrelation functions, we obtain the number of fluorescent dsDNA molecules in the focal volume of the confocal microscope and PDL. We also calculate the labeling efficiency of ssDNA. The method requires minimal amount of material. The samples have the concentration of DNA in the nano-molar/L range and the volume of tens of microliters. We verify our method by using restriction enzyme Hind III to cleave the fluorescent dsDNA. The kinetics of the reaction depends strongly on PDL, a critical parameter for quantitative biochemical measurements. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Electrokinetic acceleration of DNA hybridization in microsystems.

    Science.gov (United States)

    Lei, Kin Fong; Wang, Yun-Hsiang; Chen, Huai-Yi; Sun, Jia-Hong; Cheng, Ji-Yen

    2015-06-01

    In this work, electrokinetic acceleration of DNA hybridization was investigated by different combinations of frequencies and amplitudes of actuating electric signals. Because the frequencies from low to high can induce different kinds of electrokinetic forces, i.e., electroosmotic to electrothermal forces, this work provides an in-depth investigation of electrokinetic enhanced hybridization. Concentric circular Cr/Au microelectrodes of 350 µm in diameter were fabricated on a glass substrate and probe DNA was immobilized on the electrode surface. Target DNA labeled with fluorescent dyes suspending in solution was then applied to the electrode. Different electrokinetic forces were induced by the application of different electric signals to the circular microelectrodes. Local microfluidic vortexes were generated to increase the collision efficiency between the target DNA suspending in solution and probe DNA immobilized on the electrode surface. DNA hybridization on the electrode surface could be accelerated by the electrokinetic forces. The level of hybridization was represented by the fluorescent signal intensity ratio. Results revealed that such 5-min dynamic hybridization increased 4.5 fold of signal intensity ratio as compared to a 1-h static hybridization. Moreover, dynamic hybridization was found to have better differentiation ability between specific and non-specific target DNA. This study provides a strategy to accelerate DNA hybridization in microsystems. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Uniform silica nanoparticles encapsulating two-photon absorbing fluorescent dye

    International Nuclear Information System (INIS)

    Wu Weibing; Liu Chang; Wang Mingliang; Huang Wei; Zhou Shengrui; Jiang Wei; Sun Yueming; Cui Yiping; Xu Chunxinag

    2009-01-01

    We have prepared uniform silica nanoparticles (NPs) doped with a two-photon absorbing zwitterionic hemicyanine dye by reverse microemulsion method. Obvious solvatochromism on the absorption spectra of dye-doped NPs indicates that solvents can partly penetrate into the silica matrix and then affect the ground and excited state of dye molecules. For dye-doped NP suspensions, both one-photon and two-photon excited fluorescence are much stronger and recorded at shorter wavelength compared to those of free dye solutions with comparative overall dye concentration. This behavior is possibly attributed to the restricted twisted intramolecular charge transfer (TICT), which reduces fluorescence quenching when dye molecules are trapped in the silica matrix. Images from two-photon laser scanning fluorescence microscopy demonstrate that the dye-doped silica NPs can be actively uptaken by Hela cells with low cytotoxicity. - Graphical abstract: Water-soluble silica NPs doped with a two-photon absorbing zwitterionic hemicyanine dye were prepared. They were found of enhanced one-photon and two-photon excited fluorescence compared to free dye solutions. Images from two-photon laser scanning fluorescence microscopy demonstrate that the dye-doped silica NPs can be actively uptaken by Hela cells.

  18. Interplay between transparency and efficiency in dye sensitized solar cells.

    Science.gov (United States)

    Tagliaferro, Roberto; Colonna, Daniele; Brown, Thomas M; Reale, Andrea; Di Carlo, Aldo

    2013-02-11

    In this paper we analyze the interplay between transparency and efficiency in dye sensitized solar cells by varying fabrication parameters such as the thickness of the nano-crystalline TiO(2) layer, the dye loading and the dye type. Both transparency and efficiency show a saturation trend when plotted versus dye loading. By introducing the transparency-efficiency plot, we show that the relation between transparency and efficiency is linear and is almost independent on the TiO(2) thickness for a certain thickness range. On the contrary, the relation between transparency and efficiency depends strongly on the type of the dye. Moreover, we show that co-sensitization techniques can be effectively used to access regions of the transparency-efficiency space that are forbidden for single dye sensitization. The relation found between transparency and efficiency (T&E) can be the general guide for optimization of Dye Solar Cells in building integration applications.

  19. Biochemical activity of a fluorescent dye rhodamine 6G: Molecular modeling, electrochemical, spectroscopic and thermodynamic studies.

    Science.gov (United States)

    Al Masum, Abdulla; Chakraborty, Maharudra; Ghosh, Soumen; Laha, Dipranjan; Karmakar, Parimal; Islam, Md Maidul; Mukhopadhyay, Subrata

    2016-11-01

    Interaction of CT DNA with Rhodamine 6G (R6G) has been studied using molecular docking, electrochemical, spectroscopic and thermodynamic methods. From the study, it was illustrated that Rhodamine 6G binds to the minor groove of CT DNA. The binding was cooperative in nature. Circular voltametric study showed significant change in peak current and peak potential due to complexation. All the studies showed that the binding constant was in the order of 10 6 M -1 . Circular dichroic spectra showed significant conformational change on binding and DNA unwind during binding. Thermodynamic study showed that binding was favored by negative enthalpy and positive entropy change. From thermodynamic study it was also observed that several positive and negative free energies played significant role during binding and the unfavorable conformational free energy change was overcame by highly negative hydrophobic and salt dependent free energy changes. The experimental results were further validated using molecular docking study and the effect of structure on binding has been studied theoretically. From docking study it was found that the hydrophobic interaction and hydrogen bonds played a significant role during binding. The dye was absorbed by cell and this phenomenon was studied using fluorescent microscope. Cell survivability test showed that the dye active against Human Breast Cancer cells MDA-MB 468. ROS study showed that the activity is due to the production of reactive oxygen. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. DNA nanotechnology for nanophotonic applications.

    Science.gov (United States)

    Samanta, Anirban; Banerjee, Saswata; Liu, Yan

    2015-02-14

    DNA nanotechnology has touched the epitome of miniaturization by integrating various nanometer size particles with nanometer precision. This enticing bottom-up approach has employed small DNA tiles, large multi-dimensional polymeric structures or more recently DNA origami to organize nanoparticles of different inorganic materials, small organic molecules or macro-biomolecules like proteins, and RNAs into fascinating patterns that are difficult to achieve by other conventional methods. Here, we are especially interested in the self-assembly of nanomaterials that are potentially attractive elements in the burgeoning field of nanophotonics. These materials include plasmonic nanoparticles, quantum dots, fluorescent organic dyes, etc. DNA based self-assembly allows excellent control over distance, orientation and stoichiometry of these nano-elements that helps to engineer intelligent systems that can potentially pave the path for future technology. Many outstanding structures have been fabricated that are capable of fine tuning optical properties, such as fluorescence intensity and lifetime modulation, enhancement of Raman scattering and emergence of circular dichroism responses. Within the limited scope of this review we have tried to give a glimpse of the development of this still nascent but highly promising field to its current status as well as the existing challenges before us.

  1. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  2. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  3. Polyfluorophore Excimers and Exciplexes as FRET Donors in DNA

    Science.gov (United States)

    Teo, Yin Nah; Kool, Eric T.

    2009-01-01

    We describe studies aimed at testing whether oligomeric exciplex- and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Förster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3’ end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Förster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single

  4. Parallel and Multivalued Logic by the Two-Dimensional Photon-Echo Response of a Rhodamine–DNA Complex

    Science.gov (United States)

    2015-01-01

    Implementing parallel and multivalued logic operations at the molecular scale has the potential to improve the miniaturization and efficiency of a new generation of nanoscale computing devices. Two-dimensional photon-echo spectroscopy is capable of resolving dynamical pathways on electronic and vibrational molecular states. We experimentally demonstrate the implementation of molecular decision trees, logic operations where all possible values of inputs are processed in parallel and the outputs are read simultaneously, by probing the laser-induced dynamics of populations and coherences in a rhodamine dye mounted on a short DNA duplex. The inputs are provided by the bilinear interactions between the molecule and the laser pulses, and the output values are read from the two-dimensional molecular response at specific frequencies. Our results highlights how ultrafast dynamics between multiple molecular states induced by light–matter interactions can be used as an advantage for performing complex logic operations in parallel, operations that are faster than electrical switching. PMID:25984269

  5. Synthesis and dyeing performance of bisazo disperse dyes based on 3-[4-(4-amino-2-chlorophenoxyanilino]phenol

    Directory of Open Access Journals (Sweden)

    Rajesh H. Parab

    2016-09-01

    Full Text Available The present communication aims to develop bisazo disperse dyes based on 3-[4-(4-amino-2-chlorophenoxyanilino]phenol (DAP both as a coupling component as well as a diazonium salt. Coupling reaction of DAP was carried out with a diazonium salt of 4-aminoacetanilide to yield a monoazo disperse dye, and then it was further used as a diazonium salt and coupled with a different aromatic phenol to synthesize bisazo disperse dyes. All the disperse dyes were characterized by elemental analysis, IR, NMR and UV–Visible spectral studies with a view to determine their chemical structure. The dyeing ability of these bisazo disperse dyes has been evaluated in terms of their dyeing behavior and fastness properties on different fabrics.

  6. Use of the ultrasonic cavitation in wool dyeing process: Effect of the dye-bath temperature.

    Science.gov (United States)

    Actis Grande, G; Giansetti, M; Pezzin, A; Rovero, G; Sicardi, S

    2017-03-01

    The present work aims to study the effect of the liquid temperature on the performance of ultrasounds (US) in a dyeing process. The approach was both theoretical and experimental. In the theoretical part the simplified model of a single bubble implosion is used to demonstrate that the "maximum implosion pressure" calculated with the well known Rayleigh-Plesset equation for a single bubble can be correlated with the cavitation intensity experimentally measured with an Ultrasonic Energy Meter (by PPB Megasonics). In particular the model was used to study the influence of the fluid temperature on the cavitation intensity. The "relative" theoretical data calculated from the implosion pressure were satisfactorily correlated with the experimental ones and evidence a zone, between 50 and 60°C, were the cavitation intensity is almost constant and still sufficiently high. Hence an experimental part of wool dyeing was carried out both to validate the previous results and to verify the dyeing quality at low temperatures (40-70°C) in presence of US. A prototype dyeing equipment able to treat textile samples with US system of 600W power, was used. The dyeing performances in the presence and absence of US were verified by measuring ΔE (colour variation), R e,% (reflectance percentage), K/S (colour strength) and colour fastness. The US tests performed in the temperature range of 40-70°C were compared with the conventional wool dyeing at 98°C. The obtained results show that a temperature close to 60°C should be chosen as the recommended US dyeing condition, being a compromise between the cavitation intensity and the kinetics which rules the dyestuff diffusion within the fibres. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Novel diyne-bridged dyes for efficient dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Jing-Kun, E-mail: fjk@njust.edu.cn [Department of Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, Xiaolingwei Street No. 200, Nanjing, 210094 (China); Sun, Tengxiao [Department of Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, Xiaolingwei Street No. 200, Nanjing, 210094 (China); Tian, Yi [Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577 (Japan); Zhang, Yingjun, E-mail: ZhangYingjun@hec.cn [HEC Pharm Group, HEC R& D Center, Dongguan, 523871 (China); Jin, Chuanfei [HEC Pharm Group, HEC R& D Center, Dongguan, 523871 (China); Xu, Zhimin; Fang, Yu; Hu, Xiangyu; Wang, Haobin [Department of Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, Xiaolingwei Street No. 200, Nanjing, 210094 (China)

    2017-07-01

    Three new metal free organic dyes (FSD101-103) were synthesized to investigate the influence of diyne unit on dye molecules. FSD101 and FSD102 with diyne unit and FSD103 with monoyne unit were applied as sensitizers in the dye-sensitized solar cells (DSSCs). The optical and electrochemical properties, theoretical studies, and photovoltaic parameters of DSSCs sensitized by these dyes were systematically investigated. By replacing the monoyne unit with a diyne unit, FSD101 exhibited broader absorption spectrum, lower IP, higher EA, lower band gap energy, higher oscillator strength, more efficient electron injection ability, broader IPCE response range and higher τ{sub e} in comparison with FSD103. Hence, DSSC sensitized by FSD101 showed higher J{sub sc} and V{sub oc} values, and demonstrated a power conversion efficiency of 3.12%, about 2-fold as that of FSD103 (1.55%). FSD102 showed similar results as FSD101, with a power conversion efficiency of 2.98%, despite a stronger electron withdraw cyanoacrylic acid group was introduced. This may be due to the lower efficiency of the electron injection from dye to TiO{sub 2} and lower τ{sub e} of FSD102 than that of FSD101. These results indicate that the performance of DSSCs can be significantly improved by introducing a diyne unit into this type of organic dyes. - Highlights: • Diyne-bridge was introduced into dye molecules by a transition-metal-free protocol. • Power conversion efficiency grows from 1.55% to 3.12% by replacing monoyne unit with diyne unit. • FSD101 with diyne unit shows the highest electron lifetime resulting in a higher V{sub oc}.

  8. Decolourisations and biodegradations of model azo dye solutions using a sequence batch reactor, followed by ultrafiltration

    DEFF Research Database (Denmark)

    Korenak, J.; Ploder, J.; Trček, J.

    2018-01-01

    RNA gene and ITS1-5.8S rDNA-ITS2 sequence analysis, respectively. Serratia marcescens and Klebsiella oxytoca were the most common bacteria with the highest number present during the aerobic and anaerobic phases of the bioprocess. In addition, a high number of Elizabethkingia miricola, Morganella morganii......, Comamonas testosteroni, Trichosporon sp. and Galactomyces sp. were detected. Taken together, our results demonstrated that the sequencing batch reactor system combined with ultrafiltration is an efficient technique for treatment of wastewater containing azo dye. Moreover, the ultrafiltration effectively...

  9. Performance variation from triphenylamine- to carbazole-triphenylamine-rhodaniline-3-acetic acid dyes in dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Chien-Hsin, E-mail: yangch@nuk.edu.tw [Department of Chemical and Materials Engineering, National University of Kaohsiung, Kaohsiung 811, Taiwan (China); Lin, Wen-Churng [Department of Environmental Engineering, Kun Shan University, Tainan 710, Taiwan (China); Wang, Tzong-Liu; Shieh, Yeong-Tarng; Chen, Wen-Janq; Liao, Shao-Hong; Sun, Yu-Kuang [Department of Chemical and Materials Engineering, National University of Kaohsiung, Kaohsiung 811, Taiwan (China)

    2011-10-17

    Highlights: {yields} We synthesized an organic dye of carbazole-rhodaniline-3-acetic acid-triphenylamine. {yields} A dye-sensitized solar cell is fabricated using this dye with efficiency of 4.64%. {yields} Carbazole donor in the dye molecule provides electron in increasing efficiency. {yields} Two rhodaniline-3-acetic acids play a key role in increasing efficiency. {yields} AC impedance proves this dye's effect on enhancing charge transfer in TiO{sub 2}. - Abstract: Organic dyes have been synthesized which contain an extra-electron donor (carbazole) and electron acceptors (rhodaniline-3-acetic acid) on triphenylamines (TPA). Photophysical, electrochemical, and theoretical computational methods have categorized these compounds. Nanocrystalline TiO{sub 2}-based dye-sensitized solar cells (DSSCs) are fabricated using these dye molecules as light-harvesting sensitizers. The overall efficiency of sensitized cells has 4.64% relative to a cis-di(thiocyanato)-bis(2,2'-bipyridyl)-4,4'-dicarboxylate ruthenium (II) (N3 dye)-sensitized device (7.83%) fabricated and measured under the same conditions. Carbazole-electron donation in the dye molecules plays a key role in the increased efficiency. Two rhodaniline-3-acetic acid groups appear to help convey the charge transfer from the excited dye molecules to the conduction band of TiO{sub 2}, leading to a higher efficiency of devices using such a dye. Electrochemical impedance supports this dye's effect on enhancing charge transfer in TiO{sub 2} (e{sup -}). Computations on this dye compound also indicate the larger charge transfer efficiency in the electronically excited state.

  10. DNA analysis by single molecule stretching in nanofluidic biochips

    DEFF Research Database (Denmark)

    Abad, E.; Juarros, A.; Retolaza, A.

    2011-01-01

    Imprint Lithography (NIL) technology combined with a conventional anodic bonding of the silicon base and Pyrex cover. Using this chip, we have performed single molecule imaging on a bench-top fluorescent microscope system. Lambda phage DNA was used as a model sample to characterize the chip. Single molecules of λ-DNA......Stretching single DNA molecules by confinement in nanofluidic channels has attracted a great interest during the last few years as a DNA analysis tool. We have designed and fabricated a sealed micro/nanofluidic device for DNA stretching applications, based on the use of the high throughput Nano...... stained with the fluorescent dye YOYO-1 were stretched in the nanochannel array and the experimental results were analysed to determine the extension factor of the DNA in the chip and the geometrical average of the nanochannel inner diameter. The determination of the extension ratio of the chip provides...

  11. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  12. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  13. Process development for the removal and recovery of hazardous dye erythrosine from wastewater by waste materials-Bottom Ash and De-Oiled Soya as adsorbents

    Energy Technology Data Exchange (ETDEWEB)

    Mittal, Alok [Department of Applied Chemistry, Maulana Azad National Institute of Technology, Bhopal 462007 (India)]. E-mail: aljymittal@yahoo.co.in; Mittal, Jyoti [Department of Applied Chemistry, Maulana Azad National Institute of Technology, Bhopal 462007 (India); Kurup, Lisha [Department of Applied Chemistry, Maulana Azad National Institute of Technology, Bhopal 462007 (India); Singh, A.K. [Department of Applied Chemistry, University Institute of Technology, RGPV, Bhopal 462036 (India)

    2006-11-02

    Erythrosine is a water-soluble xanthene class of dye. It is widely used as colorant in foods, textiles, drugs and cosmetics. It is highly toxic, causes various types of allergies, thyroid activities, carcinogenicity, DNA damage behaviour, neurotoxicity and xenoestrogen nature in the humans and animals. The photochemical and biochemical degradation of the erythrosine is not recommended due to formation of toxic by-products. The present paper is an attempt to remove erythrosine from wastewater using adsorption over Bottom Ash-a power plant waste and De-Oiled Soya-an agricultural waste. Under the batch studies, effect of concentration of dye, temperature, pH of the solution, dosage of adsorbents, sieve size of adsorbents, etc., have been studied for the uptake of the dye over both adsorbents. The adsorption process verifies Langmuir and Freundlich adsorption isotherms in both the cases and based on the data different thermodynamic parameters have been evaluated. Batch studies also include kinetic measurements, rate constant study, mass transfer behaviour and establishment of mechanistic pathway for both the cases. For the bulk removal of the dye column operations have been carried out and breakthrough capacities of the Bottom Ash and De-Oiled Soya columns have been calculated. Attempts have also been made for the recovery of the adsorbed dye from exhausted columns by eluting dilute NaOH and more than 90% of the dye was recovered.

  14. Process development for the removal and recovery of hazardous dye erythrosine from wastewater by waste materials-Bottom Ash and De-Oiled Soya as adsorbents

    International Nuclear Information System (INIS)

    Mittal, Alok; Mittal, Jyoti; Kurup, Lisha; Singh, A.K.

    2006-01-01

    Erythrosine is a water-soluble xanthene class of dye. It is widely used as colorant in foods, textiles, drugs and cosmetics. It is highly toxic, causes various types of allergies, thyroid activities, carcinogenicity, DNA damage behaviour, neurotoxicity and xenoestrogen nature in the humans and animals. The photochemical and biochemical degradation of the erythrosine is not recommended due to formation of toxic by-products. The present paper is an attempt to remove erythrosine from wastewater using adsorption over Bottom Ash-a power plant waste and De-Oiled Soya-an agricultural waste. Under the batch studies, effect of concentration of dye, temperature, pH of the solution, dosage of adsorbents, sieve size of adsorbents, etc., have been studied for the uptake of the dye over both adsorbents. The adsorption process verifies Langmuir and Freundlich adsorption isotherms in both the cases and based on the data different thermodynamic parameters have been evaluated. Batch studies also include kinetic measurements, rate constant study, mass transfer behaviour and establishment of mechanistic pathway for both the cases. For the bulk removal of the dye column operations have been carried out and breakthrough capacities of the Bottom Ash and De-Oiled Soya columns have been calculated. Attempts have also been made for the recovery of the adsorbed dye from exhausted columns by eluting dilute NaOH and more than 90% of the dye was recovered

  15. Lack of genotoxic effect of food dyes amaranth, sunset yellow and tartrazine and their metabolites in the gut micronucleus assay in mice.

    Science.gov (United States)

    Poul, Martine; Jarry, Gérard; Elhkim, Mostafa Ould; Poul, Jean-Michel

    2009-02-01

    The food dyes amaranth, sunset yellow and tartrazine were administered twice, at 24h intervals, by oral gavage to mice and assessed in the in vivo gut micronucleus test for genotoxic effects (frequency of micronucleated cells) and toxicity (apoptotic and mitotic cells). The concentrations of each compound and their main metabolites (sulfanilic acid and naphthionic acid) were measured in faeces during a 24-h period after single oral administrations of the food dyes to mice. Parent dye compounds and their main aromatic amine metabolites were detected in significant amounts in the environment of colonic cells. Acute oral exposure to food dye additives amaranth, sunset yellow and tartrazine did not induce genotoxic effect in the micronucleus gut assay in mice at doses up to 2000 mg/kg b.w. Food dyes administration increased the mitotic cells at all dose levels when compared to controls. These results suggest that the transient DNA damages previously observed in the colon of mice treated by amaranth and tartrazine by the in vivo comet assay [Sasaki, Y.F., Kawaguchi, S., Kamaya, A., Ohshita, M., Kabasawa, K., Iwama, K., Taniguchi, K., Tsuda, S., 2002. The comet assay with 8 mouse organs: results with 39 currently used food additives. Mutat. Res. 519, 103-119] are unable to be fixed in stable genotoxic lesions and might be partly explained by local cytotoxicity of the dyes.

  16. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.; Oke, Muse; Hamdan, Samir

    2014-01-01

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  17. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.

    2014-11-21

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  18. Degradation of azo dyes by environmental microorganisms and helminths

    Energy Technology Data Exchange (ETDEWEB)

    Kingthom Chung; Stevens, S.E. Jr. (Memphis State Univ., TN (United States). Dept. of Biology)

    1993-11-01

    The degradation of azo dyes by environmental microorganisms, fungi, and helminths is reviewed. Azo dyes are used in a wide variety of products and can be found in the effluent of most sewage treatment facilities. Substantial quantities of these dyes have been deposited in the environment, particularly in streams and rivers. Azo dyes were shown to affect microbial activities and microbial population sizes in the sediments and in the water columns of aquatic habitats. Only a few aerobic bacteria have been found to reduce azo dyes under aerobic conditions, and little is known about the process. A substantial number of anaerobic bacteria capable of azo dye reduction have been reported. The enzyme responsible for azo dye reduction has been partially purified, and characterization of the enzyme is proceeding. The nematode Ascaris lumbricoides and the cestode Moniezia expanza have been reported to reduce azo dyes anaerobically. Recently the fungus Phanerochaete chrysoporium was reported to mineralize azo dyes via a peroxidation-mediated pathway. A possible degradation pathway for the mineralization of azo dye is proposed and future research needs are discussed.

  19. Knowledge, attitude, and practice of dyeing and printing workers

    Directory of Open Access Journals (Sweden)

    Paramasivam Parimalam

    2010-01-01

    Full Text Available Background: Millions of workers are occupationally exposed to dyes in the world, but little is known about their knowledge and attitudes toward the effects of dye on their health. Objectives: The aim of this study was to assess the fabric dyers′ and fabric printers′ knowledge, attitude, and practice toward the health hazard of dyes. Materials and Methods: The present study was taken up in the Madurai district which is situated in the Southern Tamil Nadu, India. One hundred and forty-two workers employed in small-scale dyeing and printing units participated in a face-to-face confidential interview . Results: The mean age of fabric dyers and fabric printers was 42 years (΁10.7. When enquired about whether dyes affect body organ(s, all the workers agreed that dye(s will affect skin, but they were not aware that dyes could affect other parts of the body. All the workers believed that safe methods of handling of dyes and disposal of contaminated packaging used for dyes need to be considered. It was found that 34% of the workers were using personal protective equipment (PPE such as rubber hand gloves during work. Conclusion: The workers had knowledge regarding the occupational hazards, and their attitudinal approach toward the betterment of the work environment is positive.

  20. Organic and Inorganic Dyes in Polyelectrolyte Multilayer Films

    Science.gov (United States)

    Ball, Vincent

    2012-01-01

    Polyelectrolyte multilayer films are a versatile functionalization method of surfaces and rely on the alternated adsorption of oppositely charged species. Among such species, charged dyes can also be alternated with oppositely charged polymers, which is challenging from a fundamental point of view, because polyelectrolytes require a minimal number of charges, whereas even monovalent dyes can be incorporated during the alternated adsorption process. We will not only focus on organic dyes but also on their inorganic counterparts and on metal complexes. Such films offer plenty of possible applications in dye sensitized solar cells. In addition, dyes are massively used in the textile industry and in histology to stain textile fibers or tissues. However, the excess of non bound dyes poses serious environmental problems. It is hence of the highest interest to design materials able to adsorb such dyes in an almost irreversible manner. Polyelectrolyte multilayer films, owing to their ion exchange behavior can be useful for such a task allowing for impressive overconcentration of dyes with respect to the dye in solution. The actual state of knowledge of the interactions between charged dyes and adsorbed polyelectrolytes is the focus of this review article.

  1. Significance of hair-dye base-induced sensory irritation.

    Science.gov (United States)

    Fujita, F; Azuma, T; Tajiri, M; Okamoto, H; Sano, M; Tominaga, M

    2010-06-01

    Oxidation hair-dyes, which are the principal hair-dyes, sometimes induce painful sensory irritation of the scalp caused by the combination of highly reactive substances, such as hydrogen peroxide and alkali agents. Although many cases of severe facial and scalp dermatitis have been reported following the use of hair-dyes, sensory irritation caused by contact of the hair-dye with the skin has not been reported clearly. In this study, we used a self-assessment questionnaire to measure the sensory irritation in various regions of the body caused by two model hair-dye bases that contained different amounts of alkali agents without dyes. Moreover, the occipital region was found as an alternative region of the scalp to test for sensory irritation of the hair-dye bases. We used this region to evaluate the relationship of sensitivity with skin properties, such as trans-epidermal water loss (TEWL), stratum corneum water content, sebum amount, surface temperature, current perception threshold (CPT), catalase activities in tape-stripped skin and sensory irritation score with the model hair-dye bases. The hair-dye sensitive group showed higher TEWL, a lower sebum amount, a lower surface temperature and higher catalase activity than the insensitive group, and was similar to that of damaged skin. These results suggest that sensory irritation caused by hair-dye could occur easily on the damaged dry scalp, as that caused by skin cosmetics reported previously.

  2. Pulse radiolysis of rhodamine dye solutions

    International Nuclear Information System (INIS)

    Kucherenko, E.A.; Kartasheva, L.I.; Pikaev, A.K.

    1982-01-01

    Applying the method of pulse radiolysis (5 MeV electrons) a study was made on intermediate products of rhodamine B radiolytic transformations in neutral aqueous and ethanol solutions. Rate constants of reactions of esub(aq) and OH with the dye (they are equal to (2.2+-0.3)x10 10 and (2.1+-0.3)x10 10 e/molxs, accordingly) as well as optical and kinetic characteristics of esub(aq), OH and H interaction products were measured. The nature of these products is concluded. It was found that in ethanol solutions the semirecovered form - electroneutral radical of rhodamine B - was the only intermediate product. It arises during the interaction of the dye with esub(s) (k=(9.2+-1.2)x10 9 e/molxs) and α-et hananol radical (k=(1.1+-0.1)x10 8 l/molxs). Properties of this product were investigated

  3. Radiochromic dye film studies for brachytherapy applications

    International Nuclear Information System (INIS)

    Martinez-Davalos, A.; Rodriguez-Villafuerte, M.; Diaz-Perches, R.; Arzamendi-Perez, S.

    2002-01-01

    Commercial radiochromic dye films have been used in recent years to quantify absorbed dose in several medical applications. In this study we present the characterisation of the GafChromic MD-55-2 dye film, a double sensitive layer film suitable for photon irradiation in brachytherapy applications. Dose measurements were carried out with a low dose rate 137 Cs brachytherapy source, which produces very steep dose gradients in its vicinity, and therefore requires the capability of producing high spatial resolution isodose curves. Quantification of the dose rate in water per unit air kerma strength was obtained using a high-resolution transmission commercial scanner (Agfa DuoScan T1200) with the capability of digitising up to 600 x 1200 pixels per inch using 36 bits per pixel, together with optical density measurements. The Monte Carlo calculations and experimental measurements compared well in the 0-50 Gy dose interval used in this study. (author)

  4. Synthesis and characterisation of new laser dyes

    International Nuclear Information System (INIS)

    Scala-Valero, Claudine

    1997-01-01

    Rhodamines are very efficient laser dyes for the red part of the visible spectrum: their fluorescence quantum efficiencies are about hundred per cent. However, their conversion efficiencies in dye amplifier are about fifty per cent, due to the presence of S n electronic level which is responsible of the re-absorption of a part of photons. In this research thesis, the author aims at trying to move this S n level out of the stimulated emission bandwidth. Models have been developed to propose new structures derived from rhodamines and theoretically possessing the desired properties. The so-recommended molecules have then been synthesised and characterised in terms of absorption and fluorescence spectra, of quantum efficiency, and of fluorescence lifetime. Two modifications are proposed for the rhodamine 6G structure, either by grafting methyl substitutes, or by grafting variously substituted amines. The searched result is obtained with the second modification [fr

  5. Photophysical properties of pyronin dyes in reverse micelles of AOT

    Energy Technology Data Exchange (ETDEWEB)

    Bayraktutan, Tuğba; Meral, Kadem; Onganer, Yavuz, E-mail: yonganer@atauni.edu.tr

    2014-01-15

    The photophysical properties of pyronin B (PyB) and pyronin Y (PyY) in reverse micelles formed with water/sodium bis (2-ethyl-1-hexyl) sulfosuccinate (AOT)/n-heptane were investigated by UV–vis absorption, steady-state and time-resolved fluorescence spectroscopy techniques. This study was carried out a wide range of reverse micelle sizes, with hydrodynamic radii ranging from 1.85 to 9.38 nm. Significant photophysical parameters as band shifts, fluorescence quantum yields and fluorescence lifetimes were determined to understand how photophysical and spectroscopic features of the dye compounds were affected by the variation of reverse micelle sizes. In this regard, control of reverse micelle size by changing W{sub 0}, the molar ratio of water to surfactant, allowed tuning the photophysical properties of the dyes in organic solvent via reverse micelle. Non-fluorescent H-aggregates of pyronin dyes were observed for the smaller reverse micelles whereas an increase in the reverse micelle size induced an increment in the amount of dye monomers instead of dye aggregates. Thus, the fluorescence intensities of the dyes were improved by increasing W{sub 0} due to the predomination of the fluorescent dye monomers. As a result, the fluorescence quantum yields also increased. The fluorescence lifetimes of the dyes in the reverse micelles were determined by the time-resolved fluorescence decay studies. Evaluation of the fluorescence lifetimes calculated for pyronin dyes in the reverse micelles showed that the size of reverse micelle affected the fluorescence lifetimes of pyronin dyes. -- Highlights: • The photophysical properties of pyronin dyes were examined by spectroscopic techniques. • Optical properties of the dyes were tuned by changing of W{sub 0} values. • The fluorescence lifetime and quantum yield values of the dyes in reverse micelles were discussed.

  6. Novel organic dyes based on phenyl-substituted benzimidazole for dye sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Saltan, Gözde Murat [Department of Chemistry, Faculty of Arts and Science, Celal Bayar University, Yunus Emre, 45140 Manisa (Turkey); Dinçalp, Haluk, E-mail: haluk.dincalp@cbu.edu.tr [Department of Chemistry, Faculty of Arts and Science, Celal Bayar University, Yunus Emre, 45140 Manisa (Turkey); Kıran, Merve; Zafer, Ceylan [Solar Energy Institute, Ege University, Bornova, 35100 Izmir (Turkey); Erbaş, Seçil Çelik [Celal Bayar University, Materials Engineering Department, Faculty of Engineering, Yunus Emre, 45140 Manisa (Turkey)

    2015-08-01

    Two new sensitizers derived from benzimidazole core for dye-sensitized solar cell (DSSC) applications were designed and synthesized as D–π–A structures, in which two phenyl-substituted benzimidazole group, a phenyl ring and a cyanoacrylic acid were used as the electron donor, π-conjugated linkage and the electron acceptor, respectively. Effect of methoxy- and N,N-dimetylamino- moieties attached to the phenyl groups of benzimidazole were investigated by means of optical and photovoltaic measurements. The compounds exhibit broad absorption maximum at 387 nm with the tail extending up to 500 nm on TiO{sub 2}-coated thin film. The longer wavelength absorption band around 360 nm and the much longer decay components could be attributed to the existence of charge transfer state of the dyes in solutions. DSSC device fabricated by using methoxy substituted dye (BI5a) as a sensitizer shows much better incident photon-to-current conversion efficiency (IPCE) of 64% giving cell efficiency of 2.68%. - Graphical abstract: Display Omitted - Highlights: • Long decay times suggest the delayed fluorescence caused by the existence of ICT. • The best solar energy conversion efficiency was obtained for BI5a dye (2.68%). • More fluorescent BI5a dye gives higher photocurrent generation.

  7. Molecular modification of coumarin dyes for more efficient dye sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-de-Armas, Rocio; San-Miguel, Miguel A.; Oviedo, Jaime; Sanz, Javier Fdez. [Department of Physical Chemistry, University of Seville, Seville (Spain)

    2012-05-21

    In this work, new coumarin based dyes for dye sensitized solar cells (DSSC) have been designed by introducing several substituent groups in different positions of the NKX-2311 structure. Two types of substitutions have been considered: the introduction of three electron-donating groups (-OH, -NH{sub 2}, and -OCH{sub 3}) and two different substituents with steric effect: -CH{sub 2}-CH{sub 2}-CH{sub 2}- and -CH{sub 2}-HC=CH-. The electronic absorption spectra (position and width of the first band and absorption threshold) and the position of the LUMO level related to the conduction band have been used as theoretical criteria to evaluate the efficiency of the new dyes. The introduction of a -NH{sub 2} group produces a redshift of the absorption maximum position and the absorption threshold, which could improve the cell efficiency. In contrast, the introduction of -CH{sub 2}-CH{sub 2}-CH{sub 2}- does not modify significantly the electronic structure of NKX-2311, but it might prevent aggregation. Finally, -CH{sub 2}-HC=CH- produces important changes both in the electronic spectrum and in the electronic structure of the dye, and it would be expected as an improvement of cell efficiency for these dyes.

  8. Time dependent – density functional theory characterization of organic dyes for dye-sensitized solar cells

    KAUST Repository

    Hilal, Rifaat

    2017-06-19

    We aim at providing better insight into the parameters that govern the intramolecular charge transfer (ICT) and photo-injection processes in dyes for dye-sensitised solar cells (DSSC). Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations are utilized to study the geometry, electronic structure, electrostatic potential (ESP) and absorption spectrum, for a representative donor-π bridge-acceptor (D–π–A) dye for DSSC. The coplanar geometry of the dye (D1) facilitates strong conjugation and considerable delocalization originating the π CT interaction from donor to acceptor orbitals and the hyper-conjugative interactions involving Rydberg states. A model simulating the adsorption of the dye on the TiO surface is utilized to estimate binding energies. The effect of fluorine substituents in the π-spacer on the quantum efficiency of DSSCs was investigated. Gibb’s free energy values, redox potentials, excited state lifetime, non-linear optical properties (NLO) and driving forces for D1 and its fluorinated derivatives were computed.

  9. Effects of reduction products of ortho-hydroxyl substituted azo dyes on biodecolorization of azo dyes

    Energy Technology Data Exchange (ETDEWEB)

    Liu Guangfei [Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental and Biological Science and Technology, Dalian University of Technology, Linggong Road No. 2, Dalian 116024 (China); Wang Jing, E-mail: wangjingbio@yahoo.cn [Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental and Biological Science and Technology, Dalian University of Technology, Linggong Road No. 2, Dalian 116024 (China); Lu Hong; Jin Ruofei; Zhou Jiti; Zhang Long [Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental and Biological Science and Technology, Dalian University of Technology, Linggong Road No. 2, Dalian 116024 (China)

    2009-11-15

    The mediated effects of reduction products of some ortho-hydroxyl substituted azo dyes on biodecolorization were investigated. The results indicated that the addition of reduction products could effectively accelerate dye decolorization by Shigella sp. QRZ-1. The best accelerating effect was obtained with the addition of reduction products of Acid Red 14 (AR14), resulting in an over 3-fold increase in decolorization efficiency of many azo dyes. In sequencing batch reactor experiments, the accelerating effect of reduction products of AR14 was more obvious (1.5-fold) during the startup of the system. When the dye concentration was increased to 500 mg L{sup -1}, the accelerated decolorization efficiency was still maintained around 95%. The presence of AR14 in the feed enhanced the decolorization performance of anaerobic sludge, indicating that the strategy may be beneficial for practical application. 1-Naphthol-2-amino-4-sulfonic acid, which is one of the reduction products of AR14, may function as redox mediator to speed up azo dye biodecolorization.

  10. Effects of reduction products of ortho-hydroxyl substituted azo dyes on biodecolorization of azo dyes

    International Nuclear Information System (INIS)

    Liu Guangfei; Wang Jing; Lu Hong; Jin Ruofei; Zhou Jiti; Zhang Long

    2009-01-01

    The mediated effects of reduction products of some ortho-hydroxyl substituted azo dyes on biodecolorization were investigated. The results indicated that the addition of reduction products could effectively accelerate dye decolorization by Shigella sp. QRZ-1. The best accelerating effect was obtained with the addition of reduction products of Acid Red 14 (AR14), resulting in an over 3-fold increase in decolorization efficiency of many azo dyes. In sequencing batch reactor experiments, the accelerating effect of reduction products of AR14 was more obvious (1.5-fold) during the startup of the system. When the dye concentration was increased to 500 mg L -1 , the accelerated decolorization efficiency was still maintained around 95%. The presence of AR14 in the feed enhanced the decolorization performance of anaerobic sludge, indicating that the strategy may be beneficial for practical application. 1-Naphthol-2-amino-4-sulfonic acid, which is one of the reduction products of AR14, may function as redox mediator to speed up azo dye biodecolorization.

  11. Novel organic dyes based on phenyl-substituted benzimidazole for dye sensitized solar cells

    International Nuclear Information System (INIS)

    Saltan, Gözde Murat; Dinçalp, Haluk; Kıran, Merve; Zafer, Ceylan; Erbaş, Seçil Çelik

    2015-01-01

    Two new sensitizers derived from benzimidazole core for dye-sensitized solar cell (DSSC) applications were designed and synthesized as D–π–A structures, in which two phenyl-substituted benzimidazole group, a phenyl ring and a cyanoacrylic acid were used as the electron donor, π-conjugated linkage and the electron acceptor, respectively. Effect of methoxy- and N,N-dimetylamino- moieties attached to the phenyl groups of benzimidazole were investigated by means of optical and photovoltaic measurements. The compounds exhibit broad absorption maximum at 387 nm with the tail extending up to 500 nm on TiO 2 -coated thin film. The longer wavelength absorption band around 360 nm and the much longer decay components could be attributed to the existence of charge transfer state of the dyes in solutions. DSSC device fabricated by using methoxy substituted dye (BI5a) as a sensitizer shows much better incident photon-to-current conversion efficiency (IPCE) of 64% giving cell efficiency of 2.68%. - Graphical abstract: Display Omitted - Highlights: • Long decay times suggest the delayed fluorescence caused by the existence of ICT. • The best solar energy conversion efficiency was obtained for BI5a dye (2.68%). • More fluorescent BI5a dye gives higher photocurrent generation

  12. Photolysis of rhodamine-WT dye

    Science.gov (United States)

    Tai, D.Y.; Rathbun, R.E.

    1988-01-01

    Photolysis of rhodamine-WT dye under natural sunlight conditions was determined by measuring the loss of fluorescence as a function of time. Rate coefficients at 30?? north latitude ranged from 4.77 x 10-2 day-1 for summer to 3.16 x 10-2 day-1 for winter. Experimental coefficients were in good agreement with values calculated using a laboratory-determined value of the quantum yield.

  13. Plasmonic Dye-Sensitized Solar Cells

    KAUST Repository

    Ding, I-Kang

    2010-12-14

    This image presents a scanning electron microscopy image of solid state dye-sensitized solar cell with a plasmonic back reflector, overlaid with simulated field intensity plots when monochromatic light is incident on the device. Plasmonic back reflectors, which consist of 2D arrays of silver nanodomes, can enhance absorption through excitation of plasmonic modes and increased light scattering, as reported by Michael D. McGehee, Yi Cui, and co-workers.

  14. Nanostructured dye-sensitized solar cells

    OpenAIRE

    Palma, Giuseppina

    2014-01-01

    2012/2013 Dye-sensitized solar cells (DSSCs) represent a promising alternative to silicon-based technology. From the first publications about DSSCs in the 90s, they are considered an important breakthrough for achieving high efficiency by using relatively inexpensive and abundant materials. Stability and efficiency are two crucial points in the development of this new class of hybrid photovoltaic devices. Most of the DSSC studies carried out over the past twenty years are based on the o...

  15. Characterization and biological treatment of colored textile wastewaters from the typical Tunisian hat Chechia dyeing using newly isolated Aspergillus niger

    Directory of Open Access Journals (Sweden)

    Hajer Barouni

    2016-09-01

    Full Text Available This study aimed to characterize and investigate, for the first time, the treatment of real colored wastewaters from the artisanal dyeing of the typical Tunisian hat Chechia, using a newly isolated fungal strain. This textile effluent was a mixture called Mix of colored wastewaters from the three main types of Chechia. The major pollutant of the Mix was the toxic Azo dye Amaranth Acid or Acid Red 27. The fungal strain that made the cleanup was discovered in a Chechia dyeing wastewater’s container and identified by ITS rDNA gene sequencing. This isolated Aspergillus niger showed interesting performances on the demonstration of Chechia wastewater’s biodegradation in batch cultures. In order to understand the effect of agitation, Mix dilution and inoculum size on decolourisation and pollution removal, a full factorial experimental design 23 was set up. At the optimal conditions which were 20% inoculum size, 25% Chechia Mix dilution and an agitation of 100 rpm, Aspergillus niger was able to remove color as high as 70.18±2.84% at an initial dye concentration of 1346.6±0.01 mg/L, and to reduce COD to 74.17±14.52% at an initial COD of 4157±422 mg/L. FT-IR spectra analysis confirmed the decolourisation by biodegradation and transformation of the dyes. The treatment by the isolated Aspergillus niger could be successfully applied as a sustainable method to solve one of handicraft dyeing plants environmental management issues.

  16. Characterization and Application of DNA-templated Silver Nanoclusters and Polarized Spectroscopy of Self-Assembled Nanostructures

    DEFF Research Database (Denmark)

    Carro-Temboury, Miguel R.

    In this thesis two different systems are investigated envisioning their potential applications: DNA-templated silver nanoclusters (DNA-AgNCs) and ionic self-assembled (ISA) nanostructures based on azo-dyes. Mainly Visible-NIR spectroscopy was used to probe electronic transitions with absorbance a...

  17. Heterogeneous fenton degradation of azo dyes catalyzed by modified polyacrylonitrile fiber fe complexes: QSPR (quantitative structure peorperty relationship) study.

    Science.gov (United States)

    Li, Bing; Dong, Yongchun; Ding, Zhizhong

    2013-07-01

    The amidoximated polyacrylonitrile (PAN) fiber Fe complexes were prepared and used as the heterogeneous Fenton catalysts for the degradation of 28 anionic water soluble azo dyes in water under visible irradiation. The multiple linear regression (MLR) method was employed to develop the quantitative structure property relationship (QSPR) model equations for the decoloration and mineralization of azo dyes. Moreover, the predictive ability of the QSPR model equations was assessed using Leave-one-out (LOO) and cross-validation (CV) methods. Additionally, the effect of Fe content of catalyst and the sodium chloride in water on QSPR model equations were also investigated. The results indicated that the heterogeneous photo-Fenton degradation of the azo dyes with different structures was conducted in the presence of the amidoximated PAN fiber Fe complex. The QSPR model equations for the dye decoloration and mineralization were successfully developed using MLR technique. MW/S (molecular weight divided by the number of sulphonate groups) and NN=N (the number of azo linkage) are considered as the most important determining factor for the dye degradation and mineralization, and there is a significant negative correlation between MW/S or NN=N and degradation percentage or total organic carbon (TOC) removal. Moreover, LOO and CV analysis suggested that the obtained QSPR model equations have the better prediction ability. The variation in Fe content of catalyst and the addition of sodium chloride did not alter the nature of the QSPR model equations.

  18. Efficiencies of Dye-Sensitized Solar Cells using Ferritin-Encapsulated Quantum Dots with Various Staining Methods

    Science.gov (United States)

    Perez, Luis

    Dye-sensitized solar cells (DSSC) have the potential to replace traditional and cost-inefficient crystalline silicon or ruthenium solar cells. This can only be accomplished by optimizing DSSC's energy efficiency. One of the major components in a dye-sensitized solar cell is the porous layer of titanium dioxide. This layer is coated with a molecular dye that absorbs sunlight. The research conducted for this paper focuses on the different methods used to dye the porous TiO2 layer with ferritin-encapsulated quantum dots. Multiple anodes were dyed using a method known as SILAR which involves deposition through alternate immersion in two different solutions. The efficiencies of DSSCs with ferritin-encapsulated lead sulfide dye deposited using SILAR were subsequently compared against the efficiencies produced by cells using the traditional immersion method. It was concluded that both methods resulted in similar efficiencies (? .074%) however, the SILAR method dyed the TiO2 coating significantly faster than the immersion method. On a related note, our experiments concluded that conducting 2 SILAR cycles yields the highest possible efficiency for this particular binding method. National Science Foundation.

  19. Conical Intersections, charge localization, and photoisomerization pathway selection in a minimal model of a degenerate monomethine dye

    International Nuclear Information System (INIS)

    Olsen, Seth; McKenzie, Ross H.

    2009-01-01

    We propose a minimal model Hamiltonian for the electronic structure of a monomethine dye, in order to describe the photoisomerization of such dyes. The model describes interactions between three diabatic electronic states, each of which can be associated with a valence bond structure. Monomethine dyes are characterized by a charge-transfer resonance; the indeterminacy of the single-double bonding structure dictated by the resonance is reflected in a duality of photoisomerization pathways corresponding to the different methine bonds. The possible multiplicity of decay channels complicates mechanistic models of the effect of the environment on fluorescent quantum yields, as well as coherent control strategies. We examine the extent and topology of intersection seams between the electronic states of the dye and how they relate to charge localization and selection between different decay pathways. We find that intersections between the S 1 and S 0 surfaces only occur for large twist angles. In contrast, S 2 /S 1 intersections can occur near the Franck-Condon region. When the molecule has left-right symmetry, all intersections are associated with con- or disrotations and never with single bond twists. For asymmetric molecules (i.e., where the bridge couples more strongly to one end) the S 2 and S 1 surfaces bias torsion about different bonds. Charge localization and torsion pathway biasing are correlated. We relate our observations with several recent experimental and theoretical results, which have been obtained for dyes with similar structure.

  20. DNA-based watermarks using the DNA-Crypt algorithm

    Science.gov (United States)

    Heider, Dominik; Barnekow, Angelika

    2007-01-01

    Background The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations in the genome can be corrected by the DNA-Crypt program leaving the encrypted information intact. Existing DNA cryptographic and steganographic algorithms use synthetic DNA sequences to store binary information however, although these sequences can be used for authentication, they may change the target DNA sequence when introduced into living organisms. Results The DNA-Crypt algorithm and image steganography are based on the same watermark-hiding principle, namely using the least significant base in case of DNA-Crypt and the least significant bit in case of the image steganography. It can be combined with binary encryption algorithms like AES, RSA or Blowfish. DNA-Crypt is able to correct mutations in the target DNA with several mutation correction codes such as the Hamming-code or the WDH-code. Mutations which can occur infrequently may destroy the encrypted information, however an integrated fuzzy controller decides on a set of heuristics based on three input dimensions, and recommends whether or not to use a correction code. These three input dimensions are the length of the sequence, the individual mutation rate and the stability over time, which is represented by the number of generations. In silico experiments using the Ypt7 in Saccharomyces cerevisiae shows that the DNA watermarks produced by DNA-Crypt do not alter the translation of mRNA into protein. Conclusion The program is able to store watermarks in living organisms and can maintain the original information by correcting mutations itself. Pairwise or multiple sequence alignments show that DNA-Crypt produces few mismatches between the sequences similar to all steganographic algorithms. PMID:17535434